Immunoglobulin domain genes

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

Immunoglobulin supergene family

Main article: Immunoglobulin supergene family

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)."

Alpha-1-B glycoprotein variants

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."

"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."

A1BG contains the immunoglobulin domain: cl11960 and three immunoglobulin-like domains: pfam13895, cd05751 and smart00410.

"Immunoglobulin (Ig) domain [cl11960] found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."

"This domain [pfam13895] contains immunoglobulin-like domains."

"Ig1_LILR_KIR_like: [cd05751] domain similar to the first immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILRs) and Natural killer inhibitory receptors (KIRs). This group includes LILRB1 (or LIR-1), LILRA5 (or LIR9), an activating natural cytotoxicity receptor NKp46, the immune-type receptor glycoprotein VI (GPVI), and the IgA-specific receptor Fc-alphaRI (or CD89). LILRs are a family of immunoreceptors expressed on expressed on T and B cells, on monocytes, dendritic cells, and subgroups of natural killer (NK) cells. The human LILR family contains nine proteins (LILRA1-3,and 5, and LILRB1-5). From functional assays, and as the cytoplasmic domains of various LILRs, for example LILRB1 (LIR-1), LILRB2 (LIR-2), and LILRB3 (LIR-3) contain immunoreceptor tyrosine-based inhibitory motifs (ITIMs) it is thought that LIR proteins are inhibitory receptors. Of the eight LIR family proteins, only LIR-1 (LILRB1), and LIR-2 (LILRB2), show detectable binding to class I MHC molecules; ligands for the other members have yet to be determined. The extracellular portions of the different LIR proteins contain different numbers of Ig-like domains for example, four in the case of LILRB1 (LIR-1), and LILRB2 (LIR-2), and two in the case of LILRB4 (LIR-5). The activating natural cytotoxicity receptor NKp46 is expressed in natural killer cells, and is organized as an extracellular portion having two Ig-like extracellular domains, a transmembrane domain, and a small cytoplasmic portion. GPVI, which also contains two Ig-like domains, participates in the processes of collagen-mediated platelet activation and arterial thrombus formation. Fc-alphaRI is expressed on monocytes, eosinophils, neutrophils and macrophages; it mediates IgA-induced immune effector responses such as phagocytosis, antibody-dependent cell-mediated cytotoxicity and respiratory burst."

"IG domains [smart00410] that cannot be classified into one of IGv1, IGc1, IGc2, IG."

Carcinoembryonic antigen gene family

Main article: Carcinoembryonic antigen gene family

Immunoglobulin superfamily genes

Main article: Immunoglobulin superfamily

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

Immunoglobulin domain genes

Main article: Immunoglobulin domain genes

Immunoglobulin receptor superfamily

Main article: Immunoglobulin receptor superfamily genes

Immunoglobulin domains (cl11960)

"Immunoglobulin (Ig) domain [cl11960] found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."

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)." pfam16680 Location: 31 → 100 Ig_4; T-cell surface glycoprotein CD3 delta chain.
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." cl11960 Location: 25 → 91 Ig; Immunoglobulin domain.

Gene ID: 59307 is SIGIRR single Ig and TIR domain containing on 11p15.5.

1. NP_001128525.1 single Ig IL-1-related receptor: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. All three variants encode the same protein." cl11960 Location: 8 → 111 Ig; Immunoglobulin domain.
2. NP_001128526.1 single Ig IL-1-related receptor: "Transcript Variant: This variant (1) represents the longest transcript. All three variants encode the same protein." cl11960 Location: 8 → 111 Ig; Immunoglobulin domain.
3. NP_068577.2 single Ig IL-1-related receptor: "Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. All three variants encode the same protein." cl11960 Location: 8 → 111 Ig; Immunoglobulin domain.

Gene ID: 79037 is PVRIG PVR related immunoglobulin domain containing on 7q22.1.

1. NP_076975.2 transmembrane protein PVRIG. cl11960 Location: 84 → 324 Ig; Immunoglobulin domain.

Gene ID: 79168 see Immunoglobulin like domain cd05751.

Gene ID: 126259 is TMIGD2 transmembrane and immunoglobulin domain containing 2 on 19p13.3.

1. NP_001162597.1 transmembrane and immunoglobulin domain-containing protein 2 isoform 2 precursor: "Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1." smart00410 Location: 29 → 114 IG_like; Immunoglobulin like and cl11960 Location: 27 → 133 Ig; Immunoglobulin domain.
2. NP_001295161.1 transmembrane and immunoglobulin domain-containing protein 2 isoform 3: "Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. It encodes isoform 3, which is shorter than isoform 1."
3. NP_653216.2 transmembrane and immunoglobulin domain-containing protein 2 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)." smart00410 Location: 29 → 114 IG_like; Immunoglobulin like and cl11960 Location: 27 → 133 Ig; Immunoglobulin domain.

Immunoglobulins (pfam13895)

Main article: Immunoglobulin like domain pfam13895

Immunoglobulin like domain (smart00410)

Main article: Immunoglobulin like domain smart00410

Immunoglobulins (cd05751)

Main article: Immunoglobulin like domain cd05751

Immunoglobulin domain (pfam16681)

"Ig_5 is an immunoglobulin domain found on T-cell surface glycoprotein CD3 epsilon chain. It forms a first-order complex with T-cell surface glycoprotein CD3 delta chain as part of the T-cell receptor complex."

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 pfam16681 Location: 36 → 121 Ig_5; Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain.

Immunoglobulin domain (pfam16680)

Ig_4: "This is an immunoglobulin-like domain. It is found on the T-cell surface glycoprotein CD3 delta chain. CD3delta and CD3epsilon complex together as part of the T-cell receptor complex."

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 pfam16680 Location: 40 → 111 Ig_4; T-cell surface glycoprotein CD3 delta chain.

Immunoglobulin heavy locus

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: 28385 is IGHV6-1 immunoglobulin heavy variable 6-1 on 14q32.33.

Gene ID: 28386 is IGHV5-10-1 immunoglobulin heavy variable 5-10-1 on 14q32.33.

Gene ID: 28388 is IGHV5-51 immunoglobulin heavy variable 5-51 on 14q32.33.

Gene ID: 28389 IGHV4-38-2 immunoglobulin heavy variable 4-38-2 on 14q32.33.

Gene ID: 28391 is IGHV4-61 immunoglobulin heavy variable 4-61 on 14q32.33.

Gene ID: 28392 is IGHV4-59 immunoglobulin heavy variable 4-59 on 14q32.33.

Gene ID: 28394 is IGHV4-39 immunoglobulin heavy variable 4-39 on 14q32.33.

Gene ID: 28395 is IGHV4-34 immunoglobulin heavy variable 4-34 on 14q32.33.

Gene ID: 28396 is IGHV4-31 immunoglobulin heavy variable 4-31 on 14q32.33.

Gene ID: 28397 is IGHV4-30-4 immunoglobulin heavy variable 4-30-4 on 14q32.33.

Gene ID: 28398 is IGHV4-30-2 immunoglobulin heavy variable 4-30-2 on 14q32.33.

Gene ID: 28399 is IGHV4-30-1 immunoglobulin heavy variable 4-30-1 on 14q32.33.

Gene ID: 28400 is IGHV4-28 immunoglobulin heavy variable 4-28 on 14q32.33.

Gene ID: 28401 is IGHV4-4 immunoglobulin heavy variable 4-4 on 14q32.33.

Gene ID: 28406 is IGHV3-76 immunoglobulin heavy variable 3-76 (pseudogene) on 14q32.33.

Gene ID: 28408 is IGHV3-74 immunoglobulin heavy variable 3-74 on 14q32.33.

Gene ID: 28409 is IGHV3-73 immunoglobulin heavy variable 3-73 on 14q32.33.

Gene ID: 28410 is IGHV3-72 immunoglobulin heavy variable 3-72 on 14q32.33.

Gene ID: 28412 is IGHV3-66 immunoglobulin heavy variable 3-66 on 14q32.33.

Gene ID: 28414 is IGHV3-64 immunoglobulin heavy variable 3-64 on 14q32.33.

Gene ID: 28420 is IGHV3-53 immunoglobulin heavy variable 3-53 on 14q32.33.

Gene ID: 28423 is IGHV3-49 immunoglobulin heavy variable 3-49 on 14q32.33.

Gene ID: 28424 is IGHV3-48 immunoglobulin heavy variable 3-48 on 14q32.33.

Gene ID: 28426 is IGHV3-43 immunoglobulin heavy variable 3-43 on 14q32.33.

Gene ID: 28434 is IGHV3-33 immunoglobulin heavy variable 3-33 on 14q32.33.

Gene ID: 28439 is IGHV3-30 immunoglobulin heavy variable 3-30 on 14q32.33.

Gene ID: 28442 is IGHV3-23 immunoglobulin heavy variable 3-23 on 14q32.33: "IGHV3-23 belongs to a cluster of approximately 40 functional variable (V) genes in the immunoglobulin (Ig) heavy chain locus on chromosome 14. For background information on the Ig heavy chain and the V gene cluster, see (MIM 147070)."

Gene ID: 28444 is IGHV3-21 immunoglobulin heavy variable 3-21 on 14q32.33.

Gene ID: 28445 is IGHV3-20 immunoglobulin heavy variable 3-20 on 14q32.33.

Gene ID: 28448 is IGHV3-15 immunoglobulin heavy variable 3-15 on 14q32.33.

Gene ID: 28449 is IGHV3-13 immunoglobulin heavy variable 3-13 on 14q32.33.

Gene ID: 28450 is IGHV3-11 immunoglobulin heavy variable 3-11 on 14q32.33.

Gene ID: 28451 is IGHV3-9 immunoglobulin heavy variable 3-9 on 14q32.33.

Gene ID: 28452 is IGHV3-7 immunoglobulin heavy variable 3-7 on 14q32.33.

Gene ID: 28454 is IGHV2-70 immunoglobulin heavy variable 2-70 on 14q32.33.

Gene ID: 28455 is IGHV2-26 immunoglobulin heavy variable 2-26 on 14q32.33.

Gene ID: 28457 is IGHV2-5 immunoglobulin heavy variable 2-5 on 14q32.33.

Gene ID: 28458 is IGHV1-69-2 immunoglobulin heavy variable 1-69-2 on 14q32.33.

Gene ID: 28461 is IGHV1-69 immunoglobulin heavy variable 1-69 on 14q32.33.

Gene ID: 28464 is IGHV1-58 immunoglobulin heavy variable 1-58 on 14q32.33.

Gene ID: 28465 is IGHV1-46 immunoglobulin heavy variable 1-46 on 14q32.33.

Gene ID: 28466 is IGHV1-45 immunoglobulin heavy variable 1-45 on 14q32.33.

Gene ID: 28467 is IGHV1-24 immunoglobulin heavy variable 1-24 on 14q32.33.

Gene ID: 28468 is IGHV1-18 immunoglobulin heavy variable 1-18 on 14q32.33.

Gene ID: 28472 is IGHV1-8 immunoglobulin heavy variable 1-8 on 14q32.33.

Gene ID: 28473 is IGHV1-3 immunoglobulin heavy variable 1-3 on 14q32.33.

Gene ID: 28474 is IGHV1-2 immunoglobulin heavy variable 1-2 on 14q32.33.

Gene ID: 28475 is IGHJ6 immunoglobulin heavy joining 6 on 14q32.33.

Gene ID: 28476 is IGHJ5 immunoglobulin heavy joining 5 on 14q32.33.

Gene ID: 28477 is IGHJ4 immunoglobulin heavy joining 4 on 14q32.33.

Gene ID: 28479 is IGHJ3 immunoglobulin heavy joining 3 on 14q32.33.

Gene ID: 28481 is IGHJ2 immunoglobulin heavy joining 2 on 14q32.33.

Gene ID: 28483 is IGHJ1 immunoglobulin heavy joining 1 on 14q32.33.

Gene ID: 28484 is IGHD7-27 immunoglobulin heavy diversity 7-27 on 14q32.33.

Gene ID: 28485 is IGHD6-25 immunoglobulin heavy diversity 6-25 on 14q32.33.

Gene ID: 28486 is IGHD6-19 immunoglobulin heavy diversity 6-19 on 14q32.33.

Gene ID: 28487 is IGHD6-13 immunoglobulin heavy diversity 6-13 on 14q32.33.

Gene ID: 28488 is IGHD6-6 immunoglobulin heavy diversity 6-6 on 14q32.33.

Gene ID: 28490 is IGHD5-18 immunoglobulin heavy diversity 5-18 on 14q32.33.

Gene ID: 28491 is IGHD5-12 immunoglobulin heavy diversity 5-12 on 14q32.33.

Gene ID: 28492 is IGHD5-5 immunoglobulin heavy diversity 5-5 on 14q32.33.

Gene ID: 28494 is IGHD4-17 immunoglobulin heavy diversity 4-17 on 14q32.33.

Gene ID: 28496 is IGHD4-4 immunoglobulin heavy diversity 4-4 on 14q32.33.

Gene ID: 28497 is IGHD3-22 immunoglobulin heavy diversity 3-22 on 14q32.33.

Gene ID: 28498 is IGHD3-16 immunoglobulin heavy diversity 3-16 on 14q32.33.

Gene ID: 28499 is IGHD3-10 immunoglobulin heavy diversity 3-10 on 14q32.33.

Gene ID: 28500 is IGHD3-9 immunoglobulin heavy diversity 3-9 on 14q32.33.

Gene ID: 28501 is IGHD3-3 immunoglobulin heavy diversity 3-3 on 14q32.33: "IGHD3-3 belongs to a cluster of approximately 25 functional diversity (D) genes in the immunoglobulin (Ig) heavy chain locus on chromosome 14. For background information on the Ig heavy chain and the D gene cluster, see (MIM 146910)."

Gene ID: 28502 is IGHD2-21 immunoglobulin heavy diversity 2-21 on 14q32.33.

Gene ID: 28503 is IGHD2-15 immunoglobulin heavy diversity 2-15 on 14q32.33.

Gene ID: 28504 is IGHD2-8 immunoglobulin heavy diversity 2-8 on 14q32.33.

Gene ID: 28505 is IGHD2-2 immunoglobulin heavy diversity 2-2 on 14q32.33.

Gene ID: 28506 is IGHD1-26 immunoglobulin heavy diversity 1-26 on 14q32.33.

Gene ID: 28507 is IGHD1-20 immunoglobulin heavy diversity 1-20 on 14q32.33.

Gene ID: 28509 is IGHD1-7 immunoglobulin heavy diversity 1-7 on 14q32.33.

Gene ID: 28510 is IGHD1-1 immunoglobulin heavy diversity 1-1 on 14q32.33.

Gene ID: 57289 is IGHV7-4-1 immunoglobulin heavy variable 7-4-1 on 14q32.33.

Gene ID: 57290 is IGHV3-30-3 immunoglobulin heavy variable 3-30-3 on 14q32.33.

Gene ID: 89770 is IGHV3-30-5 immunoglobulin heavy variable 3-30-5 on 14q32.33.

Immunoglobulin kappa

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: 7842 is IGKJ immunoglobulin kappa joining 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 (see MIM 146980) and joining (J) genes. 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: 11317 is RBPJL recombination signal binding protein for immunoglobulin kappa J region like on 20q13.12: "This gene encodes a member of the suppressor of hairless protein family. A similar protein in mouse is a transcription factor that binds to DNA sequences almost identical to that bound by the Notch receptor signaling pathway transcription factor recombining binding protein J. The mouse protein has been shown to activate transcription in concert with Epstein-Barr virus nuclear antigen-2. Alternative splicing results in multiple transcript variants."

1. NP_001268377.1 recombining binding protein suppressor of hairless-like protein isoform 2: "Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which leads to a translational frameshift, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1." cl15674 Location:381 → 442: "Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
2. NP_001268378.1 recombining binding protein suppressor of hairless-like protein isoform 3: "Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1."
3. NP_055091.2 recombining binding protein suppressor of hairless-like protein isoform 1: "Transcript Variant: This variant (1) encodes the longest isoform (1)."

Gene ID: 28299 is IGKV1-5 immunoglobulin kappa variable 1-5 on 2p11.2.

Gene ID: 28874 is IGKV3D-20 immunoglobulin kappa variable 3D-20 on 22q11.22.

Gene ID: 28875 is IGKV3D-15 immunoglobulin kappa variable 3D-15 on 2p11.2.

Gene ID: 28876 is IGKV3D-11 immunoglobulin kappa variable 3D-11 on 2p11.2.

Gene ID: 28877 is IGKV3D-7 immunoglobulin kappa variable 3D-7 on 2p11.2.

Gene ID: 28878 is IGKV2D-40 immunoglobulin kappa variable 2D-40 on 2p11.2.

Gene ID: 28881 is IGKV2D-30 immunoglobulin kappa variable 2D-30 on 2p11.2.

Gene ID: 28882 is IGKV2D-29 immunoglobulin kappa variable 2D-29 on 2p11.2.

Gene ID: 28883 is IGKV2D-28 immunoglobulin kappa variable 2D-28 on 2p11.2.

Gene ID: 28891 is IGKV1D-43 immunoglobulin kappa variable 1D-43 on 2p11.2.

Gene ID: 28893 is IGKV1D-39 immunoglobulin kappa variable 1D-39 on 2p11.2.

Gene ID: 28896 is IGKV1D-33 immunoglobulin kappa variable 1D-33 on 2p11.2.

Gene ID: 28900 is IGKV1D-17 immunoglobulin kappa variable 1D-17 on 2p11.2.

Gene ID: 28901 is IGKV1D-16 immunoglobulin kappa variable 1D-16 on 2p11.2.

Gene ID: 28902 is IGKV1D-13 immunoglobulin kappa variable 1D-13 on 2p11.2.

Gene ID: 28903 is IGKV1D-12 immunoglobulin kappa variable 1D-12 on 2p11.2.

Gene ID: 28904 is IGKV1D-8 immunoglobulin kappa variable 1D-8 on 2p11.2.

Gene ID: 28907 is IGKV5-2 immunoglobulin kappa variable 5-2 on 2p11.2.

Gene ID: 28908 is IGKV4-1 immunoglobulin kappa variable 4-1 on 2p11.2.

Gene ID: 28912 is IGKV3-20 immunoglobulin kappa variable 3-20 on 2p11.2.

Gene ID: 28913 is IGKV3-15 immunoglobulin kappa variable 3-15 on 2p11.2.

Gene ID: 28914 is IGKV3-11 immunoglobulin kappa variable 3-11 on 2p11.2.

Gene ID: 28916 is IGKV2-40 immunoglobulin kappa variable 2-40 on 2p11.2.

Gene ID: 28919 is IGKV2-30 immunoglobulin kappa variable 2-30 on 2p11.2.

Gene ID: 28921 is IGKV2-28 immunoglobulin kappa variable 2-28 on 2p11.2.

Gene ID: 28923 is IGKV2-24 immunoglobulin kappa variable 2-24 on 2p11.2.

Gene ID: 28930 is IGKV1-39 immunoglobulin kappa variable 1-39 on 2p11.2.

Gene ID: 28933 is IGKV1-33 immunoglobulin kappa variable 1-33 on 2p11.2.

Gene ID: 28935 is IGKV1-27 immunoglobulin kappa variable 1-27 on 2p11.2.

Gene ID: 28937 is IGKV1-17 immunoglobulin kappa variable 1-17 on 2p11.2.

Gene ID: 28938 is IGKV1-16 immunoglobulin kappa variable 1-16 on 2p11.2.

Gene ID: 28939 is IGKV1-13 immunoglobulin kappa variable 1-13 on 2p11.2.

Gene ID: 28940 is IGKV1-12 immunoglobulin kappa variable 1-12 on 2p11.2.

Gene ID: 28941 is IGKV1-9 immunoglobulin kappa variable 1-9 on 2p11.2.

Gene ID: 28942 is IGKV1-8 immunoglobulin kappa variable 1-8 on 2p11.2.

Gene ID: 28943 is IGKV1-6 immunoglobulin kappa variable 1-6 on 2p11.2.

Gene ID: 28946 is IGKJ5 immunoglobulin kappa joining 5 on 2p11.2.

Gene ID: 28947 is IGKJ4 immunoglobulin kappa joining 4 on 2p11.2.

Gene ID: 28948 is IGKJ3 immunoglobulin kappa joining 3 on 2p11.2.

Gene ID: 28949 is IGKJ2 immunoglobulin kappa joining 2 on 2p11.2.

Gene ID: 28950 is IGKJ1 immunoglobulin kappa joining 1 on 2p11.2.

Gene ID: 50802 is IGK immunoglobulin kappa locus on 2p11.2.

Immunoglobulin lambda locus

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: 8217 is IGLJ immunoglobulin lambda joining 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 (see MIM 147240) and joining (J) genes. 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: 28772 is IGLV10-54 immunoglobulin lambda variable 10-54 on 22q11.22.

Gene ID: 28773 is IGLV9-49 immunoglobulin lambda variable 9-49 on 22q11.22.

Gene ID: 28774 is IGLV8-61 immunoglobulin lambda variable 8-61 on 22q11.22.

Gene ID: 28775 is IGLV7-46 immunoglobulin lambda variable 7-46 on 22q11.22.

Gene ID: 28776 is IGLV7-43 immunoglobulin lambda variable 7-43 on 22q11.22.

Gene ID: 28778 is IGLV6-57 immunoglobulin lambda variable 6-57 on 22q11.22.

Gene ID: 28779 is IGLV5-52 immunoglobulin lambda variable 5-52 on 22q11.22.

Gene ID: 28781 is IGLV5-45 immunoglobulin lambda variable 5-45 on 22q11.22.

Gene ID: 28782 is IGLV5-39 immunoglobulin lambda variable 5-39 on 22q11.2.

Gene ID: 28783 is IGLV5-37 immunoglobulin lambda variable 5-37 on 22q11.22.

Gene ID: 28784 is IGLV4-69 immunoglobulin lambda variable 4-69 on 22q11.22.

Gene ID: 28785 is IGLV4-60 immunoglobulin lambda variable 4-60 on 22q11.22.

Gene ID: 28786 is IGLV4-3 immunoglobulin lambda variable 4-3 on 22q11.22.

Gene ID: 28791 is IGLV3-27 immunoglobulin lambda variable 3-27 on 22q11.22.

Gene ID: 28793 is IGLV3-25 immunoglobulin lambda variable 3-25 on 22q11.22.

Gene ID: 28795 is IGLV3-22 immunoglobulin lambda variable 3-22 on 22q11.22.

Gene ID: 28796 is IGLV3-21 immunoglobulin lambda variable 3-21 on 22q11.22.

Gene ID: 28797 is IGLV3-19 immunoglobulin lambda variable 3-19 on 22q11.22.

Gene ID: 28799 is IGLV3-16 immunoglobulin lambda variable 3-16 on 22q11.22.

Gene ID: 28802 is IGLV3-12 immunoglobulin lambda variable 3-12 on 22q11.22.

Gene ID: 28803 is IGLV3-10 immunoglobulin lambda variable 3-10 on 22q11.22.

Gene ID: 28804 is IGLV3-9 immunoglobulin lambda variable 3-9 on 22q11.22.

Gene ID: 28809 is IGLV3-1 immunoglobulin lambda variable 3-1 on 22q11.22.

Gene ID: 28813 is IGLV2-23 immunoglobulin lambda variable 2-23 on 22q11.22.

Gene ID: 28814 is IGLV2-18 immunoglobulin lambda variable 2-18 on 22q11.22.

Gene ID: 28815 is IGLV2-14 immunoglobulin lambda variable 2-14 on 22q11.22.

Gene ID: 28816 is IGLV2-11 immunoglobulin lambda variable 2-11 on 22q11.22.

Gene ID: 28817 is IGLV2-8 immunoglobulin lambda variable 2-8 on 22q11.22.

Gene ID: 28820 is IGLV1-51 immunoglobulin lambda variable 1-51 on 22q11.22.

Gene ID: 28822 is IGLV1-47 immunoglobulin lambda variable 1-47 on 22q11.22.

Gene ID: 28823 is IGLV1-44 immunoglobulin lambda variable 1-44 on 22q11.22.

Gene ID: 28825 is IGLV1-40 immunoglobulin lambda variable 1-40 on 22q11.22.

Gene ID: 28826 is IGLV1-36 immunoglobulin lambda variable 1-36 on 22q11.22.

Gene ID: 28827 is IGLJ7 immunoglobulin lambda joining 7 on 22q11.22.

Gene ID: 28828 is IGLJ6 immunoglobulin lambda joining 6 on 22q11.22.

Gene ID: 28831 is IGLJ3 immunoglobulin lambda joining 3 on 22q11.22.

Gene ID: 28832 is IGLJ2 immunoglobulin lambda joining 2 on 22q11.22.

Gene ID: 28833 is IGLJ1 immunoglobulin lambda joining 1 on 22q11.22.

Gene ID: 28834 is IGLC7 immunoglobulin lambda constant 7 on 22q11.22.

Immunoglobulin likes semaphorins

"Ig_Semaphorin_class III [cd05871]; Immunoglobulin (Ig)-like domain of class III semaphorins. Semaphorins are classified into various classes on the basis of structural features additional to the Sema domain. Class III semaphorins are a vertebrate class having a Sema domain, an Ig domain, a short basic domain, and are secreted. They have been shown to be axonal guidance cues and have a part in the regulation of the cardiovascular, immune and respiratory systems. Sema3A, the prototype member of this class III subfamily, induces growth cone collapse and is an inhibitor of axonal sprouting. In perinatal rat cortex, it acts as a chemoattractant and functions to direct the orientated extension of apical dendrites. It may play a role, prior to the development of apical dendrites, in signaling the radial migration of newborn cortical neurons towards the upper layers. Sema3A selectively inhibits vascular endothelial growth factor receptor (VEGF)-induced angiogenesis and induces microvascular permeability. This group also includes Sema3B, -C, -D, -E, -G."

"IG domains [smart00410] that cannot be classified into one of IGv1, IGc1, IGc2, IG."

Gene ID: 6405 is SEMA3F semaphorin 3F aka sema domain, immunoglobulin domain (Ig), short basic domain, secreted, 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." cd05871 Location: 510 → 598 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin and smart00410 Location: 513 → 597 IG_like; Immunoglobulin like.
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." cd05871 Location: 578 → 666 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin and smart00410 Location: 581 → 665 IG_like; Immunoglobulin like.
3. NP_004177.3 semaphorin-3F isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longest isoform (1)." cd05871 Location: 609 → 697 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin and smart00410 Location: 612 → 696 IG_like; Immunoglobulin like.

Gene ID: 7869 is SEMA3B semaphorin 3B on 3p21.31: "The protein encoded by this gene belongs to the class-3 semaphorin/collapsin family, whose members function in growth cone guidance during neuronal development. This family member inhibits axonal extension and has been shown to act as a tumor suppressor by inducing apoptosis. Alternative splicing of this gene results in multiple transcript variants."

1. NP_001005914.1 semaphorin-3B isoform 2 precursor: "Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (2) that is 1 aa shorter than isoform 1. The 5' terminal exon of this variant is inferred based on tiled partial transcript alignments." cd05871 Location: 574 → 664 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.
2. NP_001276989.1 semaphorin-3B isoform 1 precursor: "Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode isoform 1." cd05871 Location: 575 → 665 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.
3. NP_001276990.1 semaphorin-3B isoform 3 precursor: "Transcript Variant: This variant (4) 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 (3) is longer than isoform 1." cd05871 Location: 580 → 670 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.
4. NP_001276991.1 semaphorin-3B isoform 4: "Transcript Variant: This variant (5) lacks several 5' exons but contains alternate 5' exon structure, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 6 encode isoform 4." cl11960 Location: 232 → 322 Ig; Immunoglobulin domain.
5. NP_001276992.1 semaphorin-3B isoform 4: "Transcript Variant: This variant (6) lacks several 5' exons but contains alternate 5' exon structure, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 6 encode isoform 4." cl11960 Location: 232 → 322 Ig; Immunoglobulin domain.
6. NP_004627.1 semaphorin-3B isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1. Both variants 1 and 3 encode isoform 1. The 5' terminal exon of this variant is inferred based on tiled partial transcript alignments." cd05871 Location: 575 → 665 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.

Gene ID: 8482 is SEMA7A semaphorin 7A (John Milton Hagen blood group) on 15q24.1: "This gene encodes a member of the semaphorin family of proteins. The encoded preproprotein is proteolytically processed to generate the mature glycosylphosphatidylinositol (GPI)-anchored membrane glycoprotein. The encoded protein is found on activated lymphocytes and erythrocytes and may be involved in immunomodulatory and neuronal processes. The encoded protein carries the John Milton Hagen (JMH) blood group antigens. Mutations in this gene may be associated with reduced bone mineral density (BMD). Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed."

1. NP_001139501.1 semaphorin-7A 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. The encoded isoform (2) may undergo proteolytic processing similar to isoform 1." cl11960 Location: 535 → 605 Ig; Immunoglobulin domain.
2. NP_001139502.1 semaphorin-7A isoform 3: "Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter N-terminus and lacks a predicted signal peptide compared to isoform 1." smart00410 Location: 399 → 460 IG_like; Immunoglobulin like and cl11960 Location: 384 → 454 Ig; Immunoglobulin domain.
3. NP_003603.1 semaphorin-7A isoform 1 preproprotein: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."

Gene ID: 9037 is SEMA5A semaphorin 5A on 5p15.31: "This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene."

1. NP_003957.2 semaphorin-5A precursor.

Gene ID: 9723 is SEMA3E semaphorin 3E on 7q21.11: "Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. This gene encodes a class 4 semaphorin. This gene encodes a class 3 semaphorin. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001171600.1 semaphorin-3E isoform 2: "Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1." cd05871 Location: 525 → 610 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.
2. NP_036563.1 semaphorin-3E isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longer isoform (1)." cd05871 Location: 585 → 670 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.

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, cd05871 Location: 580 → 670 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.

Gene ID: 10500 is SEMA6C semaphorin 6C on 1q21.3: "This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration."

1. NP_001171532.1 semaphorin-6C isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."
2. NP_001171533.1 semaphorin-6C isoform 3 precursor: "Transcript Variant: This variant (3) lacks an exon in the coding region compared to variant 1. The resulting protein (isoform 3) is shorter but has the same N- and C-termini compared to isoform 1."
3. NP_112175.2 semaphorin-6C isoform 2 precursor: "Transcript Variant: This variant (2) lacks an exon in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1."

Gene ID: 10501 is SEMA6B semaphorin 6B on 19p13.3: "This gene encodes a member of the semaphorin family, a group of proteins characterized by the presence of a conserved semaphorin (sema) domain. Whereas some semaphorins are transmembrane proteins, others are secreted. Semaphorins play a major role in axon guidance. The protein encoded by this gene may be involved in both peripheral and central nervous system development."

1. NP_115484.2 semaphorin-6B precursor.

Gene ID: 10505 is SEMA4F semaphorin 4F on 2p13.1: "This gene encodes a transmembrane class IV semaphorin family protein, which plays a role in neural development. This gene may be involved in neurogenesis in prostate cancer, the development of neurofibromas, and breast cancer tumorigenesis. Alternative splicing results in multiple transcript variants."

1. NP_001258590.1 semaphorin-4F isoform 2 precursor: "Transcript Variant: This variant (2) lacks several internal exons, resulting in the loss of an in-frame segment in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1." cl11960 Location: 415 → 494 Ig; Immunoglobulin domain.
2. NP_001258591.1 semaphorin-4F isoform 3 precursor: "Transcript Variant: This variant (3) lacks an internal in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1." cl11960 Location: 537 → 616 Ig; Immunoglobulin domain.
3. NP_004254.2 semaphorin-4F isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)." cd05872 Location: 570 → 649 Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B.

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

1. NP_001135759.1 semaphorin-4D isoform 2 precursor [variant 2], cl11960 Location: 600 → 679 Ig; Immunoglobulin domain.
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], cd05873 Location: 559 → 645 Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D and smart00410 Location: 569 → 634 IG_like; Immunoglobulin like.

Gene ID: 10509 is SEMA4B semaphorin 4B on 15q26.1.

1. NP_001310958.1 semaphorin-4B isoform 2 [variant 3].
2. NP_001310959.1 semaphorin-4B isoform 3 [variant 4], cd05872 Location: 438 → 521 Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B.
3. NP_001310960.1 semaphorin-4B isoform 4 [variant 5].
4. NP_001310961.1 semaphorin-4B isoform 5 precursor [variant 6].
5. NP_001310962.1 semaphorin-4B isoform 3 precursor [variant 7], cd05872 Location: 438 → 521 Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B.
6. NP_001310963.1 semaphorin-4B isoform 6 precursor [variant 8].
7. NP_064595.2 semaphorin-4B isoform 1 precursor: "Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 are predicted to encode the same protein which is annotated as the largest open reading frame. Translation may intitiate at either of the first two AUG sites." cd05872 Location: 594 → 677 Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B.
8. NP_945119.1 semaphorin-4B isoform 1 precursor: "Transcript Variant: This variant (2) represents an alternate 5' UTR and transcription from an alternate promoter compared to variant 1. Variants 1 and 2 are predicted to encode the same protein which is annotated as the largest open reading frame. Translation may intitiate at either of the first two AUG sites." cd05872 Location: 594 → 677 Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B.

Gene ID: 10512 is SEMA3C semaphorin 3C on 7q21.11: "This gene encodes a secreted glycoprotein that belongs to the semaphorin class 3 family of neuronal guidance cues. The encoded protein contains an N-terminal sema domain, integrin and immunoglobulin-like domains, and a C-terminal basic domain. Homodimerization and proteolytic cleavage of the C-terminal propeptide are necessary for the function of the encoded protein. It binds a neuropilin co-receptor before forming a heterotrimeric complex with an associated plexin. An increase in the expression of this gene correlates with an increase in cancer cell invasion and adhesion. Naturally occurring mutations in this gene are associated with Hirschsprung disease."

1. NP_001337049.1 semaphorin-3C isoform 1: "Transcript Variant: This variant (1) encodes the longest isoform (1)." cd05871 Location: 593 → 682 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.
2. NP_001337050.1 semaphorin-3C isoform 3: "Transcript Variant: This variant (3) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1." cd05871 Location: 517 → 606 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.
3. NP_006370.1 semaphorin-3C isoform 2 precursor: "Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1." cd05871 Location: 575 → 664 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.

Gene ID: 54437 is SEMA5B semaphorin 5B on 3q21.1: "This gene encodes a member of the semaphorin protein family which regulates axon growth during development of the nervous system. The encoded protein has a characteristic Sema domain near the N-terminus, through which semaphorins bind to plexin, and five thrombospondin type 1 repeats in the C-terminal region of the protein. The protein product may be cleaved and exist as a secreted molecule (PMID: 19463192). Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001026872.2 semaphorin-5B isoform 1: "Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 2 encode the same protein (isoform 1)."
2. NP_001243275.1 semaphorin-5B isoform 1: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein (isoform 1)."
3. NP_001243276.1 semaphorin-5B isoform 2: "Transcript Variant: This variant (3) differs in the 5' UTR and coding region and uses an alternate start codon compared to variant 1. The resulting protein (isoform 2) has a longer N-terminus compared to isoform 1."
4. NP_001243277.1 semaphorin-5B isoform 3 precursor: "Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, uses a downstream start codon and uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The resulting protein (isoform 3) is shorter and has a shorter N-terminus compared to isoform 1."

Gene ID: 54910 is SEMA4C semaphorin 4C on 2q11.2.

1. NP_060259.4 semaphorin-4C precursor. cl11960 Location:560 → 647 Ig; Immunoglobulin domain, cl11960 Location: 560 → 647 Ig; Immunoglobulin domain.

Gene ID: 56920 is SEMA3G semaphorin 3G on 3p21.1.

1. NP_064548.1 semaphorin-3G precursor, cd05871 Location: 586 → 676 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin.

Gene ID: 57556 is SEMA6A semaphorin 6A on 5q23.1: "The transmembrane semaphorin SEMA6A is expressed in developing neural tissue and is required for proper development of the thalamocortical projection (Leighton et al., 2001 [PubMed 11242070])."

1. NP_001287709.1 semaphorin-6A isoform 1 precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."
2. NP_065847.1 semaphorin-6A isoform 2 precursor: "Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1."

