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    IGSF11 immunoglobulin superfamily member 11 [ Homo sapiens (human) ]

    Gene ID: 152404, updated on 10-Dec-2024

    Summary

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    Official Symbol
    IGSF11provided by HGNC
    Official Full Name
    immunoglobulin superfamily member 11provided by HGNC
    Primary source
    HGNC:HGNC:16669
    See related
    Ensembl:ENSG00000144847 MIM:608351; AllianceGenome:HGNC:16669
    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
    CT119; VSIG3; BTIGSF; Igsf13; BT-IgSF; CXADRL1
    Summary
    IGSF11 is an immunoglobulin (Ig) superfamily member that is preferentially expressed in brain and testis. It shares significant homology with coxsackievirus and adenovirus receptor (CXADR; MIM 602621) and endothelial cell-selective adhesion molecule (ESAM).[supplied by OMIM, Apr 2005]
    Expression
    Biased expression in testis (RPKM 12.0), brain (RPKM 8.3) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IGSF11 in Genome Data Viewer
    Location:
    3q13.32
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (118900557..119146020, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (121620300..121865755, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (118619404..118864867, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374060 Neighboring gene uncharacterized LOC124909417 Neighboring gene uncharacterized LOC105374059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20293 Neighboring gene IGSF11 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:118725480-118726080 Neighboring gene MPRA-validated peak4780 silencer Neighboring gene MPRA-validated peak4781 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:118763719-118764299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:118764300-118764879 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:118839208-118839745 Neighboring gene Sharpr-MPRA regulatory region 3599 Neighboring gene testis expressed 55 Neighboring gene uroplakin 1B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Structural Basis of VSIG3: The Ligand for VISTA. Xie X, et al. Front Immunol, 2021. PMID 33841409, Free PMC Article
    2. Molecular cloning of a novel immunoglobulin superfamily gene preferentially expressed by brain and testis. Suzu S, et al. Biochem Biophys Res Commun, 2002 Sep 6. PMID 12207903
    3. IGSF11 gene, frequently up-regulated in intestinal-type gastric cancer, encodes adhesion molecule homologous to CXADR, FLJ22415 and ESAM. Katoh M, et al. Int J Oncol, 2003 Aug. PMID 12851705
    4. BT-IgSF, a novel immunoglobulin superfamily protein, functions as a cell adhesion molecule. Harada H, et al. J Cell Physiol, 2005 Sep. PMID 15795899
    5. VSIG-3 as a ligand of VISTA inhibits human T-cell function. Wang J, et al. Immunology, 2019 Jan. PMID 30220083, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. IGSF11 is required for pericentric heterochromatin dissociation during meiotic diplotene.
      Title: IGSF11 is required for pericentric heterochromatin dissociation during meiotic diplotene.
    2. Structural Basis of VSIG3: The Ligand for VISTA.
      Title: Structural Basis of VSIG3: The Ligand for VISTA.
    3. this study shows that VSIG-3 as a ligand of VISTA inhibits human T-cell function
      Title: VSIG-3 as a ligand of VISTA inhibits human T-cell function.
    4. Concerted role for IgSF11 and PSD-95 in the regulation of AMPAR-mediated synaptic transmission and plasticity.
      Title: Synaptic adhesion molecule IgSF11 regulates synaptic transmission and plasticity.
    5. IGSF11 is a good candidate of cancer-testis antigen. Furthermore, suppression of IGSF11 by siRNA retarded the growth of gastric cancer cells.
      Title: Identification of immunoglobulin superfamily 11 (IGSF11) as a novel target for cancer immunotherapy of gastrointestinal and hepatocellular carcinomas.
    6. Molecular cloning of BT-IgSF which is preferentially expressed by brain and testis
      Title: Molecular cloning of a novel immunoglobulin superfamily gene preferentially expressed by brain and testis.
    7. cell adhesion-inducing function of BT-IgSF suggests a role of the cell surface molecule in the development/function of the central nervous system and spermatogenesis
      Title: BT-IgSF, a novel immunoglobulin superfamily protein, functions as a cell adhesion molecule.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Gene network analysis in a pediatric cohort identifies novel lung function genes.
    EBI GWAS Catalog
    Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC35227

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ionotropic glutamate receptor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell-cell adhesion via plasma-membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in maintenance of protein location IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of long-term synaptic potentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of mini excitatory postsynaptic potential IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of presynapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in trans-synaptic signaling IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell-cell junction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in excitatory synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    immunoglobulin superfamily member 11
    Names
    CXADR like 1
    V-set and immunoglobulin domain containing 3
    V-set and immunoglobulin domain-containing protein 3
    brain and testis-specific immunoglobin superfamily protein
    brain and testis-specific immunoglobulin superfamily protein
    cancer/testis antigen 119

    NCBI Reference Sequences (RefSeq)

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    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_001015887.3 → NP_001015887.1  immunoglobulin superfamily member 11 isoform b precursor

      See identical proteins and their annotated locations for NP_001015887.1

      Status: VALIDATED

      Source sequence(s)
      AB071618, AC007023, AC068984, AL834256, AY358141
      Consensus CDS
      CCDS46891.1
      UniProtKB/Swiss-Prot
      C9JZN0, Q5DX21, Q8N4F1, Q8N7T8, Q8NDD2
      Related
      ENSP00000377370.2, ENST00000393775.7
      Conserved Domains (3) summary
      smart00410
      Location:29 → 124
      IG_like; Immunoglobulin like
      pfam07686
      Location:27 → 141
      V-set; Immunoglobulin V-set domain
      cl11960
      Location:156 → 223
      Ig; Immunoglobulin domain

