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

Gene ID: 152404, updated on 2-Nov-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
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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: HPA RNA-seq normal tissues 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

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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)

Genotypes

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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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
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