Immunoglobulin supergene family

Associate Editor(s)-in-Chief: Henry A. Hoff

The immunoglobulin supergene family is "the group of proteins that have immunoglobulin-like domains, including histocompatibility antigens, the T-cell antigen receptor, poly-IgR, and other proteins involved in the vertebrate immune response (17)."

Immunoglobulin supergenes

Each family within the immunoglobulin supergene family has its share of human genes:

1. ATP-binding cassette (ABC) transporters: 23, 6890, 6891 - 3 genes,
2. Carcinoembryonic antigen genes: 634, 1048, 1084, 1087, 1088, 1089, 4680, 56971, 90273, 125931, 388551, 729767 - 12 genes,
3. Cell adhesion molecule genes: 214, 914, 1826, 3897, 4059, 4162, 4684, 4685, 4897, 4978, 5175, 7412, 8174, 10752, 23705, 51148, 57453, 57863, 90952, 199731, 220296, 221935, 253559 - 23 genes,
4. Cell adhesion-related genes: 50937 - 1 gene,
5. Immunoglobulin domain genes: 915, 916, 917 - 3 genes
6. Immunoglobulin receptor superfamily: 3903, 3904, 5284, 79368, 83417, 115352, 115653, 126014, 286676, 340745, 345193, 353514, 388364, 391123, 553128, 100132285 - 16 genes,
7. Immunoglobulin superfamily genes: 682, 2204, 3321, 3476, 3547, 3671, 9398, 9543, 10261, 10871, 11341, 22997, 57549, 57611, 57722, 83953, 84966, 93185, 117166, 121227, 124857, 146722, 147710, 150084, 152404, 283284, 285313, 492311 - 28 genes,
8. Immunoglobulin supergenes: 1, 7441, 29802 - 3 genes,
9. Intercellular adhesion molecule genes: 3383, 3384, 3385, 3386, 7087 - 5 genes,
10. Junction adhesion molecule genes: 50848, 58494, 83700, 120425, 340547 - 5 genes,
11. Major histocompatibility complex class I gene family: 563, 567, 696, 821, 909, 910, 911, 912, 913, 2217, 2794, 3077, 3105, 3106, 3107, 3133, 3134, 3135, 3140, 3806, 4277, 6992, 7726, 10107, 10384, 10385, 11118, 11119, 11120, 79692, 222698, 282890, 353219, 100507436 - 34 genes,
12. Major histocompatibility complex class II gene family: 972, 1302, 1388, 1616, 2968, 3108, 3109, 3111, 3112, 3113, 3115, 3117, 3118, 3119, 3120, 3121, 3122, 3123, 3125, 3126, 3127, 3833, 4261, 4904, 5089, 5252, 5696, 5698, 5863, 6015, 6046, 6048, 6222, 6257, 6293, 7922, 7923, 8705, 8831, 9277, 9278, 9374, 10471 - 43 genes,
13. Major histocompatibility complex class III gene family: 177, 578, 629, 717, 720, 721, 780, 1041, 1192, 1432, 1460, 1589, 1797, 2289, 2914, 4295, 4439, 4736, 4758, 4795, 4855, 5460, 5514, 5603, 6204, 6631, 6732, 6882, 6941, 6954, 7148, 7287, 7407, 7629, 7936, 7940, 8449, 8859, 8870, 9656, 10211, 259197 - 42 genes,
14. Major histocompatibility complex class IV gene family: 199, 3303, 3304, 3305, 6892 - 5 genes,
15. Major histocompatibility complex class V gene family: 534, 7916, 7917, 7918, 7919, 7920 - 6 genes,
16. Major histocompatibility complex class VI gene family: 4049, 4050, 7124 - 3 genes,
17. NF-kappa-B inhibitor family: 4792 - 1 gene,
18. ZAS family: 3096 - 1 gene, for a total of 233 genes.

The human gene sequence is 1, 23, 177, 199, 214, 534, 563, 567, 578, 629, 634, 682, 696, 717, 720, 721, 780, 821, 909, 910, 911, 912, 913, 914, 915, 916, 917, 972, 1041, 1048, 1084, 1087, 1088, 1089, 1192, 1302, 1388, 1432, 1460, 1589, 1616, 1797, 1826, 2204, 2217, 2289, 2794, 2914, 2968, 3077, 3096, 3105, 3106, 3107, 3108, 3109, 3111, 3112, 3113, 3115, 3117, 3118, 3119, 3120, 3121, 3122, 3123, 3125, 3126, 3127, 3133, 3134, 3135, 3140, 3303, 3304, 3305, 3321, 3383, 3384, 3385, 3386, 3476, 3547, 3671, 3806, 3833, 3897, 3903, 3904, 4049, 4050, 4059, 4162, 4261, 4277, 4295, 4439, 4680, 4684, 4736, 4758, 4792, 4795, 4855, 4897, 4904, 4978, 5089, 5175, 5252, 5284, 5460, 5514, 5603, 5696, 5698, 5863, 6015, 6046, 6048, 6204, 6222, 6257, 6293, 6631, 6732, 6882, 6890, 6891, 6892, 6941, 6954, 6992, 7087, 7124, 7148, 7287, 7407, 7412, 7441, 7629, 7726, 7916, 7917, 7918, 7919, 7920, 7922, 7923, 7936, 7940, 8174, 8449, 8705, 8831, 8859, 8870, 9277, 9278, 9374, 9398, 9543, 9656, 10107, 10211, 10261, 10384, 10385, 10471, 10752, 10871, 11118, 11119, 11120, 11341, 22997, 23705, 29802, 50848, 50937, 51148, 56971, 57453, 57549, 57611, 57722, 57863, 58494, 79368, 79692, 83417, 83700, 83953, 84966, 90273, 90952, 93185, 115352, 115653, 117166, 120425, 121227, 124857, 125931, 126014, 146722, 147710, 150084, 152404, 199731, 220296, 221935, 222698, 253559, 259197, 282890, 283284, 285313, 286676, 340547, 340745, 345193, 353219, 353514, 388364, 388551, 391123, 492311, 553128, 729767, 100132285, 100507436.

Gene ID: 1 A1BG alpha-1-B glycoprotein on 19q13.43: "The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins."

"𝛂₁B-glycoprotein(𝛂₁B) [...] consists of a single polypeptide chain N-linked to four glucosamine oligosaccharides. The polypeptide has five intrachain disulfide bonds and contains 474 amino acid residues. [...] 𝛂₁B exhibits internal duplication and consists of five repeating structural domains, each containing about 95 amino acids and one disulfide bond. [...] several domains of 𝛂₁B, especially the third, show statistically significant homology to variable regions of certain immunoglobulin light and heavy chains. 𝛂₁B [...] exhibits sequence similarity to other members of the immunoglobulin supergene family such as the receptor for transepithelial transport of IgA and IgM and the secretory component of human IgA."

"Some of the domains of 𝛂₁B show significant homology to variable (V) and constant (C) regions of certain immunoglobulins. Likewise, there is statistically significant homology between 𝛂₁B and the secretory component (SC) of human IgA (15) and also with the extracellular portion of the rabbit receptor for transepithelial transport of polymeric immunoglobulins (IgA and IgM). Mostov et al. (16) have called the later protein the poly-Ig receptor or poly-IgR and have shown that it is the precursor of SC."

Gene ID: 7441 is VPREB1 V-set pre-B cell surrogate light chain 1 on 22q11.22: "The protein encoded by this gene belongs to the immunoglobulin superfamily and is expressed selectively at the early stages of B cell development, namely, in proB and early preB cells. This gene encodes the iota polypeptide chain that is associated with the Ig-mu chain to form a molecular complex which is expressed on the surface of pre-B cells. The complex is thought to regulate Ig gene rearrangements in the early steps of B-cell differentiation. Alternative splicing results in multiple transcript variants."

1. NP_001290438.1 immunoglobulin iota chain isoform 2: "Transcript Variant: This variant (2) uses an alternate splice site in the coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1."
2. NP_009059.1 immunoglobulin iota chain isoform 1 precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 29802 is VPREB3 V-set pre-B cell surrogate light chain 3 on 22q11.23; 22q11: "The protein encoded by this gene is the human ortholog of the mouse VpreB3 (8HS20) protein, is thought to be involved in B-cell maturation, and may play a role in assembly of the pre-B cell receptor (pre-BCR). While the role of this protein in B-cell development has not yet been elucidated, studies with the chicken ortholog of this protein have found that when overexpressed, this protein localizes to the endoplasmic reticulum. The mouse ortholog of this protein has been shown to associate with membrane mu heavy chains early in the course of pre-B cell receptor biosynthesis. Expression of this gene has been observed in some lymphomas."

1. NP_037510.1 pre-B lymphocyte protein 3 precursor.

Carcinoembryonic antigen gene family

Main article: Carcinoembryonic antigen gene family

Immunoglobulin superfamily genes

Main article: Immunoglobulin superfamily

Gene ID: 682 is BSG basigin (Ok blood group) on 19p13.3: "The protein encoded by this gene is a plasma membrane protein that is important in spermatogenesis, embryo implantation, neural network formation, and tumor progression. The encoded protein is also a member of the immunoglobulin superfamily. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001309172.1 basigin isoform 2 precursor: "Transcript Variant: This variant (5), as well as variant 2, encodes isoform 2."
2. NP_001719.2 basigin isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."
3. NP_940991.1 basigin isoform 2 precursor: "Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1. Variants 2 and 5 both encode the same isoform (2)."
4. NP_940992.1 basigin isoform 3: "Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1."
5. NP_940993.1 basigin isoform 4: "Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (4) has a shorter and distinct N-terminus compared to isoform 1."

Gene ID: 2204 is FCAR Fc fragment of IgA receptor on 19q13.42: "This gene is a member of the immunoglobulin gene superfamily and encodes a receptor for the Fc region of IgA. The receptor is a transmembrane glycoprotein present on the surface of myeloid lineage cells such as neutrophils, monocytes, macrophages, and eosinophils, where it mediates immunologic responses to pathogens. It interacts with IgA-opsonized targets and triggers several immunologic defense processes, including phagocytosis, antibody-dependent cell-mediated cytotoxicity, and stimulation of the release of inflammatory mediators. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene."

1. NP_001991.1 immunoglobulin alpha Fc receptor isoform a precursor: "Transcript Variant: This variant (1, also known as a.1) represents the longest transcript and encodes the longest isoform (a)."
2. NP_579803.1 immunoglobulin alpha Fc receptor isoform b precursor: "Transcript Variant: This variant (2, also known as a.2, delta66EC2, or U06) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a."
3. NP_579805.1 immunoglobulin alpha Fc receptor isoform c precursor: "Transcript Variant: This variant (3, also known as a.3, Rla2, deltaE2, or U08) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a."
4. NP_579806.1 immunoglobulin alpha Fc receptor isoform d: "Transcript Variant: This variant (4, also known as deltaS2 or U11) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (d) is shorter than isoform a."
5. NP_579807.1 immunoglobulin alpha Fc receptor isoform e:"Transcript Variant: This variant (5, also known as U10) lacks alternate in-frame exons in the 5' and 3' coding region, compared to variant 1. The encoded isoform (e) is shorter than isoform a."
6. NP_579808.1 immunoglobulin alpha Fc receptor isoform f: "Transcript Variant: This variant (6, also known as U09) lacks an in-frame exon in the 5' coding region and uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (f) has a distinct C-terminus and is shorter than isoform a."
7. NP_579811.1 immunoglobulin alpha Fc receptor isoform g: "Transcript Variant: This variant (7, also known as deltaS2ECl or L10) lacks two in-frame exons in the 5' coding region, compared to variant 1. The encoded isoform (g) is shorter than isoform a."
8. NP_579812.1 immunoglobulin alpha Fc receptor isoform h: "Transcript Variant: This variant (8, also known as deltaS266Ec2 or U13) lacks an in-frame exon in the 5' coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (h) is shorter than isoform a."

Gene ID: 3321 is IGSF3 immunoglobulin superfamily member 3 on 1p13.1: "The protein encoded by this gene is an immunoglobulin-like membrane protein containing several V-type Ig-like domains. A mutation in this gene has been associated with bilateral nasolacrimal duct obstruction (LCDD)."

1. NP_001007238.1 immunoglobulin superfamily member 3 isoform 2 precursor: "Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1."
2. NP_001533.2 immunoglobulin superfamily member 3 isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longer isoform (1)."

Gene ID: 3476 is IGBP1 immunoglobulin binding protein 1 on Xq13.1: "The proliferation and differentiation of B cells is dependent upon a B-cell antigen receptor (BCR) complex. Binding of antigens to specific B-cell receptors results in a tyrosine phosphorylation reaction through the BCR complex and leads to multiple signal transduction pathways."

1. NP_001357121.1 immunoglobulin-binding protein 1 isoform 1 [variant 2].
2. NP_001357122.1 immunoglobulin-binding protein 1 isoform 1 [variant 3].
3. NP_001357123.1 immunoglobulin-binding protein 1 isoform 2 [variant 4].
4. NP_001542.1 immunoglobulin-binding protein 1 isoform 1 [variant 1].

Gene ID: 3547 is IGSF1 immunoglobulin superfamily member 1 on Xq26.1: "This gene encodes a member of the immunoglobulin-like domain-containing superfamily. Proteins in this superfamily contain varying numbers of immunoglobulin-like domains and are thought to participate in the regulation of interactions between cells. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001164432.1 immunoglobulin superfamily member 1 isoform 3 precursor: "Transcript Variant: This variant (3) represents the longest transcript and encodes the longest protein (isoform 3)."
2. NP_001164433.1 immunoglobulin superfamily member 1 isoform 4: "Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region and uses an alternate in-frame splice site in a 3' exon compared to variant 3. The resulting protein (isoform 4) is shorter compared to isoform 3."
3. NP_001164434.1 immunoglobulin superfamily member 1 isoform 2 precursor: "Transcript Variant: This variant (5) differs in the 5' UTR, and 3' coding region and UTR compared to variant 3. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 3. Variants 2 and 5 encode the same protein."
4. NP_001546.2 immunoglobulin superfamily member 1 isoform 1 precursor: "Transcript Variant: This variant (1) uses an alternate in-frame splice site in a 3' exon compared to variant 3. The resulting protein (isoform 1) is shorter compared to isoform 3."
5. NP_991402.1 immunoglobulin superfamily member 1 isoform 2 precursor: "Transcript Variant: This variant (2) differs in the 3' coding region and UTR compared to variant 3. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 3. Variants 2 and 5 encode the same protein."

Gene ID: 3671 is ISLR immunoglobulin superfamily containing leucine rich repeat on 15q24.1.

1. NP_005536.1 immunoglobulin superfamily containing leucine-rich repeat protein precursor: "Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein."
2. NP_958934.1 immunoglobulin superfamily containing leucine-rich repeat protein precursor: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein."

Gene ID: 9398 is CD101 CD101 molecule aka IGSF2 on 1p13.1.

1. NP_001243035.1 immunoglobulin superfamily member 2 isoform 1 precursor: "Transcript Variant: This variant (2) uses an alternate splice site in the 3' UTR, compared to variant 1. Variants 1, 2 and 3 all encode isoform 1."
2. NP_001243038.1 immunoglobulin superfamily member 2 isoform 1 precursor: "Transcript Variant: This variant (3) uses an alternate splice site in the 3' UTR, compared to variant 1. Variants 1, 2 and 3 all encode isoform 1."
3. NP_001243040.1 immunoglobulin superfamily member 2 isoform 2 precursor: "Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, and also an alternate splice site in the 3' UTR, compared to variant 1. The encoded isoform (2) is shorter than isoform 1."
4. NP_004249.2 immunoglobulin superfamily member 2 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1, 2 and 3 all encode isoform 1."

Gene ID: 9543 is IGDCC3 immunoglobulin superfamily DCC subclass member 3 on 15q22.31.

1. NP_004875.2 immunoglobulin superfamily DCC subclass member 3 precursor.

Gene ID: 10261 is IGSF6 immunoglobulin superfamily member 6 on 16p12.2.

1. NP_005840.2 immunoglobulin superfamily member 6 precursor.

Gene ID: 10871 is CD300C CD300c molecule aka IGSF16 on 17q25.1: "The CMRF35 antigen, which was identified by reactivity with a monoclonal antibody, is present on monocytes, neutrophils, and some T and B lymphocytes (Jackson et al., 1992 [PubMed 1349532])."

1. NP_006669.1 CMRF35-like molecule 6 precursor.

Gene ID: 11314 is CD300A CD300a molecule aka IGSF12 on 17q25.1: "This gene encodes a member of the CD300 glycoprotein family of cell surface proteins found on leukocytes involved in immune response signaling pathways. This gene is located on chromosome 17 in a cluster with all but one of the other family members. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001243770.1 CMRF35-like molecule 8 isoform 2 precursor: "Transcript Variant: This variant (2) lacks an exon in the 5' coding region compared to variant 1. The resulting protein (isoform 2), also referred to as IRC1c, is shorter compared to isoform 1."
2. NP_001317385.1 CMRF35-like molecule 8 isoform 3 [variant 3].
3. NP_001317386.1 CMRF35-like molecule 8 isoform 4 precursor [variant 4].
4. NP_009192.2 CMRF35-like molecule 8 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1), also referred to as IRC1a."

Gene ID: 22997 is IGSF9B immunoglobulin superfamily member 9B on 11q25.

1. NP_001264214.1 protein turtle homolog B precursor.

Gene ID: 57549 is IGSF9 immunoglobulin superfamily member 9 on 1q23.2.

1. NP_001128522.1 protein turtle homolog A isoform a precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a)."
2. NP_065840.2 protein turtle homolog A isoform b precursor: "Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a."

Gene ID: 57611 is ISLR2 immunoglobulin superfamily containing leucine rich repeat 2 on 15q24.1.

1. NP_001123608.1 immunoglobulin superfamily containing leucine-rich repeat protein 2 precursor: "Transcript Variant: This variant (1) represents the longest transcript. All four transcripts encode the same protein."
2. NP_001123609.1 immunoglobulin superfamily containing leucine-rich repeat protein 2 precursor: "Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. All four transcripts encode the same protein."
3. NP_001123610.1 immunoglobulin superfamily containing leucine-rich repeat protein 2 precursor: "Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. All four transcripts encode the same protein."
4. NP_065902.1 immunoglobulin superfamily containing leucine-rich repeat protein 2 precursor: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. All four transcripts encode the same protein."

Gene ID: 57722 is IGDCC4 immunoglobulin superfamily DCC subclass member 4 on 15q22.31.

1. NP_066013.1 immunoglobulin superfamily DCC subclass member 4 precursor.

Gene ID: 83953 is FCAMR Fc fragment of IgA and IgM receptor on 1q32.1.

1. NP_001116451.1 high affinity immunoglobulin alpha and immunoglobulin mu Fc receptor isoform a: "Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate exon in the 3' coding region resulting in a frameshift, compared to variant 3. The resulting isoform (a) has a shorter and distinct C-terminus, compared to isoform b. Both variants 1 and 2 encode the same isoform."
2. NP_001164102.1 high affinity immunoglobulin alpha and immunoglobulin mu Fc receptor isoform b: "Transcript Variant: This variant (3) represents the longest transcript and encodes the longer isoform (b)."
3. NP_114418.2 high affinity immunoglobulin alpha and immunoglobulin mu Fc receptor isoform a: "Transcript Variant: This variant (1) lacks an alternate exon in the 3' coding region resulting in a frameshift, compared to variant 3. The resulting isoform (a) has a shorter and distinct C-terminus, compared to isoform b. Both variants 1 and 2 encode the same isoform."

Gene ID: 84966 is IGSF21 immunoglobin superfamily member 21 on 1p36.13: "This gene encodes a protein which has two immunoglobulin (Ig) domains and is a member of the immunoglobulin superfamily. Proteins in this superfamily are usually found on or in cell membranes and act as receptors in immune response pathways."

1. NP_116269.3 immunoglobulin superfamily member 21 precursor.

Gene ID: 93185 is IGSF8 immunoglobulin superfamily member 8 on 1q23.2: "This gene encodes a member the EWI subfamily of the immunoglobulin protein superfamily. Members of this family contain a single transmembrane domain, an EWI (Glu-Trp-Ile)-motif and a variable number of immunoglobulin domains. This protein interacts with the tetraspanins CD81 and CD9 and may regulate their role in certain cellular functions including cell migration and viral infection. The encoded protein may also function as a tumor suppressor by inhibiting the proliferation of certain cancers. Alternate splicing results in multiple transcript variants that encode the same protein."

1. NP_001193594.1 immunoglobulin superfamily member 8 precursor: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1, 2 and 3 encode the same protein."
2. NP_001307176.1 immunoglobulin superfamily member 8 precursor: "Transcript Variant: This variant (3) differs in the 3' UTR, compared to variant 1. Variants 1, 2 and 3 encode the same protein."
3. NP_443100.1 immunoglobulin superfamily member 8 precursor: "Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein."

Gene ID: 117166 is WFIKKN1 WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1 on 16p13.3: "This gene encodes a secreted multidomain protein consisting of a signal peptide, a WAP domain, a follistatin domain, an immunoglobulin domain, two tandem Kunitz domains, and an NTR domain. These domains have been implicated frequently in inhibition of various types of proteases, suggesting that the encoded protein may be a multivalent protease inhibitor and may control the action of multiple types of serine proteases as well as metalloproteinases."

1. NP_444514.1 WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 1 precursor.

Gene ID: 121227 is LRIG3 leucine rich repeats and immunoglobulin like domains 3 on 12q14.1.

1. NP_001129523.1 leucine-rich repeats and immunoglobulin-like domains protein 3 isoform 1 precursor: "Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1)."
2. NP_700356.2 leucine-rich repeats and immunoglobulin-like domains protein 3 isoform 2 precursor: "Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region and represents the use of an alternate promoter, compared to variant 1, which results in a protein (isoform 2) with a shorter and distinct N-terminus, compared to isoform 1."

Gene ID: 124857 is WFIKKN2 WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 on 17q21.33: "The WFIKKN1 protein contains a WAP domain, follistatin domain, immunoglobulin domain, two tandem Kunitz domains, and an NTR domain. This gene encodes a WFIKKN1-related protein which has the same domain organization as the WFIKKN1 protein. The WAP-type, follistatin type, Kunitz-type, and NTR-type protease inhibitory domains may control the action of multiple types of proteases."

1. NP_001317270.1 WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2 isoform 2.
2. NP_783165.1 WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2 isoform 1 precursor.

Gene ID: 146722 is CD300LF CD300 molecule like family member f aka IgSF13 on 17q25.1: "This gene encodes a member of the CD300 protein family. Members of this family are cell surface glycoproteins with a single IgV-like extracellular domain, and are involved in the regulation of immune response. The encoded protein is an inhibitory receptor. Alternative splicing results in multiple transcript variants."

1. NP_001276011.1 CMRF35-like molecule 1 isoform 2: "Transcript Variant: This variant (2, also known as sv3) differs in its 5' UTR, uses an alternate start codon, and lacks an exon in the central coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) is shorter and has distinct N- and C-termini, compared to isoform 1."
2. NP_001276012.1 CMRF35-like molecule 1 isoform 3 precursor: "Transcript Variant: This variant (3) includes an alternate exon in the central coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1."
3. NP_001276013.1 CMRF35-like molecule 1 isoform 4: "Transcript Variant: This variant (4) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (4) is longer, compared to isoform 1."
4. NP_001276014.1 CMRF35-like molecule 1 isoform 5: "Transcript Variant: This variant (5, also known as sv1) differs in its 5' UTR, and uses an alternate start codon, compared to variant 1. The encoded isoform (5) has a longer and distinct N-terminus, compared to isoform 1."
5. NP_001276015.1 CMRF35-like molecule 1 isoform 6: "Transcript Variant: This variant (6) differs in its 5' UTR, uses an alternate start codon, and lacks an exon in the central coding region, which results in a frameshift, compared to variant 1. The encoded isoform (6) is shorter and has distinct N- and C-termini, compared to isoform 1."
6. NP_001276016.1 CMRF35-like molecule 1 isoform 7 precursor: "Transcript Variant: This variant (7) lacks an exon in the central coding region, which results in a frameshift, compared to variant (1). The encoded isoform (7) has a shorter and distinct C-terminus, compared to variant 1."
7. NP_620587.2 CMRF35-like molecule 1 isoform 1 precursor: "Transcript Variant: This variant (1) encodes isoform 1."

Gene ID: 147710 is IGSF23 immunoglobulin superfamily member 23 on 19q13.31: "This gene encodes a protein that has one immunoglobulin (Ig) domain and is a member of the immunoglobulin superfamily. Proteins in this superfamily are usually found on or in cell membranes and act as receptors in immune response pathways."

Gene ID: 150084 is IGSF5 immunoglobulin superfamily member 5 on 21q22.2.

Gene ID: 152404 is IGSF11 immunoglobulin superfamily member 11 on 3q13.32.

1. NP_001015887.1 immunoglobulin superfamily member 11 isoform b precursor [variant 2].
2. NP_001340247.1 immunoglobulin superfamily member 11 isoform c [variant 3].
3. NP_001340248.1 immunoglobulin superfamily member 11 isoform d [variant 4].
4. NP_001340249.1 immunoglobulin superfamily member 11 isoform a precursor [variant 5].
5. NP_001340250.1 immunoglobulin superfamily member 11 isoform e precursor [variant 6].
6. NP_001340251.1 immunoglobulin superfamily member 11 isoform f precursor [variant 7].
7. NP_001340252.1 immunoglobulin superfamily member 11 isoform g precursor [variant 8].
8. NP_001340253.1 immunoglobulin superfamily member 11 isoform h precursor [variant 9].
9. NP_001340254.1 immunoglobulin superfamily member 11 isoform i [variant 10].
10. NP_001340255.1 immunoglobulin superfamily member 11 isoform j [variant 11].
11. NP_689751.2 immunoglobulin superfamily member 11 isoform a precursor [variant 1].

Gene ID: 283284 is IGSF22 immunoglobulin superfamily member 22 on 11p15.1.

1. NP_775859.4 immunoglobulin superfamily member 22: "Transcript Variant: This variant (1) represents the protein-coding transcript."

Gene ID: 285313 is IGSF10 immunoglobulin superfamily member 10 on 3q25.1.

1. NP_001171616.1 immunoglobulin superfamily member 10 isoform 2: "Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1."
2. NP_001171617.1 immunoglobulin superfamily member 10 isoform 3: "Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1."
3. NP_849144.2 immunoglobulin superfamily member 10 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."

Gene ID: 492311 is IGIP IgA inducing protein on 5q31.3.

1. NP_001007190.1 IgA-inducing protein homolog precursor.

Major histocompatibility complex genes

Main article: Major histocompatibility complex

Class I

Main article: MHC class I

Main article: Major histocompatibility complex class I gene family

Class II

Main article: MHC class II

Main article: Major histocompatibility complex class II gene family

Class III

Main article: MHC class III

MHC class III region encodes for other immune components, such as complement components (e.g., C2, C4, factor B) and some that encode cytokines (e.g., TNF-α) and also HSPs. They are mainly known from their genes because their gene cluster is present between those of class I and class II. The gene cluster was discovered in between class I and class II genes on the short (p) arm of human chromosome 6. It was later found that it contains many genes for different signalling molecules such as tumour necrosis factors (TNFs) and heat shock proteins. More than 60 MHC class III genes are described, which is about 28% of the total MHC genes (224).