    2. NM_001353318.2 → NP_001340247.1  immunoglobulin superfamily member 11 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC007023, AC068984, AL834256
      Conserved Domains (2) summary
      pfam07686
      Location:77 → 191
      V-set; Immunoglobulin V-set domain
      pfam13927
      Location:208 → 269
      Ig_3; Immunoglobulin domain

    3. NM_001353319.2 → NP_001340248.1  immunoglobulin superfamily member 11 isoform d

      Status: VALIDATED

      Source sequence(s)
      AC007023, AC068984, AL834256
      Conserved Domains (2) summary
      pfam07686
      Location:77 → 191
      V-set; Immunoglobulin V-set domain
      pfam13927
      Location:208 → 269
      Ig_3; Immunoglobulin domain

    4. NM_001353320.2 → NP_001340249.1  immunoglobulin superfamily member 11 isoform a precursor

      Status: VALIDATED

      Source sequence(s)
      AC007023, AC068984, AC083800, AK292387, AL834256
      Consensus CDS
      CCDS2983.1
      Related
      ENSP00000406092.2, ENST00000425327.6
      Conserved Domains (2) summary
      pfam07686
      Location:26 → 140
      V-set; Immunoglobulin V-set domain
      pfam13927
      Location:157 → 218
      Ig_3; Immunoglobulin domain

    5. NM_001353321.2 → NP_001340250.1  immunoglobulin superfamily member 11 isoform e precursor

      Status: VALIDATED

      Source sequence(s)
      AC007023, AC068984, AL834256
      Consensus CDS
      CCDS87124.1
      UniProtKB/TrEMBL
      C9JMW0
      Related
      ENSP00000420486.1, ENST00000489689.5
      Conserved Domains (2) summary
      pfam07686
      Location:27 → 141
      V-set; Immunoglobulin V-set domain
      pfam13927
      Location:158 → 207
      Ig_3; Immunoglobulin domain

    6. NM_001353322.2 → NP_001340251.1  immunoglobulin superfamily member 11 isoform f precursor

      Status: VALIDATED

      Source sequence(s)
      AA292896, AB071618, AC068984, AC083800, AL834256, BI828564
      Consensus CDS
      CCDS87125.1
      Related
      ENSP00000401240.2, ENST00000441144.6
      Conserved Domains (2) summary
      pfam07686
      Location:26 → 140
      V-set; Immunoglobulin V-set domain
      pfam13927
      Location:157 → 206
      Ig_3; Immunoglobulin domain

    7. NM_001353323.2 → NP_001340252.1  immunoglobulin superfamily member 11 isoform g precursor

      Status: VALIDATED

      Source sequence(s)
      AC007023, AC068984, AL834256
      Consensus CDS
      CCDS87123.1
      UniProtKB/TrEMBL
      C9JBA5
      Related
      ENSP00000417413.1, ENST00000491903.1
      Conserved Domains (2) summary
      pfam07686
      Location:27 → 141
      V-set; Immunoglobulin V-set domain
      pfam13927
      Location:158 → 219
      Ig_3; Immunoglobulin domain

    8. NM_001353324.2 → NP_001340253.1  immunoglobulin superfamily member 11 isoform h precursor

      Status: VALIDATED

      Source sequence(s)
      AC007023, AC068984, AL834256
      Conserved Domains (2) summary
      pfam07686
      Location:27 → 141
      V-set; Immunoglobulin V-set domain
      pfam13927
      Location:158 → 211
      Ig_3; Immunoglobulin domain

    9. NM_001353325.2 → NP_001340254.1  immunoglobulin superfamily member 11 isoform i

      Status: VALIDATED

      Source sequence(s)
      AC007023, AC068984, AL834256
      Conserved Domains (2) summary
      pfam13927
      Location:99 → 160
      Ig_3; Immunoglobulin domain
      cl11960
      Location:8 → 78
      Ig; Immunoglobulin domain

    10. NM_001353326.2 → NP_001340255.1  immunoglobulin superfamily member 11 isoform j

      Status: VALIDATED

      Source sequence(s)
      AC007023, AC068984, AL834256
      Conserved Domains (2) summary
      pfam13927
      Location:99 → 148
      Ig_3; Immunoglobulin domain
      cl11960
      Location:8 → 78
      Ig; Immunoglobulin domain

    11. NM_152538.4 → NP_689751.2  immunoglobulin superfamily member 11 isoform a precursor

      See identical proteins and their annotated locations for NP_689751.2

      Status: VALIDATED

      Source sequence(s)
      AA292896, AB071618, AC068984, AC083800, AL834256, BI828564
      Consensus CDS
      CCDS2983.1
      UniProtKB/Swiss-Prot
      Q5DX21
      Conserved Domains (2) summary
      pfam07686
      Location:26 → 140
      V-set; Immunoglobulin V-set domain
      pfam13927
      Location:157 → 218
      Ig_3; Immunoglobulin domain

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      118900557..119146020 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      121620300..121865755 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5DX21.3 GenPept UniProtKB/Swiss-Prot:Q5DX21

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools