Immunoglobulin like domain pfam13895

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

The United States National Library of Medicine (NLM) is a biomedical library in the United States as part of the National Institutes of Health that contains "hierarchical classifications of widely distributed protein domain families [and records] conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research."[1]

"At the time of writing, the CDD version v3.17 is the live production version with 52,910 protein- and protein domain-models obtained from Pfam (1), SMART (2), the COGs collection (3), TIGRFAMS (4), the NCBI Protein Clusters collection (5), NCBIfam (6) and CDD’s in-house data curation effort (7)."[1]

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)."[2]

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."[3]

"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."[2]

"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."[2]

"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."[2]

A1BG contains the immunoglobulin domain: cl11960 and three immunoglobulin-like domains: pfam13895, cd05751 and smart00410 in the order and nucleotide sequence: cd05751 Location: 401 β†’ 493, smart00410 Location: 218 β†’ 280, pfam13895 Location: 210 β†’ 301 and cl11960 Location: 28 β†’ 110.

"This domain [pfam13895] contains immunoglobulin-like domains."[4]

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

Genes having immunoglobulin like domain pfam13895

Number of genes = 51.

Gene ID: 1 see Immunoglobulin domain genes.

Gene ID: 177 see Major histocompatibility complex class III gene family.

Gene ID: 634 see Carcinoembryonic antigen gene family.

Gene ID: 942 is CD86 CD86 molecule on 3q13.33: "This gene encodes a type I membrane protein that is a member of the immunoglobulin superfamily. This protein is expressed by antigen-presenting cells, and it is the ligand for two proteins at the cell surface of T cells, CD28 antigen and cytotoxic T-lymphocyte-associated protein 4. Binding of this protein with CD28 antigen is a costimulatory signal for activation of the T-cell. Binding of this protein with cytotoxic T-lymphocyte-associated protein 4 negatively regulates T-cell activation and diminishes the immune response. Alternative splicing results in several transcript variants encoding different isoforms."[5]

  1. NP_001193853.1 T-lymphocyte activation antigen CD86 isoform 4 precursor: "Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1."[5] Conserved Domains (1) summary: cl11960 Location: 24 β†’ 109 Ig; Immunoglobulin domain.[5]
  2. NP_001193854.1 T-lymphocyte activation antigen CD86 isoform 5: "Transcript Variant: This variant (5) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (5) is made from a downstream translation start site compared to isoform 1."[5] Conserved Domains (1) summary: cl11960 Location: 2 β†’ 31 Ig; Immunoglobulin domain.[5]
  3. NP_008820.3 T-lymphocyte activation antigen CD86 isoform 2 precursor: "Transcript Variant: This variant (2) includes an alternate exon in the 5' UTR, resulting in the use of a downstream start codon compared to variant 1. Isoform 2 has a shorter N-terminus than isoform 1."[5] Conserved Domains (2) summary: smart00406 Location: 29 β†’ 104 IGv; Immunoglobulin V-Type and smart00410 Location: 28 β†’ 104 IG_like; Immunoglobulin like.[5]
  4. NP_787058.5 T-lymphocyte activation antigen CD86 isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longest isoform (1) of this protein."[5] Conserved Domains (2) summary: cd16087 Location: 28 β†’ 133 IgV_CD86; Immunoglobulin variable domain (IgV) in CD86 and cl11960 Location: 136 β†’ 221 Ig; Immunoglobulin domain.[5]
  5. NP_795711.1 T-lymphocyte activation antigen CD86 isoform 3 precursor: "Transcript Variant: This variant (3) includes an alternate exon in the 5' UTR, resulting in the use of a downstream start codon compared to variant 1. It also lacks an in-frame exon compared to variant 1. The resulting isoform (3, also known as CD86deltaTM) has a shorter N-terminus and lacks an internal segment compared to isoform 1. This isoform is the soluble form of this protein."[5] Conserved Domains (3) summary: smart00406 Location: 29 β†’ 104 IGv; Immunoglobulin V-Type, smart00410 Location: 28 β†’ 104 IG_like; Immunoglobulin like, and pfam13895 Location: 133 β†’ 228 Ig_2; Immunoglobulin domain.[5]

Gene ID: 962 is CD48 CD48 molecule on 1q23.3: "This gene encodes a member of the CD2 subfamily of immunoglobulin-like receptors which includes SLAM (signaling lymphocyte activation molecules) proteins. The encoded protein is found on the surface of lymphocytes and other immune cells, dendritic cells and endothelial cells, and participates in activation and differentiation pathways in these cells. The encoded protein does not have a transmembrane domain, however, but is held at the cell surface by a GPI anchor via a C-terminal domain which maybe cleaved to yield a soluble form of the receptor. Multiple transcript variants encoding different isoforms have been found for this gene."[6]