Gene ID: 57715 is SEMA4G semaphorin 4G on 10q24.31: "Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_001190173.1 semaphorin-4G isoform 2 precursor: "Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1."
2. NP_060363.2 semaphorin-4G isoform 1 precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)." cd05872 Location: 572 → 655 Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B.

Gene ID: 64218 is SEMA4A semaphorin 4A on 1q22: "This gene encodes a member of the semaphorin family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass type I membrane protein containing an immunoglobulin-like C2-type domain, a PSI domain and a sema domain. It inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. It is an activator of T-cell-mediated immunity and suppresses vascular endothelial growth factor (VEGF)-mediated endothelial cell migration and proliferation in vitro and angiogenesis in vivo. Mutations in this gene are associated with retinal degenerative diseases including retinitis pigmentosa type 35 (RP35) and cone-rod dystrophy type 10 (CORD10). Multiple alternatively spliced transcript variants encoding different isoforms have been identified."

1. NP_001180229.1 semaphorin-4A isoform 1 precursor: "Transcript Variant: This variant (2) differs in the 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform (1)." cl11960 Location: 566 → 638 Ig; Immunoglobulin domain.
2. NP_001180230.1 semaphorin-4A isoform 1 precursor: "Transcript Variant: This variant (3) has an alternate 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform (1)." cl11960 Location: 566 → 638 Ig; Immunoglobulin domain.
3. NP_001180231.1 semaphorin-4A isoform 2: "Transcript Variant: This variant (4) lacks two internal exons in 5' different regions respectively, resulting in a downstream AUG start codon, as compared to variant 1. The resulting isoform (2) is shorter at the N-terminus and lacks an internal segment, as compared to isoform 1." cl11960 Location: 434 → 506 Ig; Immunoglobulin domain.
4. NP_001357496.1 semaphorin-4A isoform 1 precursor [variant 5], cl11960 Location: 566 → 638 Ig; Immunoglobulin domain.
5. NP_001357497.1 semaphorin-4A isoform 3 [variant 6], cl11960 Location: 467 → 539 Ig; Immunoglobulin domain.
6. NP_001357498.1 semaphorin-4A isoform 4 [variant 7], cl11960 Location: 397 → 469 Ig; Immunoglobulin domain.
7. NP_001357500.1 semaphorin-4A isoform 4 [variant 8], cl11960 Location: 397 → 469 Ig; Immunoglobulin domain.
8. NP_071762.2 semaphorin-4A isoform 1 precursor: "Transcript Variant: This variant (1) is the longest transcript. Variants 1-3 encode the same isoform (1)." cl11960 Location: 566 → 638 Ig; Immunoglobulin domain.

Gene ID: 80031 is SEMA6D semaphorin 6D on 15q21.1: "Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner."

1. NP_001185928.1 semaphorin-6D isoform 1 precursor [variant 7].
2. NP_001345280.1 semaphorin-6D isoform 4 precursor [variant 8].
3. NP_001345281.1 semaphorin-6D isoform 7 precursor [variant 9].
4. NP_065909.1 semaphorin-6D isoform 1 precursor [variant 1].
5. NP_079242.2 semaphorin-6D isoform 6 precursor [variant 6].
6. NP_705869.1 semaphorin-6D isoform 2 precursor [variant 2].
7. NP_705870.1 semaphorin-6D isoform 3 precursor [variant 3].
8. NP_705871.1 semaphorin-6D isoform 4 precursor [variant 4].
9. NP_705872.1 semaphorin-6D isoform 5 precursor [variant 5].

Gene ID: 223117 is SEMA3D semaphorin 3D on 7q21.11: "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 like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development."

1. NP_689967.2 semaphorin-3D precursor, cd05871 Location: 596 → 686 Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin and smart00410 Location: 611 → 680 IG_like; Immunoglobulin like.

Immunoglobulin likes

Gene ID: 7075 is TIE1 tyrosine kinase with immunoglobulin like and EGF like domains 1 on 1p34.2: "This gene encodes a member of the tyrosine protein kinase family. The encoded protein plays a critical role in angiogenesis and blood vessel stability by inhibiting angiopoietin 1 signaling through the endothelial receptor tyrosine kinase Tie2. Ectodomain cleavage of the encoded protein relieves inhibition of Tie2 and is mediated by multiple factors including vascular endothelial growth factor. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene."

1. NP_001240286.1 tyrosine-protein kinase receptor Tie-1 isoform 2: "Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1." pfam00047 Location: 84 → 165 ig; Immunoglobulin domain.
2. NP_005415.1 tyrosine-protein kinase receptor Tie-1 isoform 1 precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)." pfam00047 Location: 129 → 210 ig; Immunoglobulin domain.

Gene ID: 9860 is LRIG2 leucine rich repeats and immunoglobulin like domains 2 on 1p13.2: "This gene encodes a transmembrane protein containing leucine-rich repeats and immunoglobulin-like domains. The encoded protein promotes epidermal growth factor signalling, resulting in increased proliferation. Its expression in the cytoplasm of glioma cells is correlated with poor survival. Mutations in this gene can cause urofacial syndrome. Alternative splicing results in multiple transcript variants."

1. NP_001299615.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform 2: "Transcript Variant: This variant (2) contains an alternate exon in the 5' region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1." cd05763 Location: 516 → 590 Ig_1; Subgroup of the immunoglobulin (Ig) superfamily, pfam07679 Location: 593 → 680 I-set; Immunoglobulin I-set domain and pfam13927 Location: 394 → 481 Ig_3; Immunoglobulin domain.
2. NP_055628.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform 1 precursor: "Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1)." cd05763 Location: 619 → 693 Ig_1; Subgroup of the immunoglobulin (Ig) superfamily, smart00409 Location: 504 → 598 IG; Immunoglobulin, pfam07679 Location: 602 → 692 I-set; Immunoglobulin I-set domain, and cl11960 Location: 714 → 783 Ig; Immunoglobulin domain.

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], cd00096 Location: 512 → 586 Ig; Immunoglobulin domain, cd05763 Location: 616 → 690 Ig_1; Subgroup of the immunoglobulin (Ig) superfamily, smart00408 Location: 707 → 770 IGc2; Immunoglobulin C-2 Type, and pfam07679 Location: 599 → 689 I-set; Immunoglobulin I-set domain.

