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 [3]: 23, 6890, 6891,
2. Carcinoembryonic antigen genes [12]: 634, 1048, 1084, 1087, 1088, 1089, 4680, 56971, 90273, 125931, 388551, 729767,
3. Cell adhesion molecule genes [23]: 214, 914, 1826, 3897, 4059, 4162, 4684, 4685, 4897, 4978, 5175, 7412, 8174, 10752, 23705, 51148, 57453, 57863, 90952, 199731, 220296, 221935, 253559,
4. Cell adhesion-related genes [1]: 50937,
5. Immunoglobulin domain genes [24]: 915, 916, 917, 3492, 3493, 3494, 3495, 3496, 3497, 3500 3501, 3502, 3503, 3507, 3514, 3515, 3519, 3535, 3537, 3538, 3539, 3543, 3546, 6696, 10371, 10507,
6. Immunoglobulin receptor superfamily [36]: 1630, 2208, 2209, 2212, 2213, 2214, 3802, 3803, 3804, 3805, 3806, 3808, 3809, 3811, 3812, 3813, 3903, 3904, 5284, 10288, 10859, 26762, 79368, 83417, 115350, 115352, 115653, 126014, 286676, 340745, 345193, 353514, 388364, 391123, 553128, 100132285,
7. Immunoglobulin superfamily genes [29]: 682, 2204, 3321, 3476, 3547, 3671, 9398, 9543, 10261, 10871, 11341, 22997, 57549, 57611, 57722, 83953, 84966, 93185, 117166, 121227, 124857, 140885, 146722, 147710, 150084, 152404, 283284, 285313, 492311,
8. Immunoglobulin supergenes [3]: 1, 7441, 29802,
9. Intercellular adhesion molecule genes [5]: 3383, 3384, 3385, 3386, 7087,
10. Junction adhesion molecule genes [5]: 50848, 58494, 83700, 120425, 340547,
11. Major histocompatibility complex class I gene family [34]: 563, 567, 696, 821, 909, 910, 911, 912, 913, 2217, 2794, 3077, 3105, 3106, 3107, 3133, 3134, 3135, 3140, 4277, 6992, 7726, 10107, 10384, 10385, 11118, 11119, 11120, 79692, 222698, 282890, 353219, 100507436,
12. Major histocompatibility complex class II gene family [43]: 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,
13. Major histocompatibility complex class III gene family [42]: 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,
14. Major histocompatibility complex class IV gene family [6]: 199, 3303, 3304, 3305, 3309, 6892,
15. Major histocompatibility complex class V gene family [6]: 534, 7916, 7917, 7918, 7919, 7920,
16. Major histocompatibility complex class VI gene family [3]: 4049, 4050, 7124 - 3 genes,
17. NF-kappa-B inhibitor family [1]: 4792,
18. ZAS family [1]: 3096,
19. for a total of 272 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, 1630, 1797, 1826, 2204, 2208, 2209, 2212, 2213, 2214, 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, 3309, 3321, 3383, 3384, 3385, 3386, 3476, 3492, 3493, 3494, 3495, 3496, 3497, 3500 3501, 3502, 3503, 3507, 3514, 3515, 3519, 3535, 3537, 3538, 3539, 3547, 3671, 3802, 3803, 3804, 3805, 3806, 3808, 3809, 3811, 3812, 3813, 3833, 3897, 3903, 3904, 4049, 4050, 4059, 4162, 4261, 4277, 4295, 4439, 4680, 4684, 4685, 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, 6696, 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, 10288, 10371, 10384, 10385, 10471, 10507, 10752, 10859, 10871, 11118, 11119, 11120, 11341, 22997, 23705, 26762, 29802, 50848, 50937, 51148, 56971, 57453, 57549, 57611, 57722, 57863, 58494, 79368, 79692, 83417, 83700, 83953, 84966, 90273, 90952, 93185, 115350, 115352, 115653, 117166, 120425, 121227, 124857, 125931, 126014, 140885, 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: 140885 is SIRPA signal regulatory protein alpha on 20p13: "The protein encoded by this gene is a member of the signal-regulatory-protein (SIRP) family, and also belongs to the immunoglobulin superfamily. SIRP family members are receptor-type transmembrane glycoproteins known to be involved in the negative regulation of receptor tyrosine kinase-coupled signaling processes. This protein can be phosphorylated by tyrosine kinases. The phospho-tyrosine residues of this PTP have been shown to recruit SH2 domain containing tyrosine phosphatases (PTP), and serve as substrates of PTPs. This protein was found to participate in signal transduction mediated by various growth factor receptors. CD47 has been demonstrated to be a ligand for this receptor protein. This gene and its product share very high similarity with several other members of the SIRP family. These related genes are located in close proximity to each other on chromosome 20p13. Multiple alternatively spliced transcript variants have been determined for this gene."