  1. NP_001242959.1 CD48 antigen isoform 2 precursor: "Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 1. The resulting protein (isoform 2) is longer and has a distinct C-terminus compared to isoform 1."[6] Conserved Domains (3) summary: cd05741 Location: 38 β†’ 127 Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins, smart00410 Location: 32 β†’ 127 IG_like; Immunoglobulin like and pfam13895 Location: 148 β†’ 217 Ig_2; Immunoglobulin domain.[6]
  2. NP_001769.2 CD48 antigen isoform 1 precursor: "Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter protein (isoform 1)."[6] Conserved Domains (2) summary: pfam13895 Location: 133 β†’ 217 Ig_2; Immunoglobulin domain and cd05775 Location: 35 β†’ 128 Ig_CD2_like_N; N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2 and similar domains.[6]
  3. XP_011508473.1 CD48 antigen isoform X1, Conserved Domains (3) summary: cd05741 Location: 6 β†’ 95 Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins, smart00410 Location: 1 β†’ 95 IG_like; Immunoglobulin like and pfam13895 Location: 116 β†’ 185 Ig_2; Immunoglobulin domain.[6]
  4. XP_005245682.1 CD48 antigen isoform X2, Conserved Domains (2) summary: cd05741 Location: 38 β†’ 127 Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins and smart00410 Location: 32 β†’ 127 IG_like; Immunoglobulin like.[6]

Gene ID: 1048 see Carcinoembryonic antigen gene family.

Gene ID: 1088 see Carcinoembryonic antigen gene family.

Gene ID: 2324 is FLT4 fms related receptor tyrosine kinase 4 on 5q35.3: "This gene encodes a tyrosine kinase receptor for vascular endothelial growth factors C and D. The protein is thought to be involved in lymphangiogenesis and maintenance of the lymphatic endothelium. Mutations in this gene cause hereditary lymphedema type IA."[7]

  1. NP_001341918.1 vascular endothelial growth factor receptor 3 isoform 3 precursor: "Transcript Variant: This variant (3) contains an alternate 3' terminal exon compared to variant 1. This results in an isoform (3) with a shorter C-terminus compared to isoform 1."[7] Conserved Domains (6) summary: cd05862 Location: 245 β†’ 329 Ig_VEGFR; Immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R), cd05863 Location: 352 β†’ 418 Ig_VEGFR-3; Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3), smart00408 Location: 693 β†’ 755 IGc2; Immunoglobulin C-2 Type, smart00410 Location: 564 β†’ 657 IG_like; Immunoglobulin like, and pfam13895 Location: 137 β†’ 224 Ig_2; Immunoglobulin domain.[7]
  2. NP_002011.2 vascular endothelial growth factor receptor 3 isoform 2 precursor: "Transcript Variant: This variant (2) contains an alternate 3' terminal exon compared to variant 1. This results in an isoform (2) with a shorter C-terminus compared to isoform 1."[7] Conserved Domains (10) summary: cd05862 Location: 245 β†’ 329 Ig1_VEGFR; First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R), cd05863 Location: 352 β†’ 418 Ig2_VEGFR-3; Second immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3), smart00408 Location: 693 β†’ 755 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 564 β†’ 657 IG; Immunoglobulin, smart00410 Location: 238 β†’ 327 IG_like; Immunoglobulin like, pfam07679 Location: 678 β†’ 765 I-set; Immunoglobulin I-set domain, pfam13895 Location: 138 β†’ 224 Ig_2; Immunoglobulin domain, and cl11960 Location: 570 β†’ 658 Ig; Immunoglobulin domain.[7]
  3. NP_891555.2 vascular endothelial growth factor receptor 3 isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longest isoform (1)."[7] Conserved Domains (10) summary: cd05862 Location: 245 β†’ 329 Ig1_VEGFR; First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R), cd05863 Location: 352 β†’ 418 Ig2_VEGFR-3; Second immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3), smart00408 Location: 693 β†’ 755 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 564 β†’ 657 IG; Immunoglobulin, smart00410 Location: 238 β†’ 327 IG_like; Immunoglobulin like, pfam07679 Location: 678 β†’ 765 I-set; Immunoglobulin I-set domain, pfam13895 Location: 138 β†’ 224 Ig_2; Immunoglobulin domain and cl11960 Location: 570 β†’ 658 Ig; Immunoglobulin domain.[7]
  4. XP_011532780.1 vascular endothelial growth factor receptor 3 isoform X1, Conserved Domains (10) summary: cd05862 Location: 322 β†’ 406 Ig1_VEGFR; First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R), cd05863 Location: 429 β†’ 495 Ig2_VEGFR-3; Second immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3), smart00408 Location: 770 β†’ 832 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 641 β†’ 734 IG; Immunoglobulin, smart00410 Location: 315 β†’ 404 IG_like; Immunoglobulin like, pfam07679 Location: 755 β†’ 842 I-set; Immunoglobulin I-set domain, pfam13895 Location: 215 β†’ 301 Ig_2; Immunoglobulin domain, and cl11960 Location: 647 β†’ 735 Ig; Immunoglobulin domain.[7]
  5. XP_011532786.1 vascular endothelial growth factor receptor 3 isoform X6, Conserved Domains (10) summary: cd05862 Location: 92 β†’ 176 Ig1_VEGFR; First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R), cd05863 Location: 199 β†’ 265 Ig2_VEGFR-3; Second immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3), smart00408 Location: 540 β†’ 602 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 411 β†’ 504 IG; Immunoglobulin, smart00410 Location: 85 β†’ 174 IG_like; Immunoglobulin like, pfam07679 Location: 525 β†’ 612 I-set; Immunoglobulin I-set domain, pfam13895 Location: 1 β†’ 71 Ig_2; Immunoglobulin domain, and cl11960 Location: 417 β†’ 505 Ig; Immunoglobulin domain.[7]

Gene ID: 3339 is HSPG2 heparan sulfate proteoglycan 2 on 1p36.12: "This gene encodes the perlecan protein, which consists of a core protein to which three long chains of glycosaminoglycans (heparan sulfate or chondroitin sulfate) are attached. The perlecan protein is a large multidomain proteoglycan that binds to and cross-links many extracellular matrix components and cell-surface molecules. It has been shown that this protein interacts with laminin, prolargin, collagen type IV, FGFBP1, FBLN2, FGF7 and transthyretin, etc., and it plays essential roles in multiple biological activities. Perlecan is a key component of the vascular extracellular matrix, where it helps to maintain the endothelial barrier function. It is a potent inhibitor of smooth muscle cell proliferation and is thus thought to help maintain vascular homeostasis. It can also promote growth factor (e.g., FGF2) activity and thus stimulate endothelial growth and re-generation. It is a major component of basement membranes, where it is involved in the stabilization of other molecules as well as being involved with glomerular permeability to macromolecules and cell adhesion. Mutations in this gene cause Schwartz-Jampel syndrome type 1, Silverman-Handmaker type of dyssegmental dysplasia, and tardive dyskinesia. Alternative splicing of this gene results in multiple transcript variants."[8]

  1. NP_001278789.1 basement membrane-specific heparan sulfate proteoglycan core protein isoform a precursor: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a)."[8] Conserved Domains (18) summary: cd00096 Location: 3131 β†’ 3200 Ig; Immunoglobulin domainm cd05743 Location: 421 β†’ 498 Ig_Perlecan_D2_like; Immunoglobulin (Ig)-like domain II (D2) of the human basement membrane heparan sulfate proteoglycan perlecan, also known as HSPG2, cd05754 Location: 1772 β†’ 1857 Ig3_Perlecan_like; Third immunoglobulin (Ig)-like domain found in Perlecan and similar proteins, smart00408 Location: 1971 β†’ 2033 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 414 β†’ 490 IG; Immunoglobulin, smart00410 Location: 2058 β†’ 2135 IG_like; Immunoglobulin like, pfam07679 Location: 3582 β†’ 3659 I-set; Immunoglobulin I-set domain, pfam00047 Location: 3027 β†’ 3107 ig; Immunoglobulin domain, pfam13895 Location: 2930 β†’ 3010 Ig_2; Immunoglobulin domain, cl11960 Location: 3597 β†’ 3652 Ig; Immunoglobulin domain.[8]
  2. NP_005520.4 basement membrane-specific heparan sulfate proteoglycan core protein isoform b precursor: "Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is 1 aa shorter than isoform a."[8] Conserved Domains (18) summary: cd00096 Location: 3130 β†’ 3199 Ig; Immunoglobulin domain, cd05743 Location: 421 β†’ 498 Ig_Perlecan_D2_like; Immunoglobulin (Ig)-like domain II (D2) of the human basement membrane heparan sulfate proteoglycan perlecan, also known as HSPG2, cd05754 Location: 1771 β†’ 1856 Ig3_Perlecan_like; Third immunoglobulin (Ig)-like domain found in Perlecan and similar proteins, smart00408 Location: 1970 β†’ 2032 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 414 β†’ 490 IG; Immunoglobulin, smart00410 Location: 2057 β†’ 2134 IG_like; Immunoglobulin like, pfam07679 Location: 3581 β†’ 3658 I-set; Immunoglobulin I-set domain, pfam00047 Location: 3026 β†’ 3106 ig; Immunoglobulin domain, pfam13895 Location: 2929 β†’ 3009 Ig_2; Immunoglobulin domain, and cl11960 Location: 3596 β†’ 3651 Ig; Immunoglobulin domain.[8]
  3. XP_011539620.1 basement membrane-specific heparan sulfate proteoglycan core protein isoform X1, Conserved Domains (18) summary: cd00096 Location: 3313 β†’ 3382 Ig; Immunoglobulin domain, cd05743 Location: 438 β†’ 515 Ig_Perlecan_D2_like; Immunoglobulin (Ig)-like domain II (D2) of the human basement membrane heparan sulfate proteoglycan perlecan, also known as HSPG2, cd05754 Location: 1954 β†’ 2039 Ig3_Perlecan_like; Third immunoglobulin (Ig)-like domain found in Perlecan and similar proteins, smart00408 Location: 2153 β†’ 2215 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 431 β†’ 507 IG; Immunoglobulin, smart00410 Location: 2240 β†’ 2317 IG_like; Immunoglobulin like, pfam07679 Location: 3764 β†’ 3841 I-set; Immunoglobulin I-set domain, pfam00047 Location: 3209 β†’ 3289 ig; Immunoglobulin domain, pfam13895 Location: 3112 β†’ 3192 Ig_2; Immunoglobulin domain, cl11960 Location: 3779 β†’ 3834 Ig; Immunoglobulin domain.[8]

Gene ID: 3385 see Carcinoembryonic antigen gene family.

Gene ID: 3791 is KDR kinase insert domain receptor on 4q12: "Vascular endothelial growth factor (VEGF) is a major growth factor for endothelial cells. This gene encodes one of the two receptors of the VEGF. This receptor, known as kinase insert domain receptor, is a type III receptor tyrosine kinase. It functions as the main mediator of VEGF-induced endothelial proliferation, survival, migration, tubular morphogenesis and sprouting. The signalling and trafficking of this receptor are regulated by multiple factors, including Rab GTPase, P2Y purine nucleotide receptor, integrin alphaVbeta3, T-cell protein tyrosine phosphatase, etc.. Mutations of this gene are implicated in infantile capillary hemangiomas."[9]

  1. NP_002244.1 vascular endothelial growth factor receptor 2 precursor, Conserved Domains (10) summary: cd05862 Location: 239 β†’ 326 Ig1_VEGFR; First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R), cd05864 Location: 348 β†’ 417 Ig2_VEGFR-2; Second immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 2 (VEGFR-2), smart00408 Location: 680 β†’ 744 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 565 β†’ 661 IG; Immunoglobulin, smart00410 Location: 231 β†’ 324 IG_like; Immunoglobulin like, pfam07679 Location: 667 β†’ 754 I-set; Immunoglobulin I-set domain, pfam13895 Location: 551 β†’ 661 Ig_2; Immunoglobulin domain, and cl11960 Location: 41 β†’ 109 Ig; Immunoglobulin domain.[9]

Gene ID: 3902 is LAG3

Gene ID: 4059 see Carcinoembryonic antigen gene family.

Gene ID: 4680 see Carcinoembryonic antigen gene family.

Gene ID: 4756 is NEO1

Gene ID: 5175 see Carcinoembryonic antigen gene family.

Gene ID: 5669 is PSG1

Gene ID: 5670 is PSG2

Gene ID: 5671 is PSG3

Gene ID: 5672 is PSG4

Gene ID: 5673 is PSG5

Gene ID: 5675 is PSG6

Gene ID: 5676 is PSG7

Gene ID: 5678 is PSG9

Gene ID: 5680 is PSG11

Gene ID: 6614 is SIGLEC1

Gene ID: 7087 see Carcinoembryonic antigen gene family.

Gene ID: 7273 is TTN titin on 2q31.2: "This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma."[10]

  1. NP_001243779.1 titin isoform N2BA: "Transcript Variant: This variant (N2BA) encodes another major cardiac isoform (N2BA). It includes the N2A and N2B exons, and also the PEVK region. This variant is supported by annotation on DNA accession AJ277892.2 and by accompanying data in PMIDs 10850961 and 11717165."[10] Conserved Domains (16) summary: cd00096 Location: 5899 β†’ 5968 Ig; Immunoglobulin domain, cd05747 Location: 33485 β†’ 33576 Ig5_Titin_like; M5, fifth immunoglobulin (Ig)-like domain of human titin C terminus and similar proteins, cd05748 Location: 21720 β†’ 21791 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar proteins, smart00408 Location: 4678 β†’ 4744 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 20232 β†’ 20312 IG; Immunoglobulin, smart00410 Location: 28207 β†’ 28289, IG_like; Immunoglobulin like, pfam07679 Location: 8888 β†’ 8977 I-set; Immunoglobulin I-set domain, pfam00047 Location: 6824 β†’ 6907 ig; Immunoglobulin domain, pfam13895 Location: 13398 β†’ 13462 Ig_2; Immunoglobulin domain, and cl11960 Location: 24569 β†’ 24642 Ig; Immunoglobulin domain.[10]
  2. NP_001254479.2 titin isoform IC: "Transcript Variant: This variant (IC) represents an inferred complete model that includes all possible supported in-frame coding exons. The exons included in this inferred variant are supported by the original sequence analysis, publication data(PMID:11717165), available cDNA and EST data, and additional sequence analysis of the repetitive exons. This transcript is the longest and represents a 363-exon model encoding a predicted protein (isoform IC) of 35,991 amino acids."[10] Conserved Domains (17) summary: cd00096 Location: 7340 β†’ 7409 Ig; Immunoglobulin domain, cd05747 Location: 35126 β†’ 35217 Ig5_Titin_like; M5, fifth immunoglobulin (Ig)-like domain of human titin C terminus and similar proteins, cd05748 Location: 22567 β†’ 22640 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar proteins, smart00408 Location: 4995 β†’ 5061 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 21873 β†’ 21953 IG; Immunoglobulin, smart00410 Location: 29848 β†’ 29930 IG_like; Immunoglobulin like, pfam07679 Location: 9205 β†’ 9294 I-set; Immunoglobulin I-set domain, pfam00047 Location: 7141 β†’ 7224 ig; Immunoglobulin domain, pfam13895 Location: 15039 β†’ 15103 Ig_2; Immunoglobulin domain, and pfam16031 Location: 12286 β†’ 12406 TonB_N; TonB N-terminal region, and cl11960 Location: 26210 β†’ 26283 Ig; Immunoglobulin domain.[10]
  3. NP_003310.4 titin isoform N2-B: "Transcript Variant: This variant (N2-B) encodes the major cardiac muscle isoform (N2-B). It lacks multiple exons in the region encoding PEVK repeats. This results in a shortened PEVK region in isoform N2-B compared to isoform IC. This variant is supported by data in PMIDs 10850961 and 11717165."[10] Conserved Domains (13) summary: cd00096 Location: 24053 β†’ 24120 Ig; Immunoglobulin domain, cd05747 Location: 26061 β†’ 26152 Ig5_Titin_like; M5, fifth immunoglobulin (Ig)-like domain of human titin C terminus and similar proteins, cd05748 Location: 14296 β†’ 14367, Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar proteins, smart00408 Location: 910 β†’ 976 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 17823 β†’ 17904 IG; Immunoglobulin, smart00410 Location: 20783 β†’ 20865 IG_like; Immunoglobulin like, pfam07679 Location: 6 β†’ 97 I-set; Immunoglobulin I-set domain, pfam13895 Location: 5974 β†’ 6038 Ig_2; Immunoglobulin domain, and cl11960 Location:17145 β†’ 17218 Ig; Immunoglobulin domain.[10]
  4. NP_596869.4 titin isoform N2-A: "Transcript Variant: This variant (N2-A) encodes isoform N2-A, which is the predominant titin isoform in skeletal muscle. This variant lacks the N2B region but includes the PEVK region. This variant is supported by data in PMIDs 7569978, 10850961 and 11717165."[10] Conserved Domains (16) summary: cd00096 Location: 4972 β†’ 5041 Ig; Immunoglobulin domain, cd05747 Location: 32558 β†’ 32649 Ig5_Titin_like; M5, fifth immunoglobulin (Ig)-like domain of human titin C terminus and similar proteins, cd05748 Location: 19999 β†’ 20072 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar proteins, smart00408 Location: 3751 β†’ 3817 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 27280 β†’ 27362 IG; Immunoglobulin, smart00410 Location: 19305 β†’ 19385 IG_like; Immunoglobulin like, pfam07679 Location: 7961 β†’ 8050 I-set; Immunoglobulin I-set domain, pfam00047 Location: 5897 β†’ 5980 ig; Immunoglobulin domain, pfam13895 Location: 12471 β†’ 12535 Ig_2; Immunoglobulin domain, and cl11960 Location: 23642 β†’ 23715 Ig; Immunoglobulin domain.[10]
  5. NP_596870.2 titin isoform novex-3: "Transcript Variant: This variant (novex-3) is the shortest transcript and encodes the shortest isoform (novex-3). Its last exon is nearly 8 kb and is not found in the other variants. The novex-3 isoform, which is found in all striated muscle, lacks the PEVK region and has a C-terminal truncation compared to longer isoforms. This variant is supported by data in PMID:11717165."[10] Conserved Domains (6) summary: cd00096 Location: 3521 β†’ 3594 Ig; Immunoglobulin domain, smart00408 Location: 956 β†’ 1022 IGc2; Immunoglobulin C-2 Type, smart00410 Location: 3154 β†’ 3233 IG_like; Immunoglobulin like, pfam07679 Location: 6 β†’ 97 I-set; Immunoglobulin I-set domain, and cl11960 Location: 26 β†’ 97 Ig; Immunoglobulin domain.[10]
  6. NP_597676.3 titin isoform novex-1: "Transcript Variant: This variant (novex-1) encodes the minor cardiac muscle isoform (novex-1 or novex-1/N2B), which is nearly identical to the major cardiac isoform N2-B but contains a unique stretch of 125 aa in the I-band region. This variant is supported by data in PMID:11717165."[10] Conserved Domains (13) summary: cd00096 Location: 24178 β†’ 24245 Ig; Immunoglobulin domain, cd05747 Location: 26186 β†’ 26277 Ig5_Titin_like; M5, fifth immunoglobulin (Ig)-like domain of human titin C terminus and similar proteins, cd05748 Location: 14421 β†’ 14492 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar proteins, smart00408 Location: 910 β†’ 976, IGc2; Immunoglobulin C-2 Type, smart00409 Location: 16865 β†’ 16945 IG; Immunoglobulin, smart00410 Location: 20908 β†’ 20990 IG_like; Immunoglobulin like, pfam07679 Location: 6 β†’ 97 I-set; Immunoglobulin I-set domain, cd14104 Location: 24878 β†’ 25154 STKc_Titin; Catalytic domain of the Giant Serine/Threonine Kinase Titin, pfam13895 Location: 6099 β†’ 6163 Ig_2; Immunoglobulin domain, and cl11960 Location: 17270 β†’ 17343 Ig; Immunoglobulin domain.[10]
  7. NP_597681.4 titin isoform novex-2: "Transcript Variant: This variant (novex-2) encodes the minor cardiac and skeletal muscle isoform (novex-2 or novex-2/N2B), which is nearly identical to the major cardiac isoform N2-B but contains a unique stretch of 192 aa in the I-band region. This variant is supported by data in PMID:11717165."[10] Conserved Domains (13) summary: cd00096 Location: 24245 β†’ 24312 Ig; Immunoglobulin domain, cd05747 Location: 26253 β†’ 26344 Ig5_Titin_like; M5, fifth immunoglobulin (Ig)-like domain of human titin C terminus and similar proteins, cd05748 Location: 14488 β†’ 14559 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar proteins, smart00408 Location: 910 β†’ 976 IGc2; Immunoglobulin C-2 Type, smart00409 Location: 16932 β†’ 17012 IG; Immunoglobulin, smart00410 Location: 20975 β†’ 21057 IG_like; Immunoglobulin like, pfam07679 Location: 6 β†’ 97 I-set; Immunoglobulin I-set domain, cd14104 Location: 24945 β†’ 25221 STKc_Titin; Catalytic domain of the Giant Serine/Threonine Kinase Titin, pfam13895 Location: 6166 β†’ 6230 Ig_2; Immunoglobulin domain, and cl11960 Location: 17337 β†’ 17410 Ig; Immunoglobulin domain.[10]
  8. XP_024308867.1 titin isoform X11, Conserved Domains (11) summary: cd05747 Location: 26091 β†’ 26182 Ig_Titin_like; Immunoglobulin (Ig)-like domain of human titin C terminus and similar domains, smart00409 Location: 6004 β†’ 6068 IG; Immunoglobulin, smart00410 Location: 4753 β†’ 4823 IG_like; Immunoglobulin like, pfam07679 Location: 6 β†’ 97 I-set; Immunoglobulin I-set domain, cd05748 Location: 13532 β†’ 13605 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar domains, and cl11960 Location: 21508 β†’ 21581 Ig; Immunoglobulin domain, and cl28434 Location: 2079 β†’ 2169 I-set; Immunoglobulin I-set domain.[10]