MHC class III genes are located on chromosome 6 (6p21.3) in humans. It covers 700 kb and contains 61 genes. The gene cluster is the most gene-dense region of the human genome. They are basically similar with those of other animals. The functions of many genes are yet unknown. Many retroelements such as human endogenous retrovirus (HERV) and Alu elements are located in the cluster. The region containing genes G11/C4/Z/CYP21/X/Y, varying in size from 142 to 214 kb, is known as the most complex gene cluster in the human genome.

MHC class III genes are similar in humans, mouse, frog (Xenopus tropicalis), and gray short-tailed opossum, but not all genes are common. For example, human NCR3, MIC and MCCD1 are absent in mouse. Human NCR3 and LST1 are absent in opossum. However, birds (chicken and quail) have only a single gene, which codes for a complement component gene (C4). In fishes, the genes are distributed in different chromosomes.

Gene ID: 177 is AGER advanced glycosylation end-product specific receptor on 6p21.32: "The advanced glycosylation end product (AGE) receptor encoded by this gene is a member of the immunoglobulin superfamily of cell surface receptors. It is a multiligand receptor, and besides AGE, interacts with other molecules implicated in homeostasis, development, and inflammation, and certain diseases, such as diabetes and Alzheimer's disease. Many alternatively spliced transcript variants encoding different isoforms, as well as non-protein-coding variants, have been described for this gene (PMID:18089847)."

1. NP_001127.1 advanced glycosylation end product-specific receptor isoform 1 precursor: "Transcript Variant: This variant (1, also known as RAGE) represents the predominant transcript, and encodes isoform 1."
2. NP_001193858.1 advanced glycosylation end product-specific receptor isoform 2 precursor: "Transcript Variant: This variant (2, also known as RAGE_v5) uses an alternate in-frame donor splice site at an internal coding exon compared to variant 1. This results in a longer isoform (2) containing an additional protein segment compared to isoform 1."
3. NP_001193861.1 advanced glycosylation end product-specific receptor isoform 3 precursor: "Transcript Variant: This variant (3, also known as RAGE_v4) uses alternate in-frame acceptor and donor splice sites at two internal coding exons compared to variant 1. This results in a shorter isoform (2) missing two internal protein segments compared to isoform 1."
4. NP_001193863.1 advanced glycosylation end product-specific receptor isoform 4 precursor: "Transcript Variant: This variant (4, also known as RAGE_v6) lacks the penultimate coding exon, and uses alternate donor splice sites at two internal coding exons compared to variant 1. This results in a frame-shift and a shorter isoform (4) with a distinct C-terminus compared to isoform 1."
5. NP_001193865.1 advanced glycosylation end product-specific receptor isoform 5 precursor: "Transcript Variant: This variant (5, also known as RAGE_v9) lacks the penultimate coding exon, and uses alternate acceptor and donor splice sites at two internal coding exons compared to variant 1. This results in a frame-shift and a shorter isoform (5) with a distinct C-terminus compared to isoform 1."
6. NP_001193869.1 advanced glycosylation end product-specific receptor isoform 6 precursor: "Transcript Variant: This variant (6, also known as RAGE_v1) lacks the penultimate coding exon, and uses an alternate donor splice site at another coding exon compared to variant 1. This results in a frame-shift and a shorter isoform (6, also known as esRAGE and soluble RAGE) with a distinct C-terminus compared to isoform 1. This isoform lacks the transmembrane and intracellular domains, is secreted (PMID:18089847), and thought to function as a decoy receptor that inhibits RAGE signaling, and thus prevent the pathological progression of some pathologic conditions, such as Alzheimer's disease (PMID:18431028). Variants 6 and 9 encode the same isoform."
7. NP_001193883.1 advanced glycosylation end product-specific receptor isoform 8 precursor: "Transcript Variant: This variant (8, also known as RAGE_v8) lacks two internal coding exons, and uses an alternate donor splice site at another coding exon compared to variant 1. This results in a frame-shift, and a shorter isoform (8) with a distinct C-terminus compared to isoform 1."
8. NP_001193895.1 advanced glycosylation end product-specific receptor isoform 6 precursor: "Transcript Variant: This variant (9, also known as RAGE_v10) lacks the penultimate coding exon, and uses alternate splice sites at other exons at the 3' end compared to variant 1. This results in a frame-shift and a shorter isoform (6, also known as esRAGE and soluble RAGE) with a distinct C-terminus compared to isoform 1. Variants 6 and 9 encode the same isoform."
9. NP_751947.1 advanced glycosylation end product-specific receptor isoform 7 precursor: "Transcript Variant: This variant (7, also known as RAGE_v16) uses alternate splice sites at several internal coding exons compared to variant 1. This results in a frame-shift and a shorter isoform (7, also known as hRAGEsec) with a distinct C-terminus compared to isoform 1."

Gene ID: 578 is BAK1 BCL2 antagonist/killer 1 on 6p21.31: "The protein encoded by this gene belongs to the BCL2 protein family. BCL2 family members form oligomers or heterodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. This protein localizes to mitochondria, and functions to induce apoptosis. It interacts with and accelerates the opening of the mitochondrial voltage-dependent anion channel, which leads to a loss in membrane potential and the release of cytochrome c. This protein also interacts with the tumor suppressor P53 after exposure to cell stress."

Gene ID: 629 is CFB complement factor B on 6p21.33: "This gene encodes complement factor B, a component of the alternative pathway of complement activation. Factor B circulates in the blood as a single chain polypeptide. Upon activation of the alternative pathway, it is cleaved by complement factor D yielding the noncatalytic chain Ba and the catalytic subunit Bb. The active subunit Bb is a serine protease which associates with C3b to form the alternative pathway C3 convertase. Bb is involved in the proliferation of preactivated B lymphocytes, while Ba inhibits their proliferation. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. This cluster includes several genes involved in regulation of the immune reaction. Polymorphisms in this gene are associated with a reduced risk of age-related macular degeneration. The polyadenylation site of this gene is 421 bp from the 5' end of the gene for complement component 2."

1. NP_001701.2 complement factor B preproprotein.

Gene ID: 717 is C2 complement C2 on 6p21.33: "Component C2 is a serum glycoprotein that functions as part of the classical pathway of the complement system. Activated C1 cleaves C2 into C2a and C2b. The serine proteinase C2a then combines with complement factor 4b to create the C3 or C5 convertase. Deficiency of C2 has been reported to associated with certain autoimmune diseases and SNPs in this gene have been associated with altered susceptibility to age-related macular degeneration. This gene localizes within the class III region of the MHC on the short arm of chromosome 6. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants have been described in publications but their full-length sequence has not been determined."

1. NP_000054.2 complement C2 isoform 1 preproprotein: "Transcript Variant: This variant (1) encodes the longest isoform (1)."
2. NP_001139375.1 complement C2 isoform 2 precursor: "Transcript Variant: This variant (2) lacks two in-frame exons in the 5' coding region, compared to variant 1, that results in an isoform (2) with a shorter N-terminus that lacks one of two SUSHI repeat domains, compared to isoform 1."
3. NP_001171534.1 complement C2 isoform 3: "Transcript Variant: This variant (3) has an alternate 5' sequence and lacks an in-frame internal segment, as compared to variant 1. The resulting isoform (3) is shorter; it has a distinct N-terminus and lacks an internal segment, as compared to isoform 1."
4. NP_001269386.1 complement C2 isoform 4: "Transcript Variant: This variant (4) represents use of an alternate promoter and has multiple differences in the coding region compared to variant 1. The resulting protein (isoform 4) has a distinct N-terminus and is shorter than isoform 1."
5. NP_001269387.1 complement C2 isoform 5: "Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (5) has a shorter and distinct N-terminus compared to isoform 1."
6. NP_001269388.1 complement C2 isoform 6 precursor: "Transcript Variant: This variant (6) uses an alternate 3' exon structure, and thus differs in the 3' coding region and 3' UTR compared to variant 1. It encodes isoform 6 which is shorter and has a distinct C-terminus, compared to isoform 1."

Gene ID: 720 is C4A complement C4A (Rodgers blood group) aka MHC class III region complement on 6p21.33: "This gene encodes the acidic form of complement factor 4, part of the classical activation pathway. The protein is expressed as a single chain precursor which is proteolytically cleaved into a trimer of alpha, beta, and gamma chains prior to secretion. The trimer provides a surface for interaction between the antigen-antibody complex and other complement components. The alpha chain is cleaved to release C4 anaphylatoxin, an antimicrobial peptide and a mediator of local inflammation. Deficiency of this protein is associated with systemic lupus erythematosus and type I diabetes mellitus. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. Varying haplotypes of this gene cluster exist, such that individuals may have 1, 2, or 3 copies of this gene. Two transcript variants encoding different isoforms have been found for this gene."

1. NP_001239133.1 complement C4-A isoform 2 preproprotein: "Transcript Variant: This variant (2) lacks an alternate in-frame segment compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1."
2. NP_009224.2 complement C4-A isoform 1 preproprotein: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 721 is C4B complement C4B (Chido blood group) on 6p21.33: "This gene encodes the basic form of complement factor 4, part of the classical activation pathway. The protein is expressed as a single chain precursor which is proteolytically cleaved into a trimer of alpha, beta, and gamma chains prior to secretion. The trimer provides a surface for interaction between the antigen-antibody complex and other complement components. The alpha chain may be cleaved to release C4 anaphylatoxin, a mediator of local inflammation. Deficiency of this protein is associated with systemic lupus erythematosus. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. Varying haplotypes of this gene cluster exist, such that individuals may have 1, 2, or 3 copies of this gene. In addition, this gene exists as a long form and a short form due to the presence or absence of a 6.4 kb endogenous HERV-K retrovirus in intron 9."

1. NP_001002029.3 complement C4-B preproprotein.

Gene ID: 780 is DDR1 discoidin domain receptor tyrosine kinase 1 on 6p21.33: "Receptor tyrosine kinases play a key role in the communication of cells with their microenvironment. These kinases are involved in the regulation of cell growth, differentiation and metabolism. The protein encoded by this gene belongs to a subfamily of tyrosine kinase receptors with homology to Dictyostelium discoideum protein discoidin I in their extracellular domain, and that are activated by various types of collagen. Expression of this protein is restricted to epithelial cells, particularly in the kidney, lung, gastrointestinal tract, and brain. In addition, it has been shown to be significantly overexpressed in several human tumors. Alternatively spliced transcript variants encoding different isoforms have been described for this gene."

1. NP_001189450.1 epithelial discoidin domain-containing receptor 1 isoform 4 precursor: "Transcript Variant: This variant (4) is missing an internal coding exon compared to variant 1. This results in a frame-shift, and early translation termination, rendering this transcript a candidate for nonsense-mediated mRNA decay (NMD). However, the encoded isoform (4, also known as DDR1d) is represented as it has been detected in vivo in several colon carcinoma cell lines (PMID:11344127). This isoform is truncated and lacks the catalytic tyrosine kinase domain, therefore, most likely lacks intrinsic tyrosine kinase activity. It may function in some other regulatory capacity."
2. NP_001189451.1 epithelial discoidin domain-containing receptor 1 isoform 5 precursor: "Transcript Variant: This variant (5) is missing an internal coding exon, and uses an alternate acceptor splice site at one of the coding exons compared to variant 1. This results in localized frame-shift, and a shorter isoform (5, also known as DDR1e) compared to isoform 1. This isoform lacks the ATP binding site, therefore, most likely lacks intrinsic tyrosine kinase activity. It may function in some other regulatory capacity."
3. NP_001189452.1 epithelial discoidin domain-containing receptor 1 isoform 6 precursor: "Transcript Variant: This variant (6) contains an alternate 5' terminal exon compared to variant 1. This results in translation initiation from an in-frame upstream start codon, and a longer isoform (6) with a distinct N-terminus compared to isoform 1."
4. NP_001284581.1 epithelial discoidin domain-containing receptor 1 isoform 1 precursor: "Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1. It encodes isoform 1 (also known as DDR1a). Variants 1, 7, and 8 encode the same isoform (1)."
5. NP_001284582.1 epithelial discoidin domain-containing receptor 1 isoform 1 precursor: "Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1. It encodes isoform 1 (also known as DDR1a). Variants 1, 7, and 8 encode the same isoform (1)."
6. NP_001284583.1 epithelial discoidin domain-containing receptor 1 isoform 2 precursor: "Transcript Variant: This variant (9) contains an additional in-frame coding exon and differs in the 5' UTR compared to variant 1, resulting in a longer isoform (2, also known as DDR1b) with a 37 aa protein segment not found in isoform 1. Variants 2 and 9 encode the same isoform (2)."
7. NP_001945.3 epithelial discoidin domain-containing receptor 1 isoform 1 precursor: "Transcript Variant: This variant (1) represents the predominant transcript, and encodes isoform 1 (also known as DDR1a). Variants 1, 7, and 8 encode the same isoform (1)."
8. NP_054699.2 epithelial discoidin domain-containing receptor 1 isoform 2 precursor: "Transcript Variant: This variant (2) contains an additional in-frame coding exon compared to variant 1, resulting in a longer isoform (2, also known as DDR1b) with a 37 aa protein segment not found in isoform 1. Variants 2 and 9 encode the same isoform (2)."
9. NP_054700.2 epithelial discoidin domain-containing receptor 1 isoform 3 precursor: "Transcript Variant: This variant (3) contains an additional in-frame coding exon, and uses an alternate in-frame acceptor splice site at one of the coding exons compared to variant 1. This results in the longest isoform (3, also known as DDR1c) with additional protein segments not found in isoform 1."