1. NP_001035111.1 tyrosine-protein phosphatase non-receptor type substrate 1 isoform 1 precursor: "Transcript Variant: This variant (1) uses an alternate, in-frame, splice donor site in the 3' coding region compared to variant 4. This variant encodes a shorter protein (isoform 1) compared to isoform 2. Variants 1, 2, and 3 encode the same protein (isoform 1)."
2. NP_001035112.1 tyrosine-protein phosphatase non-receptor type substrate 1 isoform 1 precursor: "Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate, in-frame, splice donor site in the 3' coding region compared to variant 4. This variant encodes a shorter protein (isoform 1) compared to isoform 2. Variants 1, 2, and 3 encode the same protein (isoform 1)."
3. NP_001317657.1 tyrosine-protein phosphatase non-receptor type substrate 1 isoform 2 precursor: "Transcript Variant: This variant (4) encodes the longer protein (isoform 2)."
4. NP_542970.1 tyrosine-protein phosphatase non-receptor type substrate 1 isoform 1 precursor: "Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate, in-frame, splice donor site in the 3' coding region compared to variant 4. This variant encodes a shorter protein (isoform 1) compared to isoform 2. Variants 1, 2, and 3 encode the same protein (isoform 1)."

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

Main article: Major histocompatibility complex class III gene family

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: 3309 is HSPA5 heat shock protein family A (Hsp70) member 5 on 9q33.3: "The protein encoded by this gene is a member of the heat shock protein 70 (HSP70) family. It is localized in the lumen of the endoplasmic reticulum (ER), and is involved in the folding and assembly of proteins in the ER. As this protein interacts with many ER proteins, it may play a key role in monitoring protein transport through the cell."

1. NP_005338.1 endoplasmic reticulum chaperone BiP precursor.

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.

Gene ID: 3492 is IGH immunoglobulin heavy locus on 14q32.33: "Immunoglobulins recognize foreign antigens and initiate immune responses such as phagocytosis and the complement system. Each immunoglobulin molecule consists of two identical heavy chains and two identical light chains. This region represents the germline organization of the heavy chain locus. The locus includes V (variable), D (diversity), J (joining), and C (constant) segments. During B cell development, a recombination event at the DNA level joins a single D segment with a J segment; this partially rearranged D-J gene is then joined to a V segment. The rearranged V-D-J is then transcribed with the IGHM constant region; this transcript encodes a mu heavy chain. Later in development B cells generate V-D-J-Cmu-Cdelta pre-messenger RNA, which is alternatively spliced to encode either a mu or a delta heavy chain. Mature B cells in the lymph nodes undergo switch recombination, so that the V-D-J gene is brought in proximity to one of the IGHG, IGHA, or IGHE genes and each cell expresses either the gamma, alpha, or epsilon heavy chain. Recombination of many different V segments with several J segments provides a wide range of antigen recognition. Additional diversity is attained by junctional diversity, resulting from the random addition of nucleotides by terminal deoxynucleotidyltransferase, and by somatic hypermutation, which occurs during B cell maturation in the spleen and lymph nodes. Due to polymorphism, the numbers of functional V, J, and D genes differ among individuals and some V, D, J, and C segments may be pseudogenes."

Gene ID: 3493 is IGHA1 immunoglobulin heavy constant alpha 1 on 14q32.33.

Gene ID: 3494 is IGHA2 immunoglobulin heavy constant alpha 2 (A2m marker) on 14q32.33.

Gene ID: 3495 is IGHD immunoglobulin heavy constant delta on 14q32.33.

Gene ID: 3496 is IGHDOR15@ immunoglobulin heavy diversity orphans on chromosome 15 on 15q11-q12.

Gene ID: 3497 is IGHE immunoglobulin heavy constant epsilon on 14q32.33.

Gene ID: 3500 is IGHG1 immunoglobulin heavy constant gamma 1 (G1m marker) on 14q32.33.

Gene ID: 3501 is IGHG2 immunoglobulin heavy constant gamma 2 (G2m marker) on 14q32.33.

Gene ID: 3502 is IGHG3 immunoglobulin heavy constant gamma 3 (G3m marker) on 14q32.33.

Gene ID: 3503 is IGHG4 immunoglobulin heavy constant gamma 4 (G4m marker) on 14q32.33.

Gene ID: 3507 is IGHM immunoglobulin heavy constant mu on 14q32.33: "Immunoglobulins (Ig) are the antigen recognition molecules of B cells. An Ig molecule is made up of 2 identical heavy chains and 2 identical light chains (see MIM 147200) joined by disulfide bonds so that each heavy chain is linked to a light chain and the 2 heavy chains are linked together. Each Ig heavy chain has an N-terminal variable (V) region containing the antigen-binding site and a C-terminal constant (C) region, encoded by an individual C region gene, that determines the isotype of the antibody and provides effector or signaling functions. The heavy chain V region is encoded by 1 each of 3 types of genes: V genes (see MIM 147070), joining (J) genes (see MIM 147010), and diversity (D) genes (see MIM 146910). The C region genes are clustered downstream of the V region genes within the heavy chain locus on chromosome 14. The IGHM gene encodes the C region of the mu heavy chain, which defines the IgM isotype. Naive B cells express the transmembrane forms of IgM and IgD (see IGHD; MIM 1471770) on their surface. During an antibody response, activated B cells can switch to the expression of individual downstream heavy chain C region genes by a process of somatic recombination known as isotype switching. In addition, secreted Ig forms that act as antibodies can be produced by alternative RNA processing of the heavy chain C region sequences. Although the membrane forms of all Ig isotypes are monomeric, secreted IgM forms pentamers, and occasionally hexamers, in plasma (summary by Janeway et al., 2005).".

Gene ID: 3514 is IGKC immunoglobulin kappa constant on 2p11.2.

Gene ID: 3515 is IGKDEL immunoglobulin kappa deleting element or like on 2p11.2.

Gene ID: 3519 is IGKV@ immunoglobulin kappa variable cluster on 2p12: "Immunoglobulins (Ig) are the antigen recognition molecules of B cells. An Ig molecule is made up of 2 identical heavy chains (see MIM 147100) and 2 identical light chains, either kappa or lambda (see MIM 147220), joined by disulfide bonds so that each heavy chain is linked to a light chain and the 2 heavy chains are linked together. The kappa and lambda light chains have no apparent functional differences. Each Ig kappa light chain has an N-terminal variable (V) region containing the antigen-binding site and a C-terminal constant (C) region, encoded by a C region gene (IGKC; MIM 147200), that provides signaling functions. The kappa light chain V region is encoded by 2 types of genes: V genes and joining (J) genes (see MIM 146970). Random selection of just 1 gene of each type to assemble a V region accounts for the great diversity of V regions among Ig molecules. The kappa light chain locus on chromosome 2 contains approximately 40 functional V genes, followed by approximately 5 functional J genes. Due to polymorphism, the numbers of functional V and J genes differ among individuals (Janeway et al., 2005)."

Gene ID: 3535 is IGL immunoglobulin lambda locus on 22q11.22: "Immunoglobulins recognize foreign antigens and initiate immune responses such as phagocytosis and the complement system. Each immunoglobulin molecule consists of two identical heavy chains and two identical light chains. There are two classes of light chains, kappa and lambda. This region represents the germline organization of the lambda light chain locus. The locus includes V (variable), J (joining), and C (constant) segments. During B cell development, a recombination event at the DNA level joins a single V segment with a J segment; the C segment is later joined by splicing at the RNA level. Recombination of many different V segments with several J segments provides a wide range of antigen recognition. Additional diversity is attained by junctional diversity, resulting from the random additional of nucleotides by terminal deoxynucleotidyltransferase, and by somatic hypermutation, which occurs during B cell maturation in the spleen and lymph nodes. Several V segments and three C segments are known to be incapable of encoding a protein and are considered pseudogenes. The locus also includes several non-immunoglobulin genes, many of which are pseudogenes or are predicted by automated computational analysis or homology to other species. "

Gene ID: 3537 is IGLC1 immunoglobulin lambda constant 1 on 22q11.22.

Gene ID: 3538 is IGLC2 immunoglobulin lambda constant 2 on 22q11.22.

Gene ID: 3539 is IGLC3 immunoglobulin lambda constant 3 (Kern-Oz+ marker) on 22q11.22.

Gene ID: 3543 is IGLL1 immunoglobulin lambda like polypeptide 1 on 22q11.23: "The preB cell receptor is found on the surface of proB and preB cells, where it is involved in transduction of signals for cellular proliferation, differentiation from the proB cell to the preB cell stage, allelic exclusion at the Ig heavy chain gene locus, and promotion of Ig light chain gene rearrangements. The preB cell receptor is composed of a membrane-bound Ig mu heavy chain in association with a heterodimeric surrogate light chain. This gene encodes one of the surrogate light chain subunits and is a member of the immunoglobulin gene superfamily. This gene does not undergo rearrangement. Mutations in this gene can result in B cell deficiency and agammaglobulinemia, an autosomal recessive disease in which few or no gamma globulins or antibodies are made. Two transcript variants encoding different isoforms have been found for this gene."

1. NP_001356835.1 immunoglobulin lambda-like polypeptide 1 isoform c [variant 3].
2. NP_064455.1 immunoglobulin lambda-like polypeptide 1 isoform a precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a)."
3. NP_690594.1 immunoglobulin lambda-like polypeptide 1 isoform b precursor [variant 2].

Gene ID: 3546 is IGLV@ immunoglobulin lambda variable cluster on 22q11.2: "Immunoglobulins (Ig) are the antigen recognition molecules of B cells. An Ig molecule is made up of 2 identical heavy chains (see MIM 147100) and 2 identical light chains, either kappa (see MIM 147200) or lambda, joined by disulfide bonds so that each heavy chain is linked to a light chain and the 2 heavy chains are linked together. The kappa and lambda light chains have no apparent functional differences. Each Ig lambda light chain has an N-terminal variable (V) region containing the antigen-binding site and a C-terminal constant (C) region, encoded by a C region gene (IGLC1; MIM 147220), that provides signaling functions. The lambda light chain V region is encoded by 2 types of genes: V genes and joining (J) genes (see MIM 147230). Random selection of just 1 gene of each type to assemble a V region accounts for the great diversity of V regions among Ig molecules. The lambda light chain locus on chromosome 22 contains approximately 30 functional V genes, followed by approximately 4 functional J genes. Due to polymorphism, the numbers of functional V and J genes differ among individuals (Janeway et al., 2005)."

Gene ID: 6405 is SEMA3F semaphorin 3F on 3p21.31: "This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin loop and a C-terminal basic domain. This gene is expressed by the endothelial cells where it was found to act in an autocrine fashion to induce apoptosis, inhibit cell proliferation and survival, and function as an anti-tumorigenic agent. Alternative splicing results in multiple transcript variants encoding different isoforms."

1. NP_001305727.1 semaphorin-3F isoform 3: "Transcript Variant: This variant (3) has multiple differences in the 5' coding region and initiates translation at a downstream start site, compared to variant 1. It encodes isoform 3 which is shorter than isoform 1."
2. NP_001305729.1 semaphorin-3F isoform 2 precursor: "Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2 which is shorter than isoform 1."
3. NP_004177.3 semaphorin-3F isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longest isoform (1)."

Gene ID: 6696 is SPP1 secreted phosphoprotein 1 aka osteopontin/immunoglobulin alpha 1 heavy chain constant region fusion protein on 4q22.1: "The protein encoded by this gene is involved in the attachment of osteoclasts to the mineralized bone matrix. The encoded protein is secreted and binds hydroxyapatite with high affinity. The osteoclast vitronectin receptor is found in the cell membrane and may be involved in the binding to this protein. This protein is also a cytokine that upregulates expression of interferon-gamma and interleukin-12. Several transcript variants encoding different isoforms have been found for this gene."

1. NP_000573.1 osteopontin isoform OPN-b precursor: "Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 5. The resulting isoform (OPN-b, as described in PubMed: 7837791) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform e."
2. NP_001035147.1 osteopontin isoform OPN-a precursor: "Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 5. The resulting isoform (OPN-a, as described in PubMed: 7837791) has a shorter and distinct N-terminus compared to isoform e."
3. NP_001035149.1 osteopontin isoform OPN-c precursor: "Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 5. The resulting isoform (OPN-c, as described in PubMed: 7837791) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform e."
4. NP_001238758.1 osteopontin isoform 4 precursor: "Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and lacks two alternate in-frame exons compared to variant 5. The resulting isoform (4) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform e."
5. NP_001238759.1 osteopontin isoform 5: "Transcript Variant: This variant (5) represents the longest transcript and encodes the longest isoform (5)."

Gene ID: 10371 is SEMA3A semaphorin 3A on 7q21.11: "This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease."

1. NP_006071.1 semaphorin-3A precursor

Gene ID: 10507 is SEMA4D semaphorin 4D on 9q22.2.

1. NP_001135759.1 semaphorin-4D isoform 2 precursor [variant 2].
2. NP_001358123.1 semaphorin-4D isoform 1 precursor [variant 3].
3. NP_001358124.1 semaphorin-4D isoform 1 precursor [variant 4].
4. NP_001358125.1 semaphorin-4D isoform 1 precursor [variant 5].
5. NP_001358126.1 semaphorin-4D isoform 1 precursor [variant 6].
6. NP_001358127.1 semaphorin-4D isoform 2 precursor [variant 7].
7. NP_001358128.1 semaphorin-4D isoform 2 precursor [variant 8].
8. NP_001358129.1 semaphorin-4D isoform 2 precursor [variant 9].
9. NP_001358130.1 semaphorin-4D isoform 2 precursor [variant 10].
10. NP_001358131.1 semaphorin-4D isoform 3 precursor [variant 11].
11. NP_006369.3 semaphorin-4D isoform 1 precursor [variant 1].

Gene ID: 26018 is LRIG1 leucine rich repeats and immunoglobulin like domains 1 on 3p14.1.

1. NP_001364273.1 leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 2 precursor [variant 2].
2. NP_001364274.1 leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 3 [variant 3].
3. NP_001364275.1 leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 3 [variant 4].
4. NP_001364276.1 leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 4 [variant 5].
5. NP_001364277.1 leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 5 [variant 6].
6. NP_001364278.1 leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 6 [variant 7].
7. NP_056356.2 leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 1 precursor [variant 1].

Immunoglobulin receptor superfamily

Gene ID: 1630 is DCC DCC netrin 1 receptor on 18q21.2: "This gene encodes a netrin 1 receptor. The transmembrane protein is a member of the immunoglobulin superfamily of cell adhesion molecules, and mediates axon guidance of neuronal growth cones towards sources of netrin 1 ligand. The cytoplasmic tail interacts with the tyrosine kinases Src and focal adhesion kinase (FAK, also known as PTK2) to mediate axon attraction. The protein partially localizes to lipid rafts, and induces apoptosis in the absence of ligand. The protein functions as a tumor suppressor, and is frequently mutated or downregulated in colorectal cancer and esophageal carcinoma."

Gene ID: 2208 is FCER2 Fc fragment of IgE receptor II on 19p13.2: "The protein encoded by this gene is a B-cell specific antigen, and a low-affinity receptor for IgE. It has essential roles in B cell growth and differentiation, and the regulation of IgE production. This protein also exists as a soluble secreted form, then functioning as a potent mitogenic growth factor. Alternatively spliced transcript variants encoding different isoforms have been described for this gene."

1. NP_001193948.2 low affinity immunoglobulin epsilon Fc receptor isoform b: "Transcript Variant: This variant (2) contains an alternate 5' terminal exon and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (b, also known as CD23b) is shorter and has a distinct N-terminus, compared to isoform a. This variant is supported by data in PubMed IDs 12379312 and 15843555."
2. NP_001207429.1 low affinity immunoglobulin epsilon Fc receptor isoform a: "Transcript Variant: This variant (3) uses an alternate donor splice site in the 5' UTR, compared to variant 1. Both variants 1 and 3 encode the same isoform (a, also known as CD23a)."
3. NP_001993.2 low affinity immunoglobulin epsilon Fc receptor isoform a: "Transcript Variant: This variant (1) encodes the longer isoform (a, also known as CD23a). Both variants 1 and 3 encode the same isoform."

Gene ID: 2209 is FCGR1A Fc fragment of IgG receptor Ia on 1q21.2: "This gene encodes a protein that plays an important role in the immune response. This protein is a high-affinity Fc-gamma receptor. The gene is one of three related gene family members located on chromosome 1."

1. NP_000557.1 high affinity immunoglobulin gamma Fc receptor I isoform 2 precursor [variant 2].
2. NP_001365733.1 high affinity immunoglobulin gamma Fc receptor I isoform 1 precursor [variant 1].
3. NP_001365734.1 high affinity immunoglobulin gamma Fc receptor I isoform 3 precursor [variant 3].
4. NP_001365735.1 high affinity immunoglobulin gamma Fc receptor I isoform 4 precursor [variant 4].
5. NP_001365736.1 high affinity immunoglobulin gamma Fc receptor I isoform 5 [variant 5].
6. NP_001365737.1 high affinity immunoglobulin gamma Fc receptor I isoform 6 precursor [variant 6].
7. NP_001365738.1 high affinity immunoglobulin gamma Fc receptor I isoform 7 precursor [variant 7].
8. NP_001365739.1 high affinity immunoglobulin gamma Fc receptor I isoform 8 precursor [variant 8].
9. NP_001365740.1 high affinity immunoglobulin gamma Fc receptor I isoform 9 precursor [variant 9].

Gene ID: 2212 is FCGR2A Fc fragment of IgG receptor IIa on 1q23.3: "This gene encodes one member of a family of immunoglobulin Fc receptor genes found on the surface of many immune response cells. The protein encoded by this gene is a cell surface receptor found on phagocytic cells such as macrophages and neutrophils, and is involved in the process of phagocytosis and clearing of immune complexes. Alternative splicing results in multiple transcript variants."

1. NP_001129691.1 low affinity immunoglobulin gamma Fc region receptor II-a isoform 1 precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."
2. NP_001362225.1 low affinity immunoglobulin gamma Fc region receptor II-a isoform 3 precursor [variant 3].
3. NP_001362226.1 low affinity immunoglobulin gamma Fc region receptor II-a isoform 4 precursor [variant 4].
4. NP_067674.2 low affinity immunoglobulin gamma Fc region receptor II-a isoform 2 precursor: "Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1."

Gene ID: 2213 is FCGR2B Fc fragment of IgG receptor IIb on 1q23.3: "The protein encoded by this gene is a low affinity receptor for the Fc region of immunoglobulin gamma complexes. The encoded protein is involved in the phagocytosis of immune complexes and in the regulation of antibody production by B-cells. Variations in this gene may increase susceptibilty to systemic lupus erythematosus (SLE). Several transcript variants encoding different isoforms have been found for this gene."