  9. XP_024308866.1 titin isoform X9, Conserved Domains (14) summary: cd05747 Location: 32170 β†’ 32261 Ig_Titin_like; Immunoglobulin (Ig)-like domain of human titin C terminus and similar domains, smart00060 Location: 15110 β†’ 15194 FN3; Fibronectin type 3 domain, smart00409 Location: 12083 β†’ 12147 IG; Immunoglobulin, smart00410 Location: 10925 β†’ 10989 IG_like; Immunoglobulin like, pfam07679 Location: 8889 β†’ 8978 I-set; Immunoglobulin I-set domain, cd05748 Location: 19611 β†’ 19684 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar domains, cl11960 Location: 24336 β†’ 24410 Ig; Immunoglobulin domain, and cl28434 Location: 9673 β†’ 9755 I-set; Immunoglobulin I-set domain.[10]
  10. XP_024308865.1 titin isoform X8, Conserved Domains (13) summary: cd05747 Location: 32197 β†’ 32288 Ig_Titin_like; Immunoglobulin (Ig)-like domain of human titin C terminus and similar domains, smart00410 Location: 12110 β†’ 12174 IG_like; Immunoglobulin like, pfam07679 Location: 8889 β†’ 8978 I-set; Immunoglobulin I-set domain, cd05748 Location: 19638 β†’ 19711 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar domains, cl11960 Location: 24363 β†’ 24437 Ig; Immunoglobulin domain, cl28434 Location: 9673 β†’ 9755 I-set; Immunoglobulin I-set domain.[10]
  11. XP_024308864.1 titin isoform X6, Conserved Domains (15) summary: cd05747 Location: 33083 β†’ 33174 Ig_Titin_like; Immunoglobulin (Ig)-like domain of human titin C terminus and similar domains, smart00409 Location: 12996 β†’ 13060 IG; Immunoglobulin, smart00410 Location: 11745 β†’ 11815 IG_like; Immunoglobulin like, pfam07679 Location: 8889 β†’ 8978 I-set; Immunoglobulin I-set domain, cd05748 Location: 20524 β†’ 20597 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar domains, cl11960 Location: 28500 β†’ 28573 Ig; Immunoglobulin domain, and cl28434 Location: 9177 β†’ 9267 I-set; Immunoglobulin I-set domain.[10]
  12. XP_024308862.1 titin isoform X2, Conserved Domains (15) summary: cd05747 Location: 33273 β†’ 33364 Ig_Titin_like; Immunoglobulin (Ig)-like domain of human titin C terminus and similar domains, smart00409 Location: 13186 β†’ 13250 IG; Immunoglobulin, smart00410 Location: 11935 β†’ 12005 IG_like; Immunoglobulin like, pfam07679 Location: 8889 β†’ 8978 I-set; Immunoglobulin I-set domain, cd05748 Location: 20714 β†’ 20787 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar domains, cl11960 Location: 28690 β†’ 28763 Ig; Immunoglobulin domain, and cl28434 Location: 9177 β†’ 9267 I-set; Immunoglobulin I-set domain.[10]
  13. XP_024308863.1 titin isoform X3, Conserved Domains (15) summary: cd05747 Location: 33272 β†’ 33363 Ig_Titin_like; Immunoglobulin (Ig)-like domain of human titin C terminus and similar domains, smart00409 Location: 13185 β†’ 13249 IG; Immunoglobulin, smart00410 Location: 11934 β†’ 12004 IG_like; Immunoglobulin like, pfam07679 Location: 8889 β†’ 8978, I-set; Immunoglobulin I-set domain, cd05748 Location: 20713 β†’ 20786 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar domains, cl11960 Location: 28689 β†’ 28762 Ig; Immunoglobulin domain, and cl28434 Location: 9177 β†’ 9267 I-set; Immunoglobulin I-set domain.[10]
  14. XP_024308868.1 titin isoform X12, Conserved Domains (13) summary: cd05747 Location: 22709 β†’ 22800 Ig_Titin_like; Immunoglobulin (Ig)-like domain of human titin C terminus and similar domains, smart00409 Location: 2622 β†’ 2686 IG; Immunoglobulin, smart00410 Location: 1371 β†’ 1441 IG_like; Immunoglobulin like, pfam07679 Location: 20684 β†’ 20771 I-set; Immunoglobulin I-set domain, cd05748 Location: 10150 β†’ 10223 Ig_Titin_like; Immunoglobulin (Ig)-like domain of titin and similar domains, cl11960 Location: 13793 β†’ 13866 Ig; Immunoglobulin domain, and cl28434 Location: 1814 β†’ 1897 I-set; Immunoglobulin I-set domain.[10]