Gene ID: 1041 is CDSN corneodesmosin on 6p21.33: "This gene encodes a protein found in corneodesmosomes, which localize to human epidermis and other cornified squamous epithelia. The encoded protein undergoes a series of cleavages during corneocyte maturation. This gene is highly polymorphic in human populations, and variation has been associated with skin diseases such as psoriasis, hypotrichosis and peeling skin syndrome. The gene is located in the major histocompatibility complex (MHC) class I region on chromosome 6."

1. NP_001255.4 corneodesmosin precursor.

Gene ID: 1192 is CLIC1 chloride intracellular channel 1 on 6p21.33: "Chloride channels are a diverse group of proteins that regulate fundamental cellular processes including stabilization of cell membrane potential, transepithelial transport, maintenance of intracellular pH, and regulation of cell volume. Chloride intracellular channel 1 is a member of the p64 family; the protein localizes principally to the cell nucleus and exhibits both nuclear and plasma membrane chloride ion channel activity."

1. NP_001274522.1 chloride intracellular channel protein 1: "Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein."
2. NP_001274523.1 chloride intracellular channel protein 1: "Transcript Variant: This variant (3) has an alternate exon in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein."
3. NP_001279.2 chloride intracellular channel protein 1: "Transcript Variant: This variant (2) has an alternate exon in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein."

Gene ID: 1432 is MAPK14 mitogen-activated protein kinase 14 on 6p21.31: "The protein encoded by this gene is a member of the MAP kinase family. MAP kinases act as an integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. This kinase is activated by various environmental stresses and proinflammatory cytokines. The activation requires its phosphorylation by MAP kinase kinases (MKKs), or its autophosphorylation triggered by the interaction of MAP3K7IP1/TAB1 protein with this kinase. The substrates of this kinase include transcription regulator ATF2, MEF2C, and MAX, cell cycle regulator CDC25B, and tumor suppressor p53, which suggest the roles of this kinase in stress related transcription and cell cycle regulation, as well as in genotoxic stress response. Four alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported."

1. NP_001306.1 mitogen-activated protein kinase 14 isoform 1: "Transcript Variant: This variant (1) encodes the longest isoform (1) [...] STKc_p38alpha; Catalytic domain of the Serine/Threonine Kinase, p38alpha Mitogen-Activated Protein Kinase (also called MAPK14)."
2. NP_620581.1 mitogen-activated protein kinase 14 isoform 2: "Transcript Variant: This variant (2) contains a different segment within the coding region when compared to variant 1. The translation frame remains the same, and the resulting isoform 2 has an internal segment different from that of isoform 1."
3. NP_620582.1 mitogen-activated protein kinase 14 isoform 3: "Transcript Variant: This variant (3) contains a different internal segment within the coding region, and a different 3' coding region as well as a different 3' UTR, when compared to variant 1. It thus encodes an isoform that has a different internal segment, and a distinct C-terminus, as compared to isoform 1."
4. NP_620583.1 mitogen-activated protein kinase 14 isoform 4: "Transcript Variant: This variant (4) contains a different internal segment when compared to variant 1. It thus encodes an isoform that has a different and shorter internal segment, as compared to isoform 1."

Gene ID: 1460 is CSNK2B casein kinase 2 beta on 6p21.33: "This gene encodes the beta subunit of casein kinase II, a ubiquitous protein kinase which regulates metabolic pathways, signal transduction, transcription, translation, and replication. The enzyme is composed of three subunits, alpha, alpha prime and beta, which form a tetrameric holoenzyme. The alpha and alpha prime subunits are catalytic, while the beta subunit serves regulatory functions. The enzyme localizes to the endoplasmic reticulum and the Golgi apparatus. Two transcript variants encoding different isoforms have been found for this gene."

1. NP_001269314.1 casein kinase II subunit beta isoform 2: "Transcript Variant: This variant (2) uses an alternate in-frame splice junction in the 3' coding sequence compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1."
2. NP_001311.3 casein kinase II subunit beta isoform 1: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 1589 is CYP21A2 cytochrome P450 family 21 subfamily A member 2 on 6p21.33: "This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and hydroxylates steroids at the 21 position. Its activity is required for the synthesis of steroid hormones including cortisol and aldosterone. Mutations in this gene cause congenital adrenal hyperplasia. A related pseudogene is located near this gene; gene conversion events involving the functional gene and the pseudogene are thought to account for many cases of steroid 21-hydroxylase deficiency. Two transcript variants encoding different isoforms have been found for this gene."

1. NP_000491.4 steroid 21-hydroxylase isoform a: "Transcript Variant: This variant (1) encodes the longer isoform (a)."
2. NP_001122062.3 steroid 21-hydroxylase isoform b: "Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a."
3. NP_001355072.1 steroid 21-hydroxylase isoform c: "Transcript Variant: This variant (3), as well as variant 4, encodes isoform c."
4. NP_001355073.1 steroid 21-hydroxylase isoform c: "Transcript Variant: This variant (4), as well as variant 3, encodes isoform c."

Gene ID: 1797 is DXO decapping exoribonuclease aka DOM3Z on 6p21.33: "This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. The function of its protein product is unknown, but its ubiquitous expression and conservation in both simple and complex eukaryotes suggests that this may be a housekeeping gene."

1. NP_001358134.1 decapping and exoribonuclease protein isoform 1: "Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 3 encode the same protein."
2. NP_001358135.1 decapping and exoribonuclease protein isoform 1: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode the same protein."
3. NP_005501.2 decapping and exoribonuclease protein isoform 2.

Gene ID: 2289 is FKBP5 FKBP prolyl isomerase 5 on 6p21.31: "The protein encoded by this gene is a member of the immunophilin protein family, which play a role in immunoregulation and basic cellular processes involving protein folding and trafficking. This encoded protein is a cis-trans prolyl isomerase that binds to the immunosuppressants FK506 and rapamycin. It is thought to mediate calcineurin inhibition. It also interacts functionally with mature hetero-oligomeric progesterone receptor complexes along with the 90 kDa heat shock protein and P23 protein. This gene has been found to have multiple polyadenylation sites. Alternative splicing results in multiple transcript variants."

1. NP_001139247.1 peptidyl-prolyl cis-trans isomerase FKBP5 isoform 1: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1)."
2. NP_001139248.1 peptidyl-prolyl cis-trans isomerase FKBP5 isoform 1: "Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1)."
3. NP_001139249.1 peptidyl-prolyl cis-trans isomerase FKBP5 isoform 2: "Transcript Variant: This variant (4) has multiple differences in the coding region and 3' UTR compared to variant 1 which result in a frameshift. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1."
4. NP_004108.1 peptidyl-prolyl cis-trans isomerase FKBP5 isoform 1: "Transcript Variant: This variant (1) represents the shortest transcript and encodes the longer isoform (1). Variants 1, 2 and 3 encode the same isoform (1)."

Gene ID: 2914 is GRM4 glutamate metabotropic receptor 4 on 6p21.31: "L-glutamate is the major excitatory neurotransmitter in the central nervous system and activates both ionotropic and metabotropic glutamate receptors. Glutamatergic neurotransmission is involved in most aspects of normal brain function and can be perturbed in many neuropathologic conditions. The metabotropic glutamate receptors are a family of G protein-coupled receptors, that have been divided into 3 groups on the basis of sequence homology, putative signal transduction mechanisms, and pharmacologic properties. Group I includes GRM1 and GRM5 and these receptors have been shown to activate phospholipase C. Group II includes GRM2 and GRM3 while Group III includes GRM4, GRM6, GRM7 and GRM8. Group II and III receptors are linked to the inhibition of the cyclic AMP cascade but differ in their agonist selectivities. Several transcript variants encoding different isoforms have been found for this gene."

1. NP_000832.1 metabotropic glutamate receptor 4 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."
2. NP_001243738.1 metabotropic glutamate receptor 4 isoform 2: "Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence, and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform 1."
3. NP_001243740.1 metabotropic glutamate receptor 4 isoform 4 precursor: "Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1."
4. NP_001243741.1 metabotropic glutamate receptor 4 isoform 5: "Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (5) has a shorter and distinct N-terminus compared to isoform 1."
5. NP_001243742.1 metabotropic glutamate receptor 4 isoform 6: "Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (6) has a shorter and distinct N-terminus compared to isoform 1."
6. NP_001269776.1 metabotropic glutamate receptor 4 isoform 8: "Transcript Variant: This variant (8) uses an alternate 5' structure and thus differs in the 5' UTR and 5' coding region compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (8) with a shorter N-terminus, compared to isoform 1."

Gene ID: 4295 is MLN motilin on 6p21.31: "This gene encodes a small peptide hormone that is secreted by cells of the small intestine to regulate gastrointestinal contractions and motility. Proteolytic processing of the secreted protein produces the mature peptide and a byproduct referred to as motilin-associated peptide (MAP). Three transcript variants encoding different preproprotein isoforms but the same mature peptide have been found for this gene."

1. NP_001035198.1 promotilin isoform 2 preproprotein: "Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter preproprotein (isoform 2) but not affecting the mature peptide."
2. NP_001171627.1 promotilin isoform 3 preproprotein: "Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1."
3. NP_002409.1 promotilin isoform 1 preproprotein: "ranscript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."

Gene ID: 4439 is MSH5 mutS homolog 5 on 6p21.33: "This gene encodes a member of the mutS family of proteins that are involved in DNA mismatch repair and meiotic recombination. This protein is similar to a Saccharomyces cerevisiae protein that participates in segregation fidelity and crossing-over events during meiosis. This protein plays a role in promoting ionizing radiation-induced apoptosis. This protein forms hetero-oligomers with another member of this family, mutS homolog 4. Polymorphisms in this gene have been linked to various human diseases, including IgA deficiency, common variable immunodeficiency, and premature ovarian failure. Alternative splicing results multiple transcript variants. Read-through transcription also exists between this gene and the downstream chromosome 6 open reading frame 26 (C6orf26) gene."

1. NP_002432.1 mutS protein homolog 5 isoform c: "Transcript Variant: This variant (3) differs in the 5' UTR and uses alternate in-frame splice sites in both the central and 3' coding regions, compared to variant 1, resulting in an isoform (c) that is longer than isoform a. Both variants 3 and 4 encode the same isoform."
2. NP_079535.4 mutS protein homolog 5 isoform a: "Transcript Variant: This variant (1) represents the shortest transcript and encodes the shortest isoform (a)."
3. NP_751897.1 mutS protein homolog 5 isoform b: "Transcript Variant: This variant (2) uses alternate in-frame splice sites in both the central and 3' coding regions, compared to variant 1, resulting in an isoform (b) that is longer than isoform a."
4. NP_751898.1 mutS protein homolog 5 isoform c: "Transcript Variant: This variant (4) uses alternate in-frame splice sites in both the central and 3' coding regions, compared to variant 1, resulting in an isoform (c) that is longer than isoform a. Both variants 3 and 4 encode the same isoform."

Gene ID: 4736 is RPL10A ribosomal protein L10a on 6p21.31: "Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L1P family of ribosomal proteins. It is located in the cytoplasm. The expression of this gene is downregulated in the thymus by cyclosporin-A (CsA), an immunosuppressive drug. Studies in mice have shown that the expression of the ribosomal protein L10a gene is downregulated in neural precursor cells during development. This gene previously was referred to as NEDD6 (neural precursor cell expressed, developmentally downregulated 6), but it has been renamed RPL10A (ribosomal protein 10a). As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome."

Gene ID: 4758 is NEU1 neuraminidase 1 on 6p21.33: "The protein encoded by this gene is a lysosomal enzyme that cleaves terminal sialic acid residues from substrates such as glycoproteins and glycolipids. In the lysosome, this enzyme is part of a heterotrimeric complex together with beta-galactosidase and cathepsin A (the latter is also referred to as 'protective protein'). Mutations in this gene can lead to sialidosis, a lysosomal storage disease that can be type 1 (cherry red spot-myoclonus syndrome or normosomatic type), which is late-onset, or type 2 (the dysmorphic type), which occurs at an earlier age with increased severity."

1. NP_000425.1 sialidase-1 precursor.

Gene ID: 4795 is NFKBIL1 NFKB inhibitor like 1 on 6p21.33: "This gene encodes a divergent member of the I-kappa-B family of proteins. Its function has not been determined. The gene lies within the major histocompatibility complex (MHC) class I region on chromosome 6. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001138433.1 NF-kappa-B inhibitor-like protein 1 isoform 2: "Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1."
2. NP_001138434.1 NF-kappa-B inhibitor-like protein 1 isoform 3: "Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1."
3. NP_001138435.1 NF-kappa-B inhibitor-like protein 1 isoform 4: "Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (4) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 1."
4. NP_004998.3 NF-kappa-B inhibitor-like protein 1 isoform 1: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."

Gene ID: 4855 is NOTCH4 notch receptor 4 on 6p21.32: "This gene encodes a member of the NOTCH family of proteins. Members of this Type I transmembrane protein family share structural characteristics including an extracellular domain consisting of multiple epidermal growth factor-like (EGF) repeats, and an intracellular domain consisting of multiple different domain types. Notch signaling is an evolutionarily conserved intercellular signaling pathway that regulates interactions between physically adjacent cells through binding of Notch family receptors to their cognate ligands. The encoded preproprotein is proteolytically processed in the trans-Golgi network to generate two polypeptide chains that heterodimerize to form the mature cell-surface receptor. This receptor may play a role in vascular, renal and hepatic development. Mutations in this gene may be associated with schizophrenia. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed."

1. NP_004548.3 neurogenic locus notch homolog protein 4 preproprotein: "Transcript Variant: This variant (1) represents the longest transcript and encodes the protein."

Gene ID: 5460 is POU5F1 POU class 5 homeobox 1 on 6p21.33: "This gene encodes a transcription factor containing a POU homeodomain that plays a key role in embryonic development and stem cell pluripotency. Aberrant expression of this gene in adult tissues is associated with tumorigenesis. This gene can participate in a translocation with the Ewing's sarcoma gene on chromosome 21, which also leads to tumor formation. Alternative splicing, as well as usage of alternative AUG and non-AUG translation initiation codons, results in multiple isoforms. One of the AUG start codons is polymorphic in human populations. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12."

1. NP_001167002.1 POU domain, class 5, transcription factor 1 isoform 2: "Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame non-AUG (CUG) start codon, compared to variant 1. The resulting isoform (2, also known as OCT4B-190) is shorter at the N-terminus, compared to isoform 1. Variants 2 and 3 encode the same isoform (2). This variant may encode an additional isoform through the use of an alternative downstream AUG start codon. Use of alternate start codons and the non-AUG start codon is described in PMID:19489092."
2. NP_001272915.1 POU domain, class 5, transcription factor 1 isoform 4: "Transcript Variant: This variant (4, also known as OCT4B1) contains multiple differences in the 5' UTR and the 5' coding region, compared to variant 1, and initiates translation at a downstream in-frame AUG start codon. The resulting isoform (4, also known as OCT4B-164) is shorter at the N-terminus, compared to isoform 1."
3. NP_001272916.1 POU domain, class 5, transcription factor 1 isoform 3: "Transcript Variant: This variant (5, also known as OCT4B) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate AUG start codon, compared to variant 1. The resulting isoform (3, also known as OCT4B-265) is shorter and has a distinct N-terminus, compared to isoform 1. This variant represents an allele of variant 2 that contains an AUG start codon that is polymorphic in human populations (see rs3130932). This variant may encode additional isoforms through the use of alternative downstream AUG and non-AUG start codons, as described in PMID:19489092."
4. NP_002692.2 POU domain, class 5, transcription factor 1 isoform 1: "Transcript Variant: This variant (1, also known as OCT4A) represents the shortest transcript and encodes the longest isoform (1)."
5. NP_976034.4 POU domain, class 5, transcription factor 1 isoform 2: "Transcript Variant: This variant (2, also known as OCT4B) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame non-AUG (CUG) start codon, compared to variant 1. The resulting isoform (2, also known as OCT4B-190) is shorter at the N-terminus, compared to isoform 1. Variants 2 and 3 encode the same isoform (2). This variant may encode additional isoforms through the use of an alternative downstream AUG start codon, as well as an alternative upstream AUG start codon, which is polymorphic in human populations (AGG allele represented in this RefSeq; see rs3130932). Use of alternate start codons and the non-AUG start codon is described in PMID:19489092."

Gene ID: 5514 is PPP1R10 protein phosphatase 1 regulatory subunit 10 aka MHC class I region proline-rich protein CAT53 on 6p21.33: "This gene encodes a protein phosphatase 1 binding protein. The encoded protein plays a role in many cellular processes including cell cycle progression, DNA repair and apoptosis by regulating the activity of protein phosphatase 1. This gene lies within the major histocompatibility complex class I region on chromosome 6, and alternatively spliced transcript variants have been observed for this gene."

1. NP_001363124.1 serine/threonine-protein phosphatase 1 regulatory subunit 10: "Transcript Variant: This variant (3) represents the longest transcript. Variants 1 and 3 both encode the same protein."
2. NP_002705.2 serine/threonine-protein phosphatase 1 regulatory subunit 10 [variant 1?].

Gene ID: 5603 is MAPK13 mitogen-activated protein kinase 13 on 6p21.31: "This gene encodes a member of the mitogen-activated protein (MAP) kinase family. MAP kinases act as an integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. The encoded protein is a p38 MAP kinase and is activated by proinflammatory cytokines and cellular stress. Substrates of the encoded protein include the transcription factor ATF2 and the microtubule dynamics regulator stathmin. Alternatively spliced transcript variants have been observed for this gene."

1. NP_002745.1 mitogen-activated protein kinase 13: "Transcript Variant: This variant (1) represents the longer transcript and is protein-coding."

Gene ID: 6204 is RPS10 ribosomal protein S10 on 6p21.31: "Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S10E family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternate splicing results in multiple transcript variants that encode the same protein. Naturally occurring read-through transcription occurs between this locus and the neighboring locus NUDT3 (nudix (nucleoside diphosphate linked moiety X)-type motif 3)."

1. NP_001005.1 40S ribosomal protein S10: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein."
2. NP_001190174.1 40S ribosomal protein S10: "Transcript Variant: This variant (1) represents the longer transcript. Variants 1, 2 and 3 encode the same protein."
3. NP_001191020.1 40S ribosomal protein S10: "Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein."

Gene ID: 6631 is SNRPC small nuclear ribonucleoprotein polypeptide C on 6p21.31: "This gene encodes one of the specific protein components of the U1 small nuclear ribonucleoprotein (snRNP) particle required for the formation of the spliceosome. The encoded protein participates in the processing of nuclear precursor messenger RNA splicing. snRNP particles are attacked by autoantibodies frequently produced by patients with connective tissue diseases. The genome contains several pseudogenes of this functional gene. Alternative splicing results in a non-coding transcript variant."

1. NP_003084.1 U1 small nuclear ribonucleoprotein C: "Transcript Variant: This variant (1) represents the longer transcript."

Gene ID: 6732 is SRPK1 SRSF protein kinase 1 on 6p21.31: "This gene encodes a serine/arginine protein kinase specific for the SR (serine/arginine-rich domain) family of splicing factors. The protein localizes to the nucleus and the cytoplasm. It is thought to play a role in regulation of both constitutive and alternative splicing by regulating intracellular localization of splicing factors. Alternative splicing of this gene results in multiple transcript variants. Additional alternatively spliced transcript variants have been described for this gene, but their full length nature have not been determined."

1. NP_003128.3 SRSF protein kinase 1: "Transcript Variant: This variant (1) represents the shorter transcript."

Gene ID: 6882 is TAF11 TATA-box binding protein associated factor 11 on 6p21.31: "Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes a small subunit of TFIID that is present in all TFIID complexes and interacts with TBP. This subunit also interacts with another small subunit, TAF13, to form a heterodimer with a structure similar to the histone core structure. Two transcript variants encoding different isoforms have been found for this gene."

1. NP_001257417.1 transcription initiation factor TFIID subunit 11 isoform 2: "Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1."
2. NP_005634.1 transcription initiation factor TFIID subunit 11 isoform 1: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 6941 is TCF19 transcription factor 19 on 6p21.33: "This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants."

1. NP_001070979.1 transcription factor 19: "Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein."
2. NP_001305837.1 transcription factor 19: "Transcript Variant: This variant (3) lacks an alternate segment in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein."
3. NP_009040.2 transcription factor 19: "Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same protein."

Gene ID: 6954 is TCP11 t-complex 11 on 6p21.31.

1. NP_001248746.2 T-complex protein 11 homolog isoform 3: "Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1."
2. NP_001248747.1 T-complex protein 11 homolog isoform 4: "Transcript Variant: This variant (4) lacks an exon in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1."
3. NP_001248748.1 T-complex protein 11 homolog isoform 5: "Transcript Variant: This variant (5) lacks an exon and uses an alternate splice site in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (5) is shorter than isoform 1."
4. NP_001248749.1 T-complex protein 11 homolog isoform 6: "Transcript Variant: This variant (6) differs in the 5' UTR, includes an alternate internal exon in the 5' region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 6 and 7 encode the same isoform (6), which has a shorter N-terminus compared to isoform 1."
5. NP_001248750.1 T-complex protein 11 homolog isoform 6: "Transcript Variant: This variant (7) has multiple differences, including the use of a downstream, in-frame start codon, compared to variant 1. Variants 6 and 7 encode the same isoform (6), which has a shorter N-terminus compared to isoform 1."
6. NP_001353252.1 T-complex protein 11 homolog isoform 6 [variant 8].
7. NP_001353253.1 T-complex protein 11 homolog isoform 2 [variant 9].
8. NP_001353254.1 T-complex protein 11 homolog isoform 7 [variant 10].
9. NP_001353255.1 T-complex protein 11 homolog isoform 8 [variant 11].
10. NP_001353256.1 T-complex protein 11 homolog isoform 9 [variant 12].
11. NP_001353257.1 T-complex protein 11 homolog isoform 9 [variant 13].
12. NP_001353258.1 T-complex protein 11 homolog isoform 9 [variant 14].
13. NP_001353259.1 T-complex protein 11 homolog isoform 10 [variant 15].
14. NP_001353260.1 T-complex protein 11 homolog isoform 11 [variant 16].
15. NP_001353261.1 T-complex protein 11 homolog isoform 12 [variant 17].
16. NP_001357616.1 T-complex protein 11 homolog isoform 1: "Transcript Variant: This variant (1) encodes the longest isoform (1)."
17. NP_061149.1 T-complex protein 11 homolog isoform 2: "Transcript Variant: This variant (2) has multiple differences, including the use of an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1."

Gene ID: 7148 is TNXB tenascin XB on 6p21.33-p21.32: "This gene encodes a member of the tenascin family of extracellular matrix glycoproteins. The tenascins have anti-adhesive effects, as opposed to fibronectin which is adhesive. This protein is thought to function in matrix maturation during wound healing, and its deficiency has been associated with the connective tissue disorder Ehlers-Danlos syndrome. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. It is one of four genes in this cluster which have been duplicated. The duplicated copy of this gene is incomplete and is a pseudogene which is transcribed but does not encode a protein. The structure of this gene is unusual in that it overlaps the CREBL1 and CYP21A2 genes at its 5' and 3' ends, respectively. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001352205.1 tenascin-X isoform 3 precursor: "Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3). It should be noted that the exon combination of this variant lacks full-length transcript support in human; it is predicted based on a combination of partial human and homologous transcript alignments."
2. NP_061978.6 tenascin-X isoform 1 precursor: "Transcript Variant: This variant (XB) uses an alternate in-frame splice junction compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 3. It should be noted that the exon combination of this variant lacks full-length transcript support in human; it is predicted based on a combination of partial human and homologous transcript alignments."
3. NP_115859.2 tenascin-X isoform 2: "Transcript Variant: This variant (XB-S) is transcribed from a cryptic internal promoter sequence and is substantially shorter than variant 3 at the 5' end. It encodes isoform 2, which is identical to the C-terminus of the full-length protein, isoform 3."

Gene ID: 7287 is TULP1 TUB like protein 1 on 6p21.31: "This gene encodes a member of the tubby-like gene family (TULPs). Members of this family have been identified in plants, vertebrates, and invertebrates. TULP proteins share a conserved C-terminal region of approximately 200 amino acid residues. The protein encoded by this gene is thought to play a role in the physiology of photoreceptors. Mutations in this gene are associated with recessive juvenile retinitis pigmentosa and Leber congenital amaurosis-15."

1. NP_001276324.1 tubby-related protein 1 isoform 2: "Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter than isoform 1."
2. NP_003313.3 tubby-related protein 1 isoform 1: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 7407 is VARS1 valyl-tRNA synthetase 1 on 6p21.33: "Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. The protein encoded by this gene belongs to class-I aminoacyl-tRNA synthetase family and is located in the class III region of the major histocompatibility complex."

Gene ID: 7629 is ZNF76 zinc finger protein 76 on 6p21.31.

1. NP_001278961.1 zinc finger protein 76 isoform 2: "Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1."
2. NP_003418.2 zinc finger protein 76 isoform 1: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 7936 is NELFE negative elongation factor complex member E aka major histocompatibility complex gene RD on 6p21.33: "The protein encoded by this gene is part of a complex termed negative elongation factor (NELF) which represses RNA polymerase II transcript elongation. This protein bears similarity to nuclear RNA-binding proteins; however, it has not been demonstrated that this protein binds RNA. The protein contains a tract of alternating basic and acidic residues, largely arginine (R) and aspartic acid (D). The gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6."

1. NP_002895.3 negative elongation factor E.

Gene ID: 7940 is LST1 leukocyte specific transcript 1 on 6p21.33: "The protein encoded by this gene is a membrane protein that can inhibit the proliferation of lymphocytes. Expression of this gene is enhanced by lipopolysaccharide, interferon-gamma, and bacteria. Several transcript variants encoding different isoforms have been found for this gene."

1. NP_001160010.1 leukocyte-specific transcript 1 protein isoform 6: "Transcript Variant: This variant (6) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (6) that is shorter than isoform 1. The 5' UTR of this variant is incomplete because the transcripts supporting this CDS exon combination lack a complete 5' UTR, and alternative splicing choices exist further upstream."
2. NP_009092.3 leukocyte-specific transcript 1 protein isoform 1: "Transcript Variant: This variant (1) encodes the longest isoform (1). The 5' UTR of this variant is incomplete because the transcripts supporting this CDS exon combination lack a complete 5' UTR, and alternative splicing choices exist further upstream."
3. NP_995309.2 leukocyte-specific transcript 1 protein isoform 2: "Transcript Variant: This variant (2) includes an additional exon in the 5' UTR and lacks an internal exon that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1."
4. NP_995310.2 leukocyte-specific transcript 1 protein isoform 3: "Transcript Variant: This variant (3) includes an additional exon in the 5' UTR, lacks an alternate in-frame exon in the 5' coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1."
5. NP_995311.2 leukocyte-specific transcript 1 protein isoform 4: "Transcript Variant: This variant (4) includes an additional exon in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1."
6. NP_995312.2 leukocyte-specific transcript 1 protein isoform 5: "Transcript Variant: This variant (5) lacks an alternate exon in the central coding region and uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (5) has a distinct C-terminus and is shorter than isoform 1. The 5' UTR of this variant is incomplete because the transcripts supporting this CDS exon combination lack a complete 5' UTR, and alternative splicing choices exist further upstream."