1. NP_001002273.1 low affinity immunoglobulin gamma Fc region receptor II-b isoform 2 precursor: "Transcript Variant: This variant (2) lacks an alternate in-frame exon and uses an alternate in-frame splice junction at the 5' 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_001002274.1 low affinity immunoglobulin gamma Fc region receptor II-b isoform 3 precursor: "Transcript Variant: This variant (3) lacks an alternate in-frame 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_001002275.1 low affinity immunoglobulin gamma Fc region receptor II-b isoform 4 precursor: "Transcript Variant: This variant (4) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is 1 aa shorter compared to isoform 1."
4. NP_001177757.1 low affinity immunoglobulin gamma Fc region receptor II-b isoform 5: "Transcript Variant: This variant (5) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1."
5. NP_003992.3 low affinity immunoglobulin gamma Fc region receptor II-b isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."

Gene ID: 2214 is FCGR3A Fc fragment of IgG receptor IIIa on 1q23.3: "This gene encodes a receptor for the Fc portion of immunoglobulin G, and it is involved in the removal of antigen-antibody complexes from the circulation, as well as other other antibody-dependent responses. This gene (FCGR3A) is highly similar to another nearby gene (FCGR3B) located on chromosome 1. The receptor encoded by this gene is expressed on natural killer (NK) cells as an integral membrane glycoprotein anchored through a transmembrane peptide, whereas FCGR3B is expressed on polymorphonuclear neutrophils (PMN) where the receptor is anchored through a phosphatidylinositol (PI) linkage. Mutations in this gene have been linked to susceptibility to recurrent viral infections, susceptibility to systemic lupus erythematosus, and alloimmune neonatal neutropenia. Alternatively spliced transcript variants encoding different isoforms have been found for this gene."

1. NP_000560.7 low affinity immunoglobulin gamma Fc region receptor III-A isoform a precursor: "Transcript Variant: This variant (1) retains an intron in its 5' UTR and 5' coding region compared to variant 3.Variants 1, 3, 4 and 6 encode the same isoform (c).compared to isoform c."
2. NP_001121064.2 low affinity immunoglobulin gamma Fc region receptor III-A isoform b: "Transcript Variant: This variant (2) retains an intron in its 5' UTR and 5' coding region, and uses an alternate in-frame splice site in its 5' coding region compared to variant 3. The encoded isoform (2) is longer than isoform c. This isoform (b) lacks a predicted signal peptide compared to isoform c."
3. NP_001121065.1 low affinity immunoglobulin gamma Fc region receptor III-A isoform c precursor: "Transcript Variant: This variant (3) encodes isoform c. Variants 3, 4 and 6 encode the same isoform (c)."
4. NP_001121067.1 low affinity immunoglobulin gamma Fc region receptor III-A isoform c precursor: "Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 3. Variants 3, 4 and 6 encode the same isoform (c)."
5. NP_001121068.1 low affinity immunoglobulin gamma Fc region receptor III-A isoform d precursor: "Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 5' coding region compared to variant 3. The encoded isoform (d) is shorter than isoform c."
6. NP_001316049.1 low affinity immunoglobulin gamma Fc region receptor III-A isoform c precursor: "Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 3. Variants 3, 4 and 6 encode the same isoform (c)."
7. NP_001316051.1 low affinity immunoglobulin gamma Fc region receptor III-A isoform e: "Transcript Variant: This variant (7) retains an intron in its 5' UTR and 5' coding region, and lacks an alternate in-frame exon in its 3' coding region compared to variant 3. The encoded isoform is longer than isoform c. This isoform (e) lacks a predicted signal peptide compared to isoform c."

Gene ID: 3802 is KIR2DL1 killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1 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."

1. NP_055033.2 killer cell immunoglobulin-like receptor 2DL1 precursor.

Gene ID: 3803 is KIR2DL2 killer cell immunoglobulin like receptor, two Ig domains and long 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."

1. NP_055034.2 killer cell immunoglobulin-like receptor 2DL2 precursor.

Gene ID: 3804 is KIR2DL3 killer cell immunoglobulin like receptor, two 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."

1. NP_056952.2 killer cell immunoglobulin-like receptor 2DL3 precursor.

Gene ID: 3805 is KIR2DL4 killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4 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. Alternate alleles of this gene are represented on multiple alternate reference loci (ALT_REF_LOCs). Alternative splicing results in multiple transcript variants, some of which may not be annotated on the primary reference assembly."