Gene ID: 10892 is MALT1

Gene ID: 27036 is SIGLEC7

Gene ID: 51744 is CD244

Gene ID: 55243 is KIRREL1

Gene ID: 57611 see Immunoglobulin supergene family

Gene ID: 57863 see Carcinoembryonic antigen gene family.

Gene ID: 79368 see Immunoglobulin receptor superfamily genes.

Gene ID: 79827 is CLMP

Gene ID: 83416 see Immunoglobulin receptor superfamily genes.

Gene ID: 83417 see Immunoglobulin receptor superfamily genes.

Gene ID: 84033 is OBSCN

Gene ID: 84623 is KIRREL3

Gene ID: 84824 is FCRLA

Gene ID: 115350 see Immunoglobulin receptor superfamily genes.

Gene ID: 115352 see Immunoglobulin receptor superfamily genes.

Gene ID: 125931 see Carcinoembryonic antigen gene family.

Gene ID: 161357 is MDGA2

Gene ID: 220296 see Carcinoembryonic antigen gene family.

Gene ID: 255809 is C19orf38

Gene ID: 284021 is MILR1

Gene ID: 343413 see Immunoglobulin receptor superfamily genes.

Gene ID: 388551 see Carcinoembryonic antigen gene family.

Gene ID: 440533 is PSG8

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 β†’ 493, smart00410 Location: 218 β†’ 280, pfam13895 Location: 210 β†’ 301 and cl11960 Location: 28 β†’ 110.

See also

References

  1. ↑ 1.0 1.1 Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Gabriele H Marchler, James S Song, Narmada Thanki, Roxanne A Yamashita, Mingzhang Yang, Dachuan Zhang, Chanjuan Zheng, Christopher J Lanczycki, and Aron Marchler-Bauer (8 January 2020). "CDD/SPARCLE: The Conserved Domain Database in 2020". Nucleic Acids Research. 48 (D1): D265–D268. doi:10.1093/nar/gkz991. PMID 31777944. Retrieved 24 June 2020.
  2. ↑ 2.0 2.1 2.2 2.3 Noriaki Ishioka, Nobuhiro Takahashi, and Frank W. Putnam (April 1986). "Amino acid sequence of human plasma 𝛂1B-glycoprotein: Homology to the immunoglobulin supergene family" (PDF). Proceedings of the National Academy of Sciences USA. 83 (8): 2363–7. doi:10.1073/pnas.83.8.2363. PMID 3458201. Retrieved 9 March 2020.
  3. ↑ RefSeq (July 2008). "A1BG alpha-1-B glycoprotein [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 17 April 2020.
  4. ↑ NCBI (5 August 2015). "Conserved Protein Domain Family pfam13895: Ig_2". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 May 2020.
  5. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 RefSeq (May 2011). "CD86 CD86 molecule [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 25 June 2020.
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 RefSeq (December 2011). "CD48 CD48 molecule [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 25 June 2020.
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 RefSeq (July 2008). "FLT4 fms related receptor tyrosine kinase 4 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 25 June 2020.
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 RefSeq (May 2014). "HSPG2 heparan sulfate proteoglycan 2 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 25 June 2020.
  9. ↑ 9.0 9.1 RefSeq (May 2009). "KDR kinase insert domain receptor [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 21 June 2020.
  10. ↑ 10.00 10.01 10.02 10.03 10.04 10.05 10.06 10.07 10.08 10.09 10.10 10.11 10.12 10.13 10.14 10.15 10.16 10.17 10.18 10.19 10.20 10.21 RefSeq (February 2012). "TTN titin [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 19 June 2020.

External links

{{Phosphate biochemistry}}Template:Sisterlinks

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