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

    Gene ID: 79679, updated on 3-Dec-2024

    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; AllianceGenome:HGNC:28873
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VTCN1 in Genome Data Viewer
    Location:
    1p13.1-p12
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (117143587..117210927, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (117154077..117221391, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (117686209..117753549, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1580 Neighboring gene uncharacterized LOC124904387 Neighboring gene MPRA-validated peak386 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:117689065-117690264 Neighboring gene tripartite motif containing 45 Neighboring gene ribosomal protein S15a pseudogene 9 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117714175-117714737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117714738-117715299 Neighboring gene Sharpr-MPRA regulatory region 504 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:117811525-117812043 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:117842461-117842998 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117842999-117843536 Neighboring gene long intergenic non-protein coding RNA 1525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117900419-117901060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117918162-117918686 Neighboring gene mannosidase alpha class 1A member 2 Neighboring gene MPRA-validated peak388 silencer

    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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ22418

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in T cell receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of T cell activation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of T cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of T cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of interleukin-2 production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of cytokine production IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to protozoan IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in external side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    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)

    NEW Try the new Transcript table

    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_001253849.2NP_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_001253850.2NP_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
      Q0GN76, Q45VN0, Q5WPZ3, Q6P097, Q7Z7D3, Q9H6B2
      UniProtKB/TrEMBL
      Q5T2L0
      Related
      ENSP00000358470.3, ENST00000369458.8
      Conserved Domains (2) summary
      smart00410
      Location:46144
      IG_like; Immunoglobulin like
      cl11960
      Location:49146
      Ig; Immunoglobulin domain

    RNA

    1. NR_045603.2 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
    2. NR_045604.2 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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      117143587..117210927 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002335.3XP_016857824.1  V-set domain-containing T-cell activation inhibitor 1 isoform X2

      UniProtKB/TrEMBL
      Q5T2L0
      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

      UniProtKB/TrEMBL
      Q5T2L0

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      117154077..117221391 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338745.1XP_054194720.1  V-set domain-containing T-cell activation inhibitor 1 isoform X2

      UniProtKB/TrEMBL
      Q5T2L0
    2. XM_054338744.1XP_054194719.1  V-set domain-containing T-cell activation inhibitor 1 isoform X1

      UniProtKB/TrEMBL
      Q5T2L0