Gene ID: 8449 is DHX16 DEAH-box helicase 16 on 6p21.33: "DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a functional homolog of fission yeast Prp8 protein involved in cell cycle progression. This gene is mapped to the MHC region on chromosome 6p21.3, a region where many malignant, genetic and autoimmune disease genes are linked. Three transcript variants encoding different isoforms have been found for this gene."

1. NP_001157711.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform 2: "Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1."
2. NP_001350444.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform 3: "Transcript Variant: This variant (3) contains an alternate exon compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1."
3. NP_003578.2 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform 1: "Transcript Variant: This variant (1) encodes the longest isoform (1)."

Gene ID: 8859 is STK19 serine/threonine kinase 19 aka MHC class III HLA-RP1 on 6p21.33: "This gene encodes a serine/threonine kinase which localizes predominantly to the nucleus. Its specific function is unknown; it is possible that phosphorylation of this protein is involved in transcriptional regulation. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6 and expresses two transcript variants."

1. NP_004188.1 serine/threonine-protein kinase 19 isoform 1: "Transcript Variant: This variant (1) uses an alternate splice site in the coding region, compared to variant 2. It encodes isoform 1 which is shorter compared to isoform 2. Although isoforms 1 and 2 differ in the kinase domain, it appears that there is no difference in kinase activity between isoforms 1 and 2."
2. NP_115830.1 serine/threonine-protein kinase 19 isoform 2: "Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2). Although isoforms 1 and 2 differ in the kinase domain, it appears that there is no difference in kinase activity between isoforms 1 and 2."

Gene ID: 8870 is IER3 immediate early response 3 on 6p21.33: "This gene functions in the protection of cells from Fas- or tumor necrosis factor type alpha-induced apoptosis. Partially degraded and unspliced transcripts are found after virus infection in vitro, but these transcripts are not found in vivo and do not generate a valid protein."

Gene ID: 9656 is MDC1 mediator of DNA damage checkpoint 1 on 6p21.33: "The protein encoded by this gene contains an N-terminal forkhead domain, two BRCA1 C-terminal (BRCT) motifs and a central domain with 13 repetitions of an approximately 41-amino acid sequence. The encoded protein is required to activate the intra-S phase and G2/M phase cell cycle checkpoints in response to DNA damage. This nuclear protein interacts with phosphorylated histone H2AX near sites of DNA double-strand breaks through its BRCT motifs, and facilitates recruitment of the ATM kinase and meiotic recombination 11 protein complex to DNA damage foci."

Gene ID: 10211 is FLOT1 flotillin 1 on 6p21.33: "This gene encodes an protein that localizes to the caveolae, which are small domains on the inner cell membranes. This protein plays a role in vesicle trafficking and cell morphology. Alternative splicing results in multiple transcript variants."

1. NP_001305804.1 flotillin-1 isoform 2: "Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (2) is shorter than isoform 1."
2. NP_005794.1 flotillin-1 isoform 1: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 259197 is NCR3 natural cytotoxicity triggering receptor 3 on 6p21.33: "The protein encoded by this gene is a natural cytotoxicity receptor (NCR) that may aid NK cells in the lysis of tumor cells. The encoded protein interacts with CD3-zeta (CD247), a T-cell receptor. A single nucleotide polymorphism in the 5' untranslated region of this gene has been associated with mild malaria suceptibility. Three transcript variants encoding different isoforms have been found for this gene."

1. NP_001138938.1 natural cytotoxicity triggering receptor 3 isoform b: "Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region compared to variant 1, that results in a frameshift. It encodes isoform b, which has a shorter and distinct C-terminus compared to isoform a."
2. NP_001138939.1 natural cytotoxicity triggering receptor 3 isoform c: "Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region compared to variant 1, that results in a frameshift. It encodes isoform c, which has a shorter and distinct C-terminus compared to isoform a."
3. NP_667341.1 natural cytotoxicity triggering receptor 3 isoform a precursor: "Transcript Variant: This variant (1) encodes the longest isoform (a). [...] Ig; Immunoglobulin domain".

Class IV

Several "genes have been described that are encoded in the telomeric end of the Class III region and that appear to be involved in both global and specific inflammatory responses. Due to this commonality of function this gene-rich region was dubbed Class IV, and includes the TNF family, AIF1, and HSP70."

The B144/LST1 protein [...] is expressed in T cell, monocytic, and macrophage cell lines, and is also substantially expressed in both murine and human dendritic cells in culture."

"The 1C7 gene [...] is located immediately adjacent to the B144 gene. RNA for B144 and 1C7 are transcribed in convergent directions such that there is a slight overlap between the 3' ends of the two mRNAs. [Human] 1C7 also shows multiple splice forms with 9 forms of the human mRNA reported so far.(21) The major forms encode proteins containing a leader sequence, a probable trans-membrane segment, an external sequence including an immunoglobulin-like domain, and at least three alternative forms of the putative intracellular segment of the protein. One alternative splice modifies the structure of the immunoglobulin-like domain, changing it from a sequence more closely resembling those of the V regions of Ig molecules to one that is more similar to IgC2 regions. Of the three alternative putative intracellular domains, one encodes multiple proline repeats suggestive of SH3 binding domains."

"The existence of the G1 gene was initially noted as a part of a screen of MHC cosmids for embedded genes. The G1 and AIF1 transcripts appear to be derived by alternative splicing from partially overlapping genomic templates. A third human interferon gamma-responsive transcript, IRT-1, has been noted that shares some internal sequences with both G1 and AIF1, but on the basis of the predicted open reading frame it shares only limited amino acid sequences with G1."

Gene ID: 199 is AIF1 allograft inflammatory factor 1 on 6p21.33: "This gene encodes a protein that binds actin and calcium. This gene is induced by cytokines and interferon and may promote macrophage activation and growth of vascular smooth muscle cells and T-lymphocytes. Polymorphisms in this gene may be associated with systemic sclerosis. Alternative splicing results in multiple transcript variants, but the full-length and coding nature of some of these variants is not certain."

1. NP_001305899.1 allograft inflammatory factor 1 isoform 1: "Transcript Variant: This variant (4) uses an alternate splice site in the 5' region and initiates translation at a downstream start codon compared to variant 3. The encoded isoform (1) has a shorter N-terminus than isoform 3. Variants 1 and 4 encode the same isoform (1)."
2. NP_001614.3 allograft inflammatory factor 1 isoform 3: "Transcript Variant: This variant (3) encodes the longest isoform (3)."
3. NP_116573.1 allograft inflammatory factor 1 isoform 1: "Transcript Variant: This variant (1, also known as G1) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 3. The encoded isoform (1) has a shorter N-terminus than isoform 3. Variants 1 and 4 encode the same isoform (1)."

"AIF-1 (allograft inflammatory factor-1) is a Ca²⁺ binding protein predominantly expressed by activated monocytes, originally identified in rat cardiac allografts with chronic rejection.(22) The human cDNA homologue is 86% identical to the rat (90% identical to the amino acid sequence) and was identified by reverse transcriptase-PCR of endomyocardial biopsy specimens from human heart transplants and in macrophage cell lines.(23)"

Gene ID: 3303 is HSPA1A heat shock protein family A (Hsp70) member 1A on 6p21.33: "This intronless gene encodes a 70kDa heat shock protein which is a member of the heat shock protein 70 family. In conjuction with other heat shock proteins, this protein stabilizes existing proteins against aggregation and mediates the folding of newly translated proteins in the cytosol and in organelles. It is also involved in the ubiquitin-proteasome pathway through interaction with the AU-rich element RNA-binding protein 1. The gene is located in the major histocompatibility complex class III region, in a cluster with two closely related genes which encode similar proteins."

Gene ID: 3304 is HSPA1B heat shock protein family A (Hsp70) member 1B on 6p21.33: "This intronless gene encodes a 70kDa heat shock protein which is a member of the heat shock protein 70 family. In conjuction with other heat shock proteins, this protein stabilizes existing proteins against aggregation and mediates the folding of newly translated proteins in the cytosol and in organelles. It is also involved in the ubiquitin-proteasome pathway through interaction with the AU-rich element RNA-binding protein 1. The gene is located in the major histocompatibility complex class III region, in a cluster with two closely related genes which encode similar proteins."

Gene ID: 3305 is HSPA1L heat shock protein family A (Hsp70) member 1 like on 6p21.33: "This gene encodes a 70kDa heat shock protein. In conjunction with other heat shock proteins, this protein stabilizes existing proteins against aggregation and mediates the folding of newly translated proteins in the cytosol and in organelles. The gene is located in the major histocompatibility complex class III region, in a cluster with two closely related genes which also encode isoforms of the 70kDa heat shock protein."

Gene ID: 6892 is TAPBP TAP binding protein on 6p21.32: "This gene encodes a transmembrane glycoprotein which mediates interaction between newly assembled major histocompatibility complex (MHC) class I molecules and the transporter associated with antigen processing (TAP), which is required for the transport of antigenic peptides across the endoplasmic reticulum membrane. This interaction is essential for optimal peptide loading on the MHC class I molecule. Up to four complexes of MHC class I and this protein may be bound to a single TAP molecule. This protein contains a C-terminal double-lysine motif (KKKAE) known to maintain membrane proteins in the endoplasmic reticulum. This gene lies within the major histocompatibility complex on chromosome 6. Alternative splicing results in three transcript variants encoding different isoforms."

1. NP_003181.3 tapasin isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1. [...] Ig; Immunoglobulin domain"
2. NP_757345.2 tapasin isoform 2 precursor: "Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is longer than isoform 1."
3. NP_757346.2 tapasin isoform 3 precursor: "Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1."

Class V

"Vacuolar ATPase is a multi-subunit protein complex that transports H⁺ ions. It functions in general to mediate acidification of cellular vacuoles, and consequently in receptor recycling, lysosome formation, and cellular pH control. [Sequences] centromeric to the BAT1 gene [...] encode exons of a gene, ATP6G, homologous to the G subunit of the vacuolar H⁺ ATPase of a number of species.(26) The mRNA for this gene had two alternative splice forms, with the shorter form removing the presumptive translation initiation codon of the longer form and therefore removing an amino terminal region of high homology to other G subunits. The longer splice form was selectively expressed in some B and T cell lines as compared with myelomonocytic lines. Vacuolar ATPase subunit G is up-regulated in neutrophils exposed to non-pathogenic bacteria (Yeramilli and Weissman, unpublished). The ATPase is also up-regulated in neutrophils by GM-CSF or phorbol myristic acid. Up-regulation of the ATPase is one of the mechanisms that may delay apoptosis in activated neutrophils. However a specific role for the ATP6G in inflammation remains to be established by more specific means."

Gene ID: 534 is ATP6V1G2 ATPase H+ transporting V1 subunit G2 on 6p21.33: "This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of intracellular compartments of eukaryotic cells. V-ATPase dependent acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c", and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This encoded protein is one of three V1 domain G subunit proteins. This gene had previous gene symbols of ATP6G and ATP6G2. Alternatively spliced transcript variants encoding different isoforms have been described. Read-through transcription also exists between this gene and the downstream DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B) gene."

1. NP_001191007.1 V-type proton ATPase subunit G 2 isoform c.
2. NP_569730.1 V-type proton ATPase subunit G 2 isoform a.
3. NP_612139.1 V-type proton ATPase subunit G 2 isoform b.

Gene ID: 7916 is PRRC2A proline rich coiled-coil 2A aka G2; BAT2; D6S51; D6S51E on 6p21.33: "A cluster of genes, BAT1-BAT5, has been localized in the vicinity of the genes for TNF alpha and TNF beta. These genes are all within the human major histocompatibility complex class III region. This gene has microsatellite repeats which are associated with the age-at-onset of insulin-dependent diabetes mellitus (IDDM) and possibly thought to be involved with the inflammatory process of pancreatic beta-cell destruction during the development of IDDM. This gene is also a candidate gene for the development of rheumatoid arthritis. Two transcript variants encoding the same protein have been found for this gene."

1. NP_004629.3 protein PRRC2A: "Transcript Variant: This variant (2) represents the longer transcript. Variants 1 and 2 both encode the same protein."
2. NP_542417.2 protein PRRC2A: "Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 2. Variants 1 and 2 both encode the same protein."

Gene ID: 7917 is BAG6 BAG cochaperone 6 aka G3; BAT3 on 6p21.33: "This gene was first characterized as part of a cluster of genes located within the human major histocompatibility complex class III region. This gene encodes a nuclear protein that is cleaved by caspase 3 and is implicated in the control of apoptosis. In addition, the protein forms a complex with E1A binding protein p300 and is required for the acetylation of p53 in response to DNA damage. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001092004.1 large proline-rich protein BAG6 isoform b: "Transcript Variant: This variant (4) differs in the 5' UTR and utilizes an alternative in-frame splice site in the 5' coding region, compared to variant 1. Variants 2, 3, and 4 encode the same isoform (b), which is 6 aa shorter than isoform a."
2. NP_001186626.1 large proline-rich protein BAG6 isoform c: "Transcript Variant: This variant (5) differs in the 5' UTR and lacks three alternate in-frame segments compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a."
3. NP_001186627.1 large proline-rich protein BAG6 isoform d: "Transcript Variant: This variant (6) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform a."
4. NP_542433.1 large proline-rich protein BAG6 isoform b: "Transcript Variant: This variant (2) differs in the 5' UTR and utilizes an alternative in-frame splice site in the 5' coding region, compared to variant 1. Variants 2, 3, and 4 encode the same isoform (b), which is 6 aa shorter than isoform a."
5. NP_542434.1 large proline-rich protein BAG6 isoform b: "Transcript Variant: This variant (3) utilizes an alternative in-frame splice site in the 5' coding region, compared to variant 1. Variants 2, 3, and 4 encode the same isoform (b), which is 6 aa shorter than isoform a."

