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)."

𝛂₁B-glycoprotein

"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."

Human genes

Gene ID: 634 is CEACAM1 CEA cell adhesion molecule 1: "This gene encodes a member of the carcinoembryonic antigen (CEA) gene family, which belongs to the immunoglobulin superfamily. Two subgroups of the CEA family, the CEA cell adhesion molecules and the pregnancy-specific glycoproteins, are located within a 1.2 Mb cluster on the long arm of chromosome 19. Eleven pseudogenes of the CEA cell adhesion molecule subgroup are also found in the cluster. The encoded protein was originally described in bile ducts of liver as biliary glycoprotein. Subsequently, it was found to be a cell-cell adhesion molecule detected on leukocytes, epithelia, and endothelia. The encoded protein mediates cell adhesion via homophilic as well as heterophilic binding to other proteins of the subgroup. Multiple cellular activities have been attributed to the encoded protein, including roles in the differentiation and arrangement of tissue three-dimensional structure, angiogenesis, apoptosis, tumor suppression, metastasis, and the modulation of innate and adaptive immune responses. Multiple transcript variants encoding different isoforms have been reported, but the full-length nature of all variants has not been defined."

1. NP_001020083.1 carcinoembryonic antigen-related cell adhesion molecule 1 isoform 2 precursor: "Transcript Variant: This variant (2) lacks an exon in the 3' coding region that results in a frameshift and an early stop codon, compared to variant 1. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1. This variant has been referred to by multiple names, including BGPc, transmembrane carcinoembryonic antigen 3, TM3-CEA, and CEACAM1-4S."
2. NP_001171742.1 carcinoembryonic antigen-related cell adhesion molecule 1 isoform 4 precursor: "Transcript Variant: This variant (4) lacks an alternate, in-frame, exon, compared to variant 1. The resulting protein (isoform 3) is shorter when it was compared to isoform 1."
3. NP_001171744.1 carcinoembryonic antigen-related cell adhesion molecule 1 isoform 3 precursor: "Transcript Variant: This variant (3) has one and lacks a different alternate, in-frame, segment, compared to variant 1. The resulting protein (isoform 3) is shorter when it was compared to isoform 1. This variant has been referred to as 'alternative spliced isoform 3S' and 'short form 3'."
4. NP_001171745.1 carcinoembryonic antigen-related cell adhesion molecule 1 isoform 5 precursor: "Transcript Variant: This variant (5) lacks two coding region segments, one of which shifts the reading frame, compared to variant 1. The resulting protein (isoform 5) has a shorter and distinct C-terminus when it is compared to isoform 1."
5. NP_001192273.1 carcinoembryonic antigen-related cell adhesion molecule 1 isoform 6 precursor: "Transcript Variant: This variant (6) lacks a segment, which results in a frameshift, compared to variant 1. The resulting protein (isoform 6) has a distinct C-terminus, compared to isoform 1."
6. NP_001703.2 carcinoembryonic antigen-related cell adhesion molecule 1 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1). This variant has been referred to by multiple names, including transmembrane carcinoembryonic antigen BGPa, TM1-CEA, and CEACAM1-4L."

Gene ID: 3105 is HLA-A major histocompatibility complex, class I, A: "HLA-A belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from the endoplasmic reticulum lumen. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domains, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. Hundreds of HLA-A alleles have been described."

1. NP_001229687.1 HLA class I histocompatibility antigen, A alpha chain A*01:01:01:01 precursor: "Transcript Variant: This variant (2) represents the A*01:01:01:01 allele of the HLA-A gene, as found in the alternate locus group ALT_REF_LOCI_2 of the reference genome and in the RefSeqGene NG_029217."
2. NP_002107.3 HLA class I histocompatibility antigen, A alpha chain A*03:01:0:01 precursor: "Transcript Variant: This variant (1) represents the A*03:01:0:01 allele of the HLA-A gene, as found in the primary assembly of the reference genome."

Gene ID: 3106 is HLA-B major histocompatibility complex, class I, B: "HLA-B belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from the endoplasmic reticulum lumen. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon 1 encodes the leader peptide, exon 2 and 3 encode the alpha1 and alpha2 domains, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. Hundreds of HLA-B alleles have been described."

1. NP_005505.2 major histocompatibility complex, class I, B precursor.

Gene ID: 3107 is HLA-C major histocompatibility complex, class I, C: "HLA-C belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from endoplasmic reticulum lumen. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domain, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. Over one hundred HLA-C alleles have been described."

1. NP_001229971.1 HLA class I histocompatibility antigen, C alpha chain precursor: "Transcript Variant: This variant (2) represents the C*07:01:01:01 allele of the HLA-C gene, as represented in the alternate locus group ALT_REF_LOCI_2 of the reference genome."
2. NP_002108.4 HLA class I histocompatibility antigen, C alpha chain precursor: "Transcript Variant: This variant (1) represents the C*07:02:01 allele of the HLA-C gene, as represented in the assembled chromosome 6 in the primary assembly of the reference genome."

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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