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    IGSF3 immunoglobulin superfamily member 3 [ Homo sapiens (human) ]

    Gene ID: 3321, updated on 27-Nov-2024

    Summary

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    Official Symbol
    IGSF3provided by HGNC
    Official Full Name
    immunoglobulin superfamily member 3provided by HGNC
    Primary source
    HGNC:HGNC:5950
    See related
    Ensembl:ENSG00000143061 MIM:603491; AllianceGenome:HGNC:5950
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    V8; LCDD; EWI-3
    Summary
    The protein encoded by this gene is an immunoglobulin-like membrane protein containing several V-type Ig-like domains. A mutation in this gene has been associated with bilateral nasolacrimal duct obstruction (LCDD). [provided by RefSeq, Jun 2016]
    Expression
    Broad expression in esophagus (RPKM 8.2), skin (RPKM 7.8) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IGSF3 in Genome Data Viewer
    Location:
    1p13.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (116574398..116667755, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (116584842..116678201, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (117117020..117210377, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CD58 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1565 Neighboring gene nucleosome assembly protein 1 like 4 pseudogene 1 Neighboring gene uncharacterized LOC105378925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1566 Neighboring gene Sharpr-MPRA regulatory region 4262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1571 Neighboring gene microRNA 548ac Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1232 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1233 Neighboring gene uncharacterized LOC124904385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1572 Neighboring gene uncharacterized LOC105378924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:117142207-117142708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:117150835-117151334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117156699-117157269 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:117161725-117162232 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:117184821-117185506 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117185507-117186190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117188080-117188811 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117188812-117189542 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117189543-117190273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1235 Neighboring gene microRNA 320b-1 Neighboring gene CRISPRi-validated cis-regulatory element chr1.8052 Neighboring gene long intergenic non-protein coding RNA 2868 Neighboring gene uncharacterized LOC105378926

    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
    • 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. Molecular cloning of a human cDNA IGSF3 encoding an immunoglobulin-like membrane protein: expression and mapping to chromosome band 1p13. Saupe S, et al. Genomics, 1998 Sep 15. PMID 9790749
    2. IGSF3 mutation identified in patient with severe COPD alters cell function and motility. Schweitzer KS, et al. JCI Insight, 2020 Jul 23. PMID 32573489, Free PMC Article
    3. Identification of an IGSF3 mutation in a family with congenital nasolacrimal duct obstruction. Foster J 2nd, et al. Clin Genet, 2014 Dec. PMID 24372406
    4. Osteoclastogenesis inhibition by mutated IGSF23 results in human osteopetrosis. Yuan Y, et al. Cell Prolif, 2019 Nov. PMID 31560140, Free PMC Article
    5. Rank-based genome-wide analysis reveals the association of ryanodine receptor-2 gene variants with childhood asthma among human populations. Ding L, et al. Hum Genomics, 2013 Jul 5. PMID 23829686, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Associated conditions

    Description Tests
    Familial congenital nasolacrimal duct obstruction
    MedGen: C1835612 OMIM: 149700 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Rank-based genome-wide analysis reveals the association of ryanodine receptor-2 gene variants with childhood asthma among human populations.
    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

    • MGC117164

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in lacrimal gland development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell surface HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    immunoglobulin superfamily member 3
    Names
    glu-Trp-Ile EWI motif-containing protein 3
    immunoglobin superfamily, member 3

    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.

    Genomic

    1. NG_050917.1 RefSeqGene

      Range
      5023..98348
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001007237.3 → NP_001007238.1  immunoglobulin superfamily member 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001007238.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AB007935, AI968231, BC110651
      Consensus CDS
      CCDS30813.1
      UniProtKB/Swiss-Prot
      A6NJZ6, A6NMC7, O75054
      Related
      ENSP00000358498.4, ENST00000369486.8
      Conserved Domains (6) summary
      smart00409
      Location:293 → 389
      IG; Immunoglobulin
      pfam07686
      Location:687 → 784
      V-set; Immunoglobulin V-set domain
      pfam13927
      Location:410 → 514
      Ig_3; Immunoglobulin domain
      cd00096
      Location:689 → 692
      Ig; Ig strand A' [structural motif]
      cd00099
      Location:152 → 251
      IgV; Immunoglobulin variable domain (IgV)
      cl11960
      Location:821 → 920
      Ig; Immunoglobulin domain

    2. NM_001542.4 → NP_001533.2  immunoglobulin superfamily member 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001533.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB007935, AF031174, AI968231, BC110651
      Consensus CDS
      CCDS30814.1
      UniProtKB/Swiss-Prot
      O75054
      Related
      ENSP00000358495.1, ENST00000369483.5
      Conserved Domains (4) summary
      smart00406
      Location:163 → 247
      IGv; Immunoglobulin V-Type
      smart00410
      Location:707 → 830
      IG_like; Immunoglobulin like
      pfam07686
      Location:707 → 830
      V-set; Immunoglobulin V-set domain
      cl11960
      Location:34 → 141
      Ig; 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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      116574398..116667755 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419052.1 → XP_047275008.1  immunoglobulin superfamily member 3 isoform X3

    2. XM_047419070.1 → XP_047275026.1  immunoglobulin superfamily member 3 isoform X5

      UniProtKB/Swiss-Prot
      A6NJZ6, A6NMC7, O75054

    3. XM_047419042.1 → XP_047274998.1  immunoglobulin superfamily member 3 isoform X3

    4. XM_011541315.2 → XP_011539617.1  immunoglobulin superfamily member 3 isoform X2

      See identical proteins and their annotated locations for XP_011539617.1

      UniProtKB/Swiss-Prot
      O75054
      Related
      ENSP00000321184.6, ENST00000318837.6
      Conserved Domains (4) summary
      smart00406
      Location:163 → 247
      IGv; Immunoglobulin V-Type
      smart00410
      Location:707 → 830
      IG_like; Immunoglobulin like
      pfam07686
      Location:707 → 830
      V-set; Immunoglobulin V-set domain
      cl11960
      Location:34 → 141
      Ig; Immunoglobulin domain

    5. XM_006710593.4 → XP_006710656.1  immunoglobulin superfamily member 3 isoform X1

      Conserved Domains (4) summary
      smart00406
      Location:168 → 252
      IGv; Immunoglobulin V-Type
      smart00410
      Location:712 → 835
      IG_like; Immunoglobulin like
      pfam07686
      Location:712 → 835
      V-set; Immunoglobulin V-set domain
      cl11960
      Location:39 → 146
      Ig; Immunoglobulin domain

    6. XM_005270794.5 → XP_005270851.1  immunoglobulin superfamily member 3 isoform X4

      Conserved Domains (4) summary
      smart00406
      Location:168 → 252
      IGv; Immunoglobulin V-Type
      smart00410
      Location:692 → 815
      IG_like; Immunoglobulin like
      pfam07686
      Location:692 → 815
      V-set; Immunoglobulin V-set domain
      cl11960
      Location:39 → 146
      Ig; Immunoglobulin domain

    7. XM_011541316.3 → XP_011539618.1  immunoglobulin superfamily member 3 isoform X6

      Conserved Domains (3) summary
      smart00410
      Location:150 → 273
      IG_like; Immunoglobulin like
      pfam07686
      Location:150 → 273
      V-set; Immunoglobulin V-set domain
      cl11960
      Location:284 → 395
      Ig; Immunoglobulin domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      116584842..116678201 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336231.1 → XP_054192206.1  immunoglobulin superfamily member 3 isoform X3

    2. XM_054336229.1 → XP_054192204.1  immunoglobulin superfamily member 3 isoform X2

    3. XM_054336233.1 → XP_054192208.1  immunoglobulin superfamily member 3 isoform X5

    4. XM_054336230.1 → XP_054192205.1  immunoglobulin superfamily member 3 isoform X3

    5. XM_054336228.1 → XP_054192203.1  immunoglobulin superfamily member 3 isoform X1

    6. XM_054336232.1 → XP_054192207.1  immunoglobulin superfamily member 3 isoform X4

    7. XM_054336234.1 → XP_054192209.1  immunoglobulin superfamily member 3 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75054.3 GenPept UniProtKB/Swiss-Prot:O75054

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

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