Gene ID: 26103 is LRIT1 leucine rich repeat, Ig-like and transmembrane domains 1 on 10q23.1.

1. NP_056428.1 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1 precursor, smart00410 Location: 267 → 345 IG_like; Immunoglobulin like and cl11960 Location: 267 → 345 Ig; Immunoglobulin domain.

Gene ID: 54841 is BIVM basic, immunoglobulin-like variable motif containing on 13q33.1.

1. NP_001153068.1 basic immunoglobulin-like variable motif-containing protein isoform b: "Transcript Variant: This variant (2) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant 1. The encoded protein (isoform b) is shorter than isoform a."
2. NP_060163.2 basic immunoglobulin-like variable motif-containing protein isoform a: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a)."

Gene ID: 158038 is LINGO2 leucine rich repeat and Ig domain containing 2 on 9p21.2-p21.1.

1. NP_001245211.1 leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 2 precursor [variant 2], pfam07679 Location: 410 → 500 I-set; Immunoglobulin I-set domain.
2. NP_001341503.1 leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 2 precursor [variant 3], pfam07679 Location: 410 → 500 I-set; Immunoglobulin I-set domain.
3. NP_001341504.1 leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 2 precursor [variant 4], pfam07679 Location: 410 → 500 I-set; Immunoglobulin I-set domain.
4. NP_689783.1 leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 2 precursor [variant 1], pfam07679 Location: 410 → 500 I-set; Immunoglobulin I-set domain.

Gene ID: 339398 is LINGO4 leucine rich repeat and Ig domain containing 4 on 1q21.3.

1. NP_001004432.1 leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 4 precursor, smart00410 Location: 420 → 501 IG_like; Immunoglobulin like and cl11960 Location: 431 → 501 Ig; Immunoglobulin domain.

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." smart00408 Location: 267 → 334 IGc2; Immunoglobulin C-2 Type and pfam07679 Location: 253 → 344 I-set; Immunoglobulin I-set domain.
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)." smart00408 Location: 267 → 344 IGc2; Immunoglobulin C-2 Type and pfam07679 Location: 253 → 354 I-set; Immunoglobulin I-set domain.

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. smart00410 Location: 267 → 345 IG_like; Immunoglobulin like and cl11960 Location: 267 → 345 Ig; Immunoglobulin domain.

Osteopontin (pfam00865)

"pfam00865 is a member of the superfamily cl02425."

"osteopontin/immunoglobulin alpha 1 heavy"

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: 11326 is VSIG4 V-set and immunoglobulin domain containing 4 on Xq12: "This gene encodes a v-set and immunoglobulin-domain containing protein that is structurally related to the B7 family of immune regulatory proteins. The encoded protein may be a negative regulator of T-cell responses. This protein is also a receptor for the complement component 3 fragments C3b and iC3b. Alternate splicing results in multiple transcript variants."

1. NP_001093901.1 V-set and immunoglobulin domain-containing protein 4 isoform 2 precursor: "Transcript Variant: This variant (2), also known as CRIg(S), lacks an alternate in-frame segment compared to variant 1, resulting in a shorter isoform (2), compared to isoform 1." smart00410 Location: 26 → 116 IG_like; Immunoglobulin like and cl11960 Location: 35 → 136 Ig; Immunoglobulin domain.
2. NP_001171759.1 V-set and immunoglobulin domain-containing protein 4 isoform 4 precursor: "Transcript Variant: This variant (4) differs in the 3' UTR and 3' coding region, compared to variant 1. The encoded isoform (4) has a shorter C-terminus, compared to isoform 4." cd00096 Location: 161 → 223 Ig; Immunoglobulin domain, smart00410 Location: 154 → 223 IG_like; Immunoglobulin like, and cl11960 Location: 35 → 136 Ig; Immunoglobulin domain.
3. NP_001171760.1 V-set and immunoglobulin domain-containing protein 4 isoform 3 precursor: "Transcript Variant: This variant (3) has multiple differences, compared to variant 1. The encoded isoform (3) is shorter than isoform 1." smart00410 Location: 26 → 116 IG_like; Immunoglobulin like and cl11960 Location: 35 → 136 Ig; Immunoglobulin domain.
4. NP_001244332.1 V-set and immunoglobulin domain-containing protein 4 isoform 5 precursor: "Transcript Variant: This variant (5) uses an alternate splice junction at the 5' end of a coding exon compared to variant 1. The resulting isoform (5) has a shorter and distinct C-terminus compared to isoform 1." cd00096 Location: 161 → 223 Ig; Immunoglobulin domain, smart00410 Location: 154 → 223 IG_like; Immunoglobulin like, and cl11960 Location: 35 → 136 Ig; Immunoglobulin domain.
5. NP_009199.1 V-set and immunoglobulin domain-containing protein 4 isoform 1 precursor: "Transcript Variant: This variant (1) is also called CRIg(L). It encodes the longest isoform (1)." cd16082 Location: 146 → 231 IgC_CRIg; Immunoglobulin (Ig) constant domain in complement receptor of the immunoglobulin superfamily (CRIg) and cd16089 Location: 26 → 137 IgV_CRIg; Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin superfamily (CRIg).

Gene ID: 23584 is VSIG2 V-set and immunoglobulin domain containing 2 on 11q24.2.

1. NP_001316849.1 V-set and immunoglobulin domain-containing protein 2 isoform 2 precursor: "Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the C-terminus compared to isoform 1."
2. NP_055127.2 V-set and immunoglobulin domain-containing protein 2 isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longer isoform (1)." pfam07686 Location: 31 → 142 V-set; Immunoglobulin V-set domain and cd00096 Location: 164 → 231 Ig; Immunoglobulin domain.

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.
3. The function of A1BG is the same as other immunoglobulin genes possessing the immunoglobulin domain cl11960 and/or any of three immunoglobulin-like domains: pfam13895, cd05751 and smart00410 in the order and nucleotide sequence: cd05751 Location: 401 → 493, smart00410 Location: 218 → 280, pfam13895 Location: 210 → 301 and cl11960 Location: 28 → 110.

See also

• Alpha-1-B glycoprotein
• Nuclear factor gene transcriptions
• SCAN domain

External links

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

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