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IGSF21 immunoglobin superfamily member 21 [ Homo sapiens (human) ]

Gene ID: 84966, updated on 5-Mar-2024

Summary

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Official Symbol
IGSF21provided by HGNC
Official Full Name
immunoglobin superfamily member 21provided by HGNC
Primary source
HGNC:HGNC:28246
See related
Ensembl:ENSG00000117154 AllianceGenome:HGNC:28246
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
Summary
This gene encodes a protein which has two immunoglobulin (Ig) domains and is a member of the immunoglobulin superfamily. Proteins in this superfamily are usually found on or in cell membranes and act as receptors in immune response pathways. [provided by RefSeq, Sep 2011]
Expression
Biased expression in brain (RPKM 11.7), spleen (RPKM 6.4) and 6 other tissues See more
Orthologs
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Genomic context

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See IGSF21 in Genome Data Viewer
Location:
1p36.13
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (18107798..18378483)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (17927918..18198544)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (18434292..18704977)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376812 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:18404738-18404927 Neighboring gene long intergenic non-protein coding RNA 1654 Neighboring gene Sharpr-MPRA regulatory region 487 Neighboring gene NANOG hESC enhancer GRCh37_chr1:18425418-18425940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18468715-18469332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18469333-18469948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18473111-18473612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18473613-18474112 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18482493-18483371 Neighboring gene IGSF21 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18501697-18502198 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18502199-18502698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18525748-18526248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18526249-18526749 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18527418-18527918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18538061-18538884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18557491-18558139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18575476-18575976 Neighboring gene uncharacterized LOC124903864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18606867-18607381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18607382-18607895 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:18609585-18610784 Neighboring gene uncharacterized LOC124903863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18620236-18621123 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18622899-18623785 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18624079-18624604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18626609-18627236 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:18633258-18633415 Neighboring gene Sharpr-MPRA regulatory region 11488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18672835-18673336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18673337-18673836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18709612-18710411 Neighboring gene uncharacterized LOC124903865 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18733166-18733860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18733861-18734554 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:18794765-18794938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18806502-18807374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18807375-18808246 Neighboring gene kelch domain containing 7A

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. Association between LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms and diabetic retinopathy of type 2 diabetes mellitus in the Chinese Han population. Lin X, et al. J Gene Med, 2016 Oct. PMID 27607899
  2. IgSF21 promotes differentiation of inhibitory synapses via binding to neurexin2α. Tanabe Y, et al. Nat Commun, 2017 Sep 1. PMID 28864826, Free PMC Article
  3. Genome-wide association study to identify single nucleotide polymorphisms (SNPs) associated with the development of erectile dysfunction in African-American men after radiotherapy for prostate cancer. Kerns SL, et al. Int J Radiat Oncol Biol Phys, 2010 Dec 1. PMID 20932654, Free PMC Article
  4. Genome-wide meta-analysis for severe diabetic retinopathy. Grassi MA, et al. Hum Mol Genet, 2011 Jun 15. PMID 21441570, Free PMC Article
  5. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Trynka G, et al. Gut, 2009 Aug. PMID 19240061

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Results suggest that LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms influence the development of diabetic retinopathy (DR).
    Title: Association between LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms and diabetic retinopathy of type 2 diabetes mellitus in the Chinese Han population.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
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
Genome-wide association study to identify single nucleotide polymorphisms (SNPs) associated with the development of erectile dysfunction in African-American men after radiotherapy for prostate cancer.
EBI GWAS Catalog
Genome-wide meta-analysis for severe diabetic retinopathy.
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

  • FLJ41177, MGC15730

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synapse maturation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in external side of plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in inhibitory synapse ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
  
located_in presynaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
immunoglobulin superfamily member 21

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_027535.2 RefSeqGene

    Range
    5053..275738
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_032880.5 → NP_116269.3  immunoglobulin superfamily member 21 precursor

    See identical proteins and their annotated locations for NP_116269.3

    Status: REVIEWED

    Source sequence(s)
    AK075316, AL356101, BC007618
    Consensus CDS
    CCDS184.1
    UniProtKB/Swiss-Prot
    Q8NBR8, Q96ID5
    Related
    ENSP00000251296.1, ENST00000251296.4
    Conserved Domains (2) summary
    smart00410
    Location:353 → 430
    IG_like; Immunoglobulin like
    cl11960
    Location:369 → 432
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    18107798..18378483
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011542319.4 → XP_011540621.1  immunoglobulin superfamily member 21 isoform X3

    Conserved Domains (2) summary
    smart00410
    Location:156 → 233
    IG_like; Immunoglobulin like
    cl11960
    Location:172 → 235
    Ig; Immunoglobulin domain

  2. XM_017002604.3 → XP_016858093.1  immunoglobulin superfamily member 21 isoform X1

    Conserved Domains (2) summary
    smart00410
    Location:347 → 424
    IG_like; Immunoglobulin like
    cl11960
    Location:363 → 426
    Ig; Immunoglobulin domain

  3. XM_017002605.1 → XP_016858094.1  immunoglobulin superfamily member 21 isoform X2

    Conserved Domains (2) summary
    smart00410
    Location:276 → 353
    IG_like; Immunoglobulin like
    cl11960
    Location:292 → 355
    Ig; Immunoglobulin domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    17927918..18198544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339280.1 → XP_054195255.1  immunoglobulin superfamily member 21 isoform X3

  2. XM_054339278.1 → XP_054195253.1  immunoglobulin superfamily member 21 isoform X1

  3. XM_054339279.1 → XP_054195254.1  immunoglobulin superfamily member 21 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96ID5.1 GenPept UniProtKB/Swiss-Prot:Q96ID5

Gene LinkOut

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

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