Gene ID: 7918 is GPANK1 G-patch domain and ankyrin repeats 1 aka G5; BAT4, on 6p21.33: "This gene is located in a cluster of HLA-B-associated transcripts, which is included in the human major histocompatability complex III region. This gene encodes a protein which is thought to play a role in immunity. Multiple alternatively spliced variants, encoding the same protein, have been identified."

1. NP_001186166.1 G patch domain and ankyrin repeat-containing protein 1: "Transcript Variant: This variant (1) represents the longest transcript."
2. NP_001186167.1 G patch domain and ankyrin repeat-containing protein 1: "Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4, and 5 encode the same protein."
3. NP_001186168.1 G patch domain and ankyrin repeat-containing protein 1: "Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4, and 5 encode the same protein."
4. NP_001186169.1 G patch domain and ankyrin repeat-containing protein 1: "Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4, and 5 encode the same protein."
5. NP_149417.1 G patch domain and ankyrin repeat-containing protein 1: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4, and 5 encode the same protein."

Gene ID: 7919 is DDX39B DExD-box helicase 39B aka BAT1 on 6p21.33: "This gene encodes a member of the DEAD box family of RNA-dependent ATPases that mediate ATP hydrolysis during pre-mRNA splicing. The encoded protein is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. This gene belongs to a cluster of genes localized in the vicinity of the genes encoding tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. Mutations in this gene may be associated with rheumatoid arthritis. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on both chromosomes 6 and 11. Read-through transcription also occurs between this gene and the upstream ATP6V1G2 (ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2) gene."

1. NP_004631.1 spliceosome RNA helicase DDX39B: "Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same protein."
2. NP_542165.1 spliceosome RNA helicase DDX39B: "Transcript Variant: This variant (2) uses an alternative splice site in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein."

Gene ID: 7920 is ABHD16A abhydrolase domain containing 16A, phospholipase, aka BAT5 on 6p21.33: "A cluster of genes, BAT1-BAT5, has been localized in the vicinity of the genes for tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. The protein encoded by this gene is thought to be involved in some aspects of immunity. Alternatively spliced transcript variants have been described."

1. NP_001170986.1 phosphatidylserine lipase ABHD16A isoform b: "Transcript Variant: This variant (2) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at an alternate AUG and result in an isoform (b) with a shorter, distinct N-terminus, compared to isoform 1."
2. NP_066983.1 phosphatidylserine lipase ABHD16A isoform a: "Transcript Variant: This variant (1) encodes the longer isoform (a)."

Class VI

"A cluster of genes for three related cytokines/cytokine receptors, tumor necrosis factor (TNF, formerly known as TNF-alpha or cachectin), lymphotoxin alpha (LTA), and lymphotoxin beta (LTB), lies in the Class IV region shortly before the most centromeric Class I related genes. TNF has been very extensively studied(5) and plays an important role in inflammation, bacterial(6) and viral infection,(7) tumor cachexia and the immune response. It is produced by a variety of cells including prominently monocytes, macrophages, and some T cell subsets."

"LTB (also called TNF C) is a membrane bound molecule that forms a heterotrimer with LTA.(12) This LTA-LTB complex can then induce activation of NF kappa B in certain cell lines by binding with the LTB receptor, a member of the TNF receptor family.(13) (14) NF kappa B is a pleiotropic transcription factor capable of activating the expression of a great variety of genes critical for the Immunoin flammatory response.(14)"

The region within the MHC class III gene cluster that contains genes for TNFs is also known as MHC class VI or the inflammatory region.

Gene ID: 4049 is LTA lymphotoxin alpha on 6p21.33: "The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene."

1. NP_000586.2 lymphotoxin-alpha precursor: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein."
2. NP_001153212.1 lymphotoxin-alpha precursor: "Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein."

Gene ID: 4050 is LTB lymphotoxin beta on 6p21.33: "Lymphotoxin beta is a type II membrane protein of the TNF family. It anchors lymphotoxin-alpha to the cell surface through heterotrimer formation. The predominant form on the lymphocyte surface is the lymphotoxin-alpha 1/beta 2 complex (e.g. 1 molecule alpha/2 molecules beta) and this complex is the primary ligand for the lymphotoxin-beta receptor. The minor complex is lymphotoxin-alpha 2/beta 1. LTB is an inducer of the inflammatory response system and involved in normal development of lymphoid tissue. Lymphotoxin-beta isoform b is unable to complex with lymphotoxin-alpha suggesting a function for lymphotoxin-beta which is independent of lympyhotoxin-alpha. Alternative splicing results in multiple transcript variants encoding different isoforms."

1. NP_002332.1 lymphotoxin-beta isoform a: "Transcript Variant: This variant (1) represents the longer transcript, encodes the longer isoform (a), and can form the heterotrimeric complex with lymphotoxin-alpha."
2. NP_033666.1 lymphotoxin-beta isoform b: "Transcript Variant: This splice variant (2) lacks an exon in the coding region, compared to variant 1. The encoded protein (isoform b) has a premature stop codon and lacks the majority of the extracellular domain, compared to isoform a. This loss impairs its ability to complex with lympytoxin-alpha."

Gene ID: 7124 is TNF tumor necrosis factor on 6p21.33: "This gene encodes a multifunctional proinflammatory cytokine that belongs to the tumor necrosis factor (TNF) superfamily. This cytokine is mainly secreted by macrophages. It can bind to, and thus functions through its receptors TNFRSF1A/TNFR1 and TNFRSF1B/TNFBR. This cytokine is involved in the regulation of a wide spectrum of biological processes including cell proliferation, differentiation, apoptosis, lipid metabolism, and coagulation. This cytokine has been implicated in a variety of diseases, including autoimmune diseases, insulin resistance, and cancer. Knockout studies in mice also suggested the neuroprotective function of this cytokine."

ATP-binding cassette (ABC) transporters

Gene ID: 23 is ABCF1 ATP binding cassette subfamily F member 1, on 6p21.33: "The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the GCN20 subfamily. Unlike other members of the superfamily, this protein lacks the transmembrane domains which are characteristic of most ABC transporters. This protein may be regulated by tumor necrosis factor-alpha and play a role in enhancement of protein synthesis and the inflammation process."

1. NP_001020262.1 ATP-binding cassette sub-family F member 1 isoform a: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a)."
2. NP_001081.1 ATP-binding cassette sub-family F member 1 isoform b: "Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The resulting protein (isoform b) is shorter than isoform a."

Gene ID: 6890 is TAP1 transporter 1, ATP binding cassette subfamily B member aka transporter, ATP-binding cassette, major histocompatibility complex, 1 on 6p21.32: "The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. The protein encoded by this gene is involved in the pumping of degraded cytosolic peptides across the endoplasmic reticulum into the membrane-bound compartment where class I molecules assemble. Mutations in this gene may be associated with ankylosing spondylitis, insulin-dependent diabetes mellitus, and celiac disease. Two transcript variants encoding different isoforms have been found for this gene."

1. NP_000584.3 antigen peptide transporter 1 isoform 1: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."
2. NP_001278951.1 antigen peptide transporter 1 isoform 2: "Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1."

Gene ID: 6891 is TAP2 transporter 2, ATP binding cassette subfamily B member on 6p21.32: "The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. This gene is located 7 kb telomeric to gene family member ABCB2. The protein encoded by this gene is involved in antigen presentation. This protein forms a heterodimer with ABCB2 in order to transport peptides from the cytoplasm to the endoplasmic reticulum. Mutations in this gene may be associated with ankylosing spondylitis, insulin-dependent diabetes mellitus, and celiac disease. Alternative splicing of this gene produces products which differ in peptide selectivity and level of restoration of surface expression of MHC class I molecules."

1. NP_000535.3 antigen peptide transporter 2 isoform 1: "Transcript Variant: This variant (1, B allele) represents the longer transcript and encodes the longest isoform (1). An allele (variant 1, A allele) exists in which a single nt change creates an internal stop codon, leading to a protein that is 17 aa shorter at the C-terminus."
2. NP_001276972.1 antigen peptide transporter 2 isoform 3: "Transcript Variant: This variant (1, A allele) differs at 3 nt positions compared to variant 1, B allele. The resulting isoform (3) is shorter at the C-terminus compared to isoform 1."
3. NP_061313.2 antigen peptide transporter 2 isoform 2: "Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (2) is shorter and has a distinct C-terminus compared to isoform 1."

Immunoglobulin domain genes

Gene ID: 915 is CD3D CD3d molecule on 11q23.3: "The protein encoded by this gene is part of the T-cell receptor/CD3 complex (TCR/CD3 complex) and is involved in T-cell development and signal transduction. The encoded membrane protein represents the delta subunit of the CD3 complex, and along with four other CD3 subunits, binds either TCR alpha/beta or TCR gamma/delta to form the TCR/CD3 complex on the surface of T-cells. Defects in this gene are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (SCIDBNK). Two transcript variants encoding different isoforms have been found for this gene. Other variants may also exist, but the full-length natures of their transcripts has yet to be defined."

1. NP_000723.1 T-cell surface glycoprotein CD3 delta chain isoform A precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (A)."
2. NP_001035741.1 T-cell surface glycoprotein CD3 delta chain isoform B precursor: "Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1. The encoded protein (B) is shorter and lacks the transmembrane domain, compared to isoform A."

Gene ID: 916 is CD3E CD3e molecule on 11q23.3: "The protein encoded by this gene is the CD3-epsilon polypeptide, which together with CD3-gamma, -delta and -zeta, and the T-cell receptor alpha/beta and gamma/delta heterodimers, forms the T-cell receptor-CD3 complex. This complex plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. The genes encoding the epsilon, gamma and delta polypeptides are located in the same cluster on chromosome 11. The epsilon polypeptide plays an essential role in T-cell development. Defects in this gene cause immunodeficiency. This gene has also been linked to a susceptibility to type I diabetes in women."

1. NP_000724.1 T-cell surface glycoprotein CD3 epsilon chain precursor.

Gene ID: 917 is CD3G CD3g molecule on 11q23.3: "The protein encoded by this gene is the CD3-gamma polypeptide, which together with CD3-epsilon, -delta and -zeta, and the T-cell receptor alpha/beta and gamma/delta heterodimers, forms the T-cell receptor-CD3 complex. This complex plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. The genes encoding the epsilon, gamma and delta polypeptides are located in the same cluster on chromosome 11. Defects in this gene are associated with T cell immunodeficiency."

1. NP_000064.1 T-cell surface glycoprotein CD3 gamma chain precursor.

Immunoglobulin receptor superfamily

Gene ID: 3903 is LAIR1 leukocyte associated immunoglobulin like receptor 1 on 19q13.42: "The protein encoded by this gene is an inhibitory receptor found on peripheral mononuclear cells, including natural killer cells, T cells, and B cells. Inhibitory receptors regulate the immune response to prevent lysis of cells recognized as self. The gene is a member of both the immunoglobulin superfamily and the leukocyte-associated inhibitory receptor family. The gene maps to a region of 19q13.4 called the leukocyte receptor cluster, which contains at least 29 genes encoding leukocyte-expressed receptors of the immunoglobulin superfamily. The encoded protein has been identified as an anchor for tyrosine phosphatase SHP-1, and may induce cell death in myeloid leukemias. Alternative splicing results in multiple transcript variants."

1. NP_001275952.2 leukocyte-associated immunoglobulin-like receptor 1 isoform c precursor: "Transcript Variant: This variant (c) lacks an in-frame exon and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (c) is shorter, compared to isoform a."
2. NP_001275954.2 leukocyte-associated immunoglobulin-like receptor 1 isoform e precursor: "Transcript Variant: This variant (e) uses an alternate in-frame splice site in the central coding region. The encoded isoform (e) is shorter, compared to isoform a."
3. NP_001275955.2 leukocyte-associated immunoglobulin-like receptor 1 isoform f: "Transcript Variant: This variant (f) differs in the 5' UTR, lacks part of the 5' coding region, and uses an alternate start codon, compared to variant a. The encoded isoform (f) has a shorter and distinct N-terminus, compared to isoform a."
4. NP_001275956.2 leukocyte-associated immunoglobulin-like receptor 1 isoform g: "Transcript Variant: This variant (g) differs in the 5' UTR, lacks part of the 5' coding region, and uses an alternate start codon, compared to variant a. The encoded isoform (g) has a shorter and distinct N-terminus, compared to isoform a."
5. NP_002278.2 leukocyte-associated immunoglobulin-like receptor 1 isoform a precursor: "Transcript Variant: This variant (a) encodes the longest isoform (a)."
6. NP_068352.2 leukocyte-associated immunoglobulin-like receptor 1 isoform b precursor: "Transcript Variant: This variant (b) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (b) is shorter, compared to isoform a."

Gene ID: 3904 is LAIR2 leukocyte associated immunoglobulin like receptor 2 on 19q13.42: "The protein encoded by this gene is a member of the immunoglobulin superfamily. It was identified by its similarity to leukocyte-associated immunoglobulin-like receptor 1, a membrane-bound receptor that modulates innate immune response. The protein encoded by this locus is a soluble receptor that may play roles in both inhibition of collagen-induced platelet aggregation and vessel formation during placental implantation. This gene maps to a region of 19q13.4, termed the leukocyte receptor cluster, which contains 29 genes in the immunoglobulin superfamily. Alternatively spliced transcript variants have been described for this gene."

1. NP_002279.2 leukocyte-associated immunoglobulin-like receptor 2 isoform a precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a)."
2. NP_067154.1 leukocyte-associated immunoglobulin-like receptor 2 isoform b precursor: "Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1, resulting in an isoform (b) which is shorter compared to isoform a."

Gene ID: 5284 is PIGR polymeric immunoglobulin receptor on 1q32.1: "This gene is a member of the immunoglobulin superfamily. The encoded poly-Ig receptor binds polymeric immunoglobulin molecules at the basolateral surface of epithelial cells; the complex is then transported across the cell to be secreted at the apical surface. A significant association was found between immunoglobulin A nephropathy and several SNPs in this gene."

1. NP_002635.2 polymeric immunoglobulin receptor precursor.

Gene ID: 79368 is FCRL2 Fc receptor like 2 on 1q23.1: "This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein has four extracellular C2-type immunoglobulin domains, a transmembrane domain and a cytoplasmic domain that contains one immunoreceptor-tyrosine activation motif and two immunoreceptor-tyrosine inhibitory motifs. This protein may be a prognostic marker for chronic lymphocytic leukemia. Alternatively spliced transcript variants have been described, but their biological validity has not been determined."

1. NP_001152960.1 Fc receptor-like protein 2 isoform 2 precursor: "Transcript Variant: This variant (2) lacks three alternate exons in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1."
2. NP_110391.2 Fc receptor-like protein 2 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1)."

Gene ID: 83416 is FCRL5 Fc receptor like 5 on 1q23.1: "This gene encodes a member of the immunoglobulin receptor superfamily and the Fc-receptor like family. This gene and several other Fc receptor-like gene members are clustered on the long arm of chromosome 1. The encoded protein is a single-pass type I membrane protein and contains 8 immunoglobulin-like C2-type domains. This gene is implicated in B cell development and lymphomagenesis. Alternatively spliced transcript variants encoding different isoforms have been identified."

1. NP_001182317.1 Fc receptor-like protein 5 isoform 2 precursor: "Transcript Variant: This variant (2) has an alternate splice site in the 3' coding region, resulting in frame-shift, as compared to variant 1. The resulting isoform (2) has a different and longer C-terminus, as compared to isoform 1."
2. NP_112571.2 Fc receptor-like protein 5 isoform 1 precursor: "Transcript Variant: This variant (1) encodes the dominant isoform (1)."

Gene ID: 83417 is FCRL4 Fc receptor like 4 on 1q23.1: "This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein has four extracellular C2-type immunoglobulin domains, a transmembrane domain and a cytoplasmic domain that contains three immune-receptor tyrosine-based inhibitory motifs. This protein may play a role in the function of memory B-cells in the epithelia. Aberrations in the chromosomal region encoding this gene are associated with non-Hodgkin lymphoma and multiple myeloma."

1. NP_112572.1 Fc receptor-like protein 4 precursor.

Gene ID: 115352 is FCRL3 Fc receptor like 3 aka immunoglobulin superfamily receptor translocation associated protein 3 on 1q23.1: "This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein contains immunoreceptor-tyrosine activation motifs and immunoreceptor-tyrosine inhibitory motifs in its cytoplasmic domain and may play a role in regulation of the immune system. Mutations in this gene have been associated with rheumatoid arthritis, autoimmune thyroid disease, and systemic lupus erythematosus. Alternative splicing results in multiple transcript variants."

1. NP_001307262.1 Fc receptor-like protein 3 isoform 3 precursor: "Transcript Variant: This variant (3) encodes the longer isoform (3)."
2. NP_443171.2 Fc receptor-like protein 3 isoform 1 precursor [variant 1].

Gene ID: 115653 is KIR3DL3 killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3 on 19q13.42: "Killer cell immunoglobulin-like receptors (KIRs) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. The KIR genes are polymorphic and highly homologous and they are found in a cluster on chromosome 19q13.4 within the 1 Mb leukocyte receptor complex (LRC). The gene content of the KIR gene cluster varies among haplotypes, although several "framework" genes are found in all haplotypes (KIR3DL3, KIR3DP1, KIR3DL4, KIR3DL2). The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The ligands for several KIR proteins are subsets of HLA class I molecules; thus, KIR proteins are thought to play an important role in regulation of the immune response. This gene is one of the "framework" loci that is present on all haplotypes."

1. NP_703144.3 killer cell immunoglobulin-like receptor 3DL3 precursor.

Gene ID: 126014 is OSCAR osteoclast associated Ig-like receptor on 19q13.42: "Osteoclasts are multinucleated cells that resorb bone and are essential for bone homeostasis. This gene encodes an osteoclast-associated receptor (OSCAR), which is a member of the leukocyte receptor complex protein family that plays critical roles in the regulation of both innate and adaptive immune responses. The encoded protein may play a role in oxidative stress-mediated atherogenesis as well as monocyte adhesion. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene."

1. NP_001269278.1 osteoclast-associated immunoglobulin-like receptor isoform 6 precursor: "Transcript Variant: This variant (6) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (6) is shorter, compared to isoform 1."
2. NP_001269279.1 osteoclast-associated immunoglobulin-like receptor isoform 7 precursor: "Transcript Variant: This variant (7) lacks two in-frame exons in the central coding region, compared to variant 1. The encoded isoform (7) is shorter, compared to isoform 1."
3. NP_570127.3 osteoclast-associated immunoglobulin-like receptor isoform 3 precursor: "Transcript Variant: This variant (3) lacks an internal segment in its 3' coding region, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1."
4. NP_573398.2 osteoclast-associated immunoglobulin-like receptor isoform 5 precursor: "Transcript Variant: This variant (5) lacks two in-frame exons in the central coding region and lacks an internal segment in its 3' coding region, compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1."
5. NP_573399.2 osteoclast-associated immunoglobulin-like receptor isoform 4 precursor: "Transcript Variant: This variant (4) lacks an in-frame exon in the central coding region and lacks an internal segment in its 3' coding region, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1."
6. NP_996554.2 osteoclast-associated immunoglobulin-like receptor isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."

Gene ID: 286676 is ILDR1 immunoglobulin like domain containing receptor 1 on 3q13.33: "This gene encodes a protein that contains an immunoglobulin-like domain. The encoded protein may function as a multimeric receptor at the cell surface. The expression of this gene may be a diagnostic marker for cancer progression. Alternatively spliced transcript variants encoding multiple protein isoforms have been observed for this gene."

1. NP_001186728.1 immunoglobulin-like domain-containing receptor 1 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."
2. NP_001186729.1 immunoglobulin-like domain-containing receptor 1 isoform 3 precursor: "Transcript Variant: This variant (3) lacks multiple exons in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1."
3. NP_787120.1 immunoglobulin-like domain-containing receptor 1 isoform 2 precursor: "Transcript Variant: This variant (2) lacks an exon in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1."

Gene ID: 340745 is LRIT2 leucine rich repeat, Ig-like and transmembrane domains 2 on 10q23.1.

1. NP_001017924.1 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 2 isoform 2 precursor: "Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1."
2. NP_001271152.1 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 2 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 345193 is LRIT3 leucine rich repeat, Ig-like and transmembrane domains 3 on 4q25: "This gene encodes a protein that has a fibronectin type III domain and a C-terminal transmembrane domain, as well as a leucine-rich repeat domain and immunoglobulin-like domain near the N-terminus. The encoded protein may regulate fibroblast growth factor receptors and affect the modification of these receptors, which are glycosylated differently in the Golgi and endoplasmic reticulum. Mutations in this gene are associated with congenital stationary night blindness, type 1F."

1. NP_940908.3 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3 precursor.

Gene ID: 353514 is LILRA5 leukocyte immunoglobulin like receptor A5 on 19q13.42: "The protein encoded by this gene is a member of the leukocyte immunoglobulin-like receptor (LIR) family. LIR family members are known to have activating and inibitory functions in leukocytes. Crosslink of this receptor protein on the surface of monocytes has been shown to induce calcium flux and secretion of several proinflammatory cytokines, which suggests the roles of this protein in triggering innate immune responses. This gene is one of the leukocyte receptor genes that form a gene cluster on the chromosomal region 19q13.4. Four alternatively spliced transcript variants encoding distinct isoforms have been described."

1. NP_067073.1 leukocyte immunoglobulin-like receptor subfamily A member 5 isoform 1 precursor: "Transcript Variant: This variant (1), also known as LIR9m1, encodes the longest isoform (1)."
2. NP_870994.1 leukocyte immunoglobulin-like receptor subfamily A member 5 isoform 3: "Transcript Variant: This variant (3), also known as LIR9s1, differs in the 3' end-region, which includes a part of the coding region, as compared to variant 1. The resulting isoform (3) has a distinct and shorter C-terminus, as compared to isoform 1."
3. NP_871714.1 leukocyte immunoglobulin-like receptor subfamily A member 5 isoform 2: "Transcript Variant: This variant (2), also known as LIR9m2, lacks an in-frame coding segment, as compared to variant 1. The resulting isoform (2) lacks an internal region, as compared to isoform 1."
4. NP_871715.1 leukocyte immunoglobulin-like receptor subfamily A member 5 isoform 4: "Transcript Variant: This variant (4), also known as LIR9s2, lacks an in-frame coding segment and differs in the 3' end-region, as compared to variant 1. The resulting isoform (4) lacks an internal region and has a distinct and shorter C-terminus as compared to isoform 1."

Gene ID: 388364 is TMIGD1 transmembrane and immunoglobulin domain containing 1 on 17q11.2.

1. NP_001306871.1 transmembrane and immunoglobulin domain-containing protein 1 isoform 2 precursor: "Transcript Variant: This variant (2) lacks an exon in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1."
2. NP_996663.1 transmembrane and immunoglobulin domain-containing protein 1 isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longer isoform (1)."

Gene ID: 391123 is VSIG8 V-set and immunoglobulin domain containing 8 on 1q23.2.

1. NP_001013683.1 V-set and immunoglobulin domain-containing protein 8 precursor.

Gene ID: 553128 is KIR2DL5B killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 5B on 19p13.3: "Killer cell immunoglobulin-like receptors (KIRs) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. The KIR genes are polymorphic and highly homologous and they are found in a cluster on chromosome 19q13.4 within the 1 Mb leukocyte receptor complex (LRC). The gene content of the KIR gene cluster varies among haplotypes, although several "framework" genes are found in all haplotypes (KIR3DL3, KIR3DP1, KIR3DL4, KIR3DL2). The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The ligands for several KIR proteins are subsets of HLA class I molecules; thus, KIR proteins are thought to play an important role in regulation of the immune response."

1. NP_001018091.1 killer cell immunoglobulin-like receptor 2DL5B precursor.

Gene ID: 100132285 is KIR2DS2 killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2 on 19q13.4: "Killer cell immunoglobulin-like receptors (KIRs) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. The KIR genes are polymorphic and highly homologous and they are found in a cluster on chromosome 19q13.4 within the 1 Mb leukocyte receptor complex (LRC). The gene content of the KIR gene cluster varies among haplotypes, although several "framework" genes are found in all haplotypes (KIR3DL3, KIR3DP1, KIR3DL4, KIR3DL2). The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The ligands for several KIR proteins are subsets of HLA class I molecules; thus, KIR proteins are thought to play an important role in regulation of the immune response. This gene represents a haplotype-specific family member that encodes a protein with a short cytoplasmic tail. Alternative splicing results in multiple transcript variants."

1. NP_001278624.1 killer cell immunoglobulin-like receptor 2DS2 isoform b precursor: "Transcript Variant: This variant (2) uses an alternate splice site in its 3' terminal exon, and it thus differs in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is longer than isoform a."
2. NP_001278625.1 killer cell immunoglobulin-like receptor 2DS2 isoform c precursor: "Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (c, also known as nkat5-delta-Ig1) that is shorter than isoform a."
3. NP_001278629.1 killer cell immunoglobulin-like receptor 2DS2 isoform d precursor: "Transcript Variant: This variant (4) lacks two alternate in-frame exons that encompass parts of the 5' and central coding regions, compared to variant 1. The encoded isoform (d) is shorter than isoform a."
4. NP_001278630.1 killer cell immunoglobulin-like receptor 2DS2 isoform e precursor: "Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (e) that is shorter than isoform a."
5. NP_036444.1 killer cell immunoglobulin-like receptor 2DS2 isoform a precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a."

NF-kappa-B inhibitor family

Gene ID: 4792 is NFKBIA NFKB inhibitor alpha aka major histocompatibility complex enhancer-binding protein [mitotic arrest deficient 3] MAD3 on 14q13.2: "This gene encodes a member of the NF-kappa-B inhibitor family, which contain multiple ankrin repeat domains. The encoded protein interacts with REL dimers to inhibit NF-kappa-B/REL complexes which are involved in inflammatory responses. The encoded protein moves between the cytoplasm and the nucleus via a nuclear localization signal and CRM1-mediated nuclear export. Mutations in this gene have been found in ectodermal dysplasia anhidrotic with T-cell immunodeficiency autosomal dominant disease."

ZAS family

Gene ID: 3096 is HIVEP1 HIVEP zinc finger 1 aka major histocompatibility complex binding protein 1 on 6p24.1: "This gene encodes a transcription factor belonging to the ZAS family, members of which are large proteins that contain a ZAS domain - a modular protein structure consisting of a pair of C2H2 zinc fingers with an acidic-rich region and a serine/threonine-rich sequence. These proteins bind specifically to the DNA sequence motif, GGGACTTTCC, found in the enhancer elements of several viral promoters, including human immunodeficiency virus (HIV), and to related sequences found in the enhancer elements of a number of cellular promoters. This protein binds to this sequence motif, suggesting a role in the transcriptional regulation of both viral and cellular genes."

1. NP_002105.3 zinc finger protein 40.

Hypotheses

1. Downstream core promoters may work as transcription factors even as their complements or inverses.
2. In addition to the DNA binding sequences listed above, the transcription factors that can open up and attach through the local epigenome need to be known and specified.

See also

• Alpha-1-B glycoprotein
• SCAN domain

External links

• GenomeNet KEGG database
• Home - Gene - NCBI
• NCBI All Databases Search
• NCBI Site Search

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