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VTCN1 V-set domain containing T cell activation inhibitor 1 [ Homo sapiens (human) ]

Gene ID: 79679, updated on 13-Feb-2019

Summary

Official Symbol
VTCN1provided by HGNC
Official Full Name
V-set domain containing T cell activation inhibitor 1provided by HGNC
Primary source
HGNC:HGNC:28873
See related
Ensembl:ENSG00000134258 MIM:608162
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
B7X; B7H4; B7S1; B7-H4; B7h.5; VCTN1; PRO1291
Summary
This gene encodes a protein belonging to the B7 costimulatory protein family. Proteins in this family are present on the surface of antigen-presenting cells and interact with ligand bound to receptors on the surface of T cells. Studies have shown that high levels of the encoded protein has been correlated with tumor progression. A pseudogene of this gene is located on chromosome 20. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
Expression
Biased expression in kidney (RPKM 5.0), pancreas (RPKM 2.8) and 9 other tissues See more
Orthologs

Genomic context

See VTCN1 in Genome Data Viewer
Location:
1p13.1-p12
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (117143587..117210985, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (117686209..117753582, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene tripartite motif containing 45 Neighboring gene ribosomal protein S15a pseudogene 9 Neighboring gene long intergenic non-protein coding RNA 1525 Neighboring gene mannosidase alpha class 1A member 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Identification of a novel susceptibility locus for juvenile idiopathic arthritis by genome-wide association analysis.
NHGRI GWA Catalog

Pathways from BioSystems

  • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
    Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
    Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ22418

Gene Ontology Provided by GOA

Function Evidence Code Pubs
molecular_function ND
No biological Data available
more info
 
signaling receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
T cell receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
interferon-gamma secretion IEA
Inferred from Electronic Annotation
more info
 
interleukin-4 secretion IEA
Inferred from Electronic Annotation
more info
 
negative regulation of T cell activation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of T cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of T cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of interleukin-2 secretion IEA
Inferred from Electronic Annotation
more info
 
regulation of immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to protozoan IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
V-set domain-containing T-cell activation inhibitor 1
Names
B7 family member, H4
B7 homolog 4
B7 superfamily member 1
T cell costimulatory molecule B7x
immune costimulatory protein B7-H4

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001253849.1NP_001240778.1  V-set domain-containing T-cell activation inhibitor 1 isoform 2

    See identical proteins and their annotated locations for NP_001240778.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region and uses a downstream start codon compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AI686571, AK303466, AL391476
    Consensus CDS
    CCDS58019.1
    UniProtKB/Swiss-Prot
    Q7Z7D3
    Related
    ENSP00000444724.1, ENST00000539893.5
    Conserved Domains (1) summary
    cl11960
    Location:244
    Ig; Immunoglobulin domain
  2. NM_001253850.1NP_001240779.1  V-set domain-containing T-cell activation inhibitor 1 isoform 3

    See identical proteins and their annotated locations for NP_001240779.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.
    Source sequence(s)
    AI686571, AL391476, DQ103757
    Consensus CDS
    CCDS58020.1
    UniProtKB/Swiss-Prot
    Q7Z7D3
    Related
    ENSP00000328168.3, ENST00000328189.7
  3. NM_024626.4NP_078902.2  V-set domain-containing T-cell activation inhibitor 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_078902.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
    Source sequence(s)
    AI686571, AL391476, AY280972, CN259811, DB198367
    Consensus CDS
    CCDS894.1
    UniProtKB/Swiss-Prot
    Q7Z7D3
    Related
    ENSP00000358470.3, ENST00000369458.7
    Conserved Domains (2) summary
    smart00410
    Location:46144
    IG_like; Immunoglobulin like
    cl11960
    Location:49146
    Ig; Immunoglobulin domain

RNA

  1. NR_045603.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI686571, AL391476, BC065717, DC347131
  2. NR_045604.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI686571, AK310812, AL391476, DC347131

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    117143587..117210985 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002335.2XP_016857824.1  V-set domain-containing T-cell activation inhibitor 1 isoform X2

    Conserved Domains (2) summary
    smart00410
    Location:51149
    IG_like; Immunoglobulin like
    cl11960
    Location:54151
    Ig; Immunoglobulin domain
  2. XM_011542143.2XP_011540445.2  V-set domain-containing T-cell activation inhibitor 1 isoform X1

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