1. NP_001074239.1 killer cell immunoglobulin-like receptor 2DL4 isoform c precursor: "Transcript Variant: This variant (3) lacks an internal exon in the coding region, compared to variant 1. It encodes isoform c, which is shorter than isoform a."
2. NP_001074241.1 killer cell immunoglobulin-like receptor 2DL4 isoform b precursor: "Transcript Variant: This variant (2) is one nt shorter than variant 1. It encodes isoform b, which is shorter and has a distinct C-terminus, compared to isoform a."
3. NP_002246.5 killer cell immunoglobulin-like receptor 2DL4 isoform a precursor: "This variant (1) represents the longest transcript and encodes the longest isoform (1)."

Gene ID: 3806 is KIR2DS1 killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1 aka MHC class I NK cell receptor Eb6 ActI 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."

1. NP_055327.1 killer cell immunoglobulin-like receptor 2DS1 precursor.

Gene ID: 3808 is KIR2DS3 killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 3 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."

1. NP_036445.1 killer cell immunoglobulin-like receptor 2DS3 precursor.

Gene ID: 3809 is KIR2DS4 killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4 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."

1. NP_001268900.1 killer cell immunoglobulin-like receptor 2DS4 isoform 2 precursor: "Transcript Variant: This variant (2) represents the 22nt deletion allele KIR2DS4*003 which results in a frameshift and loss of the C-terminal membrane binding domain. The resulting protein (isoform 2) has a distinct C-teminus and is likely secreted."
2. NP_001268901.1 killer cell immunoglobulin-like receptor 2DS4 isoform 3 precursor: "Transcript Variant: This variant (3) represents a 22nt deletion allele which also lacks a coding exon. The resulting protein (isoform 3) is frameshifted and lacks the C-terminal membrane binding domain found in the functional allele (KRI2DS4*001)."
3. NP_036446.3 killer cell immunoglobulin-like receptor 2DS4 isoform 1 precursor: "Transcript Variant: This variant (1) represents the functional allele (KIR2DS4*001) and encodes a functional, membrane-bound, activating receptor (isoform 1)."

Gene ID: 3810 is KIR2DS5 killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5: "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_055328.2 killer cell immunoglobulin-like receptor 2DS5 precursor.

Gene ID: 3811 is KIR3DL1 killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1 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."

1. NP_001309097.1 killer cell immunoglobulin-like receptor 3DL1 precursor: "Transcript Variant: This variant (2) represents an alternate allele of the KIR3DL1 gene, as represented in ALT_REF_LOCI_30."
2. NP_037421.2 killer cell immunoglobulin-like receptor 3DL1 precursor: "Transcript Variant: This variant (1) represents the reference genome allele of the KIR3DL1 gene."

Gene ID: 3812 is KIR3DL2 killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2 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. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene."

1. NP_001229796.1 killer cell immunoglobulin-like receptor 3DL2 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."
2. NP_006728.2 killer cell immunoglobulin-like receptor 3DL2 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 3813 is KIR3DS1 killer cell immunoglobulin like receptor, three Ig domains and short cytoplasmic tail 1 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene."

1. NP_001077008.1 killer cell immunoglobulin-like receptor 3DS1 isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longest isoform (1)."
2. NP_001269099.1 killer cell immunoglobulin-like receptor 3DS1 isoform 2 precursor: "Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1."
3. NP_001269100.1 killer cell immunoglobulin-like receptor 3DS1 isoform 3: "Transcript Variant: This variant (3) lacks two consecutive exons in the 5' coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1."

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: 10288 is LILRB2 leukocyte immunoglobulin like receptor B2 on 19q13.42: "This gene is a member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein belongs to the subfamily B class of LIR receptors which contain two or four extracellular immunoglobulin domains, a transmembrane domain, and two to four cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs). The receptor is expressed on immune cells where it binds to MHC class I molecules on antigen-presenting cells and transduces a negative signal that inhibits stimulation of an immune response. It is thought to control inflammatory responses and cytotoxicity to help focus the immune response and limit autoreactivity. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001074447.2 leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 2 precursor: "Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1. Both variants 2 and 3 encode the same isoform."
2. NP_001265332.2 leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 2 precursor: "Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1. Both variants 2 and 3 encode the same isoform."
3. NP_001265333.2 leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 3: "Transcript Variant: This variant (4) lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1."
4. NP_001265334.2 leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 4 precursor: "Transcript Variant: This variant (5) has a shorter 5' UTR, and lacks an internal exon which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct C-terminus, compared to isoform 1."
5. NP_001265335.2 leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 5 precursor: "Transcript Variant: This variant (6) has a shorter 5' UTR, lacks several exons, and its 3'-terminal exon extends past a splice site that is used in variant 1. The resulting protein (isoform 5) has a shorter and distinct C-terminus, compared to isoform 1. Isoform 5 lacks the transmembrane domain found in isoform 1 and is suspected to be soluble (PMID: 19658091)."
6. NP_005865.3 leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."

Gene ID: 10859 is LILRB1 leukocyte immunoglobulin like receptor B1 on 19q13.42: "This gene is a member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein belongs to the subfamily B class of LIR receptors which contain two or four extracellular immunoglobulin domains, a transmembrane domain, and two to four cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs). The receptor is expressed on immune cells where it binds to MHC class I molecules on antigen-presenting cells and transduces a negative signal that inhibits stimulation of an immune response. It is thought to control inflammatory responses and cytotoxicity to help focus the immune response and limit autoreactivity. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001075106.2 leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 2 precursor: "Transcript Variant: This variant (2) has a shorter 5' UTR and uses two alternate in-frame splice sites in the coding region, compared to variant 1. The resulting protein (isoform 2) is longer, compared to isoform 1."
2. NP_001075107.2 leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 3 precursor: "Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central coding region and differs in the 5' UTR, compared to variant 1. The resulting protein (isoform 3) is longer, compared to isoform 1."
3. NP_001075108.2 leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 4 precursor: "Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 3' coding region and differs in the 5' UTR, compared to variant 1. The resulting protein (isoform 4) is longer, compared to isoform 1."
4. NP_001265327.2 leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 5 precursor: "Transcript Variant: This variant (5) has a shorter 5' UTR, lacks an internal in-frame exon, and uses an alternate splice site in the central coding region, compared to variant 1. The resulting protein (isoform 5) is shorter, compared to isoform 1."
5. NP_001265328.2 leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 6 precursor: "Transcript Variant: This variant (6) has a shorter 5' UTR, lacks several exons, and its 3'-terminal exon extends past a splice site that is used in variant 1. The resulting protein (isoform 6) has a shorter and distinct C-terminus, compared to isoform 1. Isoform 6 lacks the transmembrane domain found in isoform 1 and is suspected to be soluble (PMID: 19658091)."
6. NP_006660.4 leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1."

Gene ID: 26762 is HAVCR1 hepatitis A virus cellular receptor 1 on 5q33.3: "The protein encoded by this gene is a membrane receptor for both human hepatitis A virus (HHAV) and TIMD4. The encoded protein may be involved in the moderation of asthma and allergic diseases. The reference genome represents an allele that retains a MTTVP amino acid segment that confers protection against atopy in HHAV seropositive individuals. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 4, 12 and 19."

1. NP_001166864.1 hepatitis A virus cellular receptor 1 isoform a precursor: "Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode isoform a."
2. NP_001295085.1 hepatitis A virus cellular receptor 1 isoform b precursor: "Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is longer than isoform a."
3. NP_036338.2 hepatitis A virus cellular receptor 1 isoform a precursor: "Transcript Variant: This variant (1) encodes the shorter isoform (a). Both variants 1 and 3 encode isoform a."

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: 84868 is HAVCR2 hepatitis A virus cellular receptor 2 on 5q33.3: "The protein encoded by this gene belongs to the immunoglobulin superfamily, and TIM family of proteins. CD4-positive T helper lymphocytes can be divided into types 1 (Th1) and 2 (Th2) on the basis of their cytokine secretion patterns. Th1 cells are involved in cell-mediated immunity to intracellular pathogens and delayed-type hypersensitivity reactions, whereas, Th2 cells are involved in the control of extracellular helminthic infections and the promotion of atopic and allergic diseases. This protein is a Th1-specific cell surface protein that regulates macrophage activation, and inhibits Th1-mediated auto- and alloimmune responses, and promotes immunological tolerance."

1. NP_116171.3 hepatitis A virus cellular receptor 2 precursor.

Gene ID: 115350 is FCRL1 Fc receptor like 1 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 three extracellular C2-like immunoglobulin domains, a transmembrane domain and a cytoplasmic domain with two immunoreceptor-tyrosine activation motifs. This protein may play a role in the regulation of cancer cell growth. Alternative splicing results in multiple transcript variants."

1. NP_001152869.1 Fc receptor-like protein 1 isoform 2 precursor: "Transcript Variant: This variant (2) uses an alternate exon in the 3' coding region compared to variant 1, that results in a frameshift. This variant encodes isoform 2, which is shorter and has a distinct C-terminus compared to isoform 1."
2. NP_001152870.1 Fc receptor-like protein 1 isoform 3 precursor: "Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This variant encodes isoform 3, which is shorter than isoform 1."
3. NP_443170.1 Fc receptor-like protein 1 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."

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: 343413 is FCRL6 Fc receptor like 6 on 1q23.2.

1. NP_001004310.2 Fc receptor-like protein 6 isoform 1 precursor: "Transcript Variant: This variant (1) represents the shorter transcript but encodes the longer protein (isoform 1)."
2. NP_001271146.1 Fc receptor-like protein 6 isoform 2: "Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus."

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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