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IGSF9 immunoglobulin superfamily member 9 [ Homo sapiens (human) ]

Gene ID: 57549, updated on 5-Mar-2024

Summary

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Official Symbol
IGSF9provided by HGNC
Official Full Name
immunoglobulin superfamily member 9provided by HGNC
Primary source
HGNC:HGNC:18132
See related
Ensembl:ENSG00000085552 MIM:609738; AllianceGenome:HGNC:18132
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
Nrt1; IGSF9A; FP18798
Summary
Predicted to enable cell-cell adhesion mediator activity. Predicted to be involved in axon guidance; dendrite self-avoidance; and homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to act upstream of or within dendrite development and regulation of synapse organization. Predicted to be located in dendrite and inhibitory synapse. Predicted to be integral component of membrane. Predicted to be active in axon and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in skin (RPKM 12.2), stomach (RPKM 7.5) and 8 other tissues See more
Orthologs
mouse all
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Genomic context

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See IGSF9 in Genome Data Viewer
Location:
1q23.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (159927041..159945613, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159064110..159082679, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (159896831..159915403, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904435 Neighboring gene Sharpr-MPRA regulatory regions 3039 and 8536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159882219-159882720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:159887707-159888596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1910 Neighboring gene uncharacterized LOC124904437 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:159893727-159894926 Neighboring gene transgelin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159904768-159905268 Neighboring gene uncharacterized LOC124904438 Neighboring gene Sharpr-MPRA regulatory region 11999 Neighboring gene SLAM family member 9 Neighboring gene long intergenic non-protein coding RNA 1133 Neighboring gene Fc receptor like 6 pseudogene 1 Neighboring gene uncharacterized LOC124904436 Neighboring gene ribosomal protein L27a pseudogene 2

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. Immunoglobulin superfamily 9 (IGSF9) is trans-activated by p53, inhibits breast cancer metastasis via FAK. Li Y, et al. Oncogene, 2022 Oct. PMID 36088502, Free PMC Article
  2. Rethinking isolated cleft lip and palate as a syndrome. Koruyucu M, et al. Oral Surg Oral Med Oral Pathol Oral Radiol, 2018 Apr. PMID 29500156
  3. Cloning and characterization of Igsf9 in mouse and human: a new member of the immunoglobulin superfamily expressed in the developing nervous system. Doudney K, et al. Genomics, 2002 May. PMID 11991715
  4. The ALDH2, IGSF9, and PRDM16 Proteins as Predictive Biomarkers for Prognosis in Breast Cancer. Han Y, et al. Clin Breast Cancer, 2023 Apr. PMID 36639264
  5. Genomic alterations and evolution of cell clusters in metastatic invasive micropapillary carcinoma of the breast. Shi Q, et al. Nat Commun, 2022 Jan 10. PMID 35013309, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The ALDH2, IGSF9, and PRDM16 Proteins as Predictive Biomarkers for Prognosis in Breast Cancer.
    Title: The ALDH2, IGSF9, and PRDM16 Proteins as Predictive Biomarkers for Prognosis in Breast Cancer.
  2. Immunoglobulin superfamily 9 (IGSF9) is trans-activated by p53, inhibits breast cancer metastasis via FAK.
    Title: Immunoglobulin superfamily 9 (IGSF9) is trans-activated by p53, inhibits breast cancer metastasis via FAK.
  3. Genomic alterations and evolution of cell clusters in metastatic invasive micropapillary carcinoma of the breast.
    Title: Genomic alterations and evolution of cell clusters in metastatic invasive micropapillary carcinoma of the breast.
  4. In the group that combined individuals affected by isolated cleft lip and palate, tooth agenesis, supernumerary teeth, molar incisor hypomineralization, or dental caries, we found an association with rs622260 but not with the rs10798049 marker. We determined that the allele C of rs622260 was overrepresented in all individuals studied compared with a group of unrelated individuals who did not present any of
    Title: Rethinking isolated cleft lip and palate as a syndrome.
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

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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Homology

Clone Names

  • KIAA1355

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell-cell adhesion mediator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in dendrite development IEA
Inferred from Electronic Annotation
more info
  
involved_in dendrite self-avoidance 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 regulation of synapse organization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in axon IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
located_in inhibitory synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein turtle homolog A
Names
immunoglobulin superfamily member 9A
turtle homolog A

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_001135050.2 → NP_001128522.1  protein turtle homolog A isoform a precursor

    See identical proteins and their annotated locations for NP_001128522.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AB037776, AI758999, AL513485, CK299326
    Consensus CDS
    CCDS44254.1
    UniProtKB/Swiss-Prot
    Q9P2J2
    Related
    ENSP00000357073.1, ENST00000368094.6
    Conserved Domains (7) summary
    cd00096
    Location:154 → 220
    Ig; Immunoglobulin domain
    smart00410
    Location:233 → 319
    IG_like; Immunoglobulin like
    cd00063
    Location:625 → 715
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:136 → 223
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:511 → 596
    fn3; Fibronectin type III domain
    pfam13927
    Location:226 → 305
    Ig_3; Immunoglobulin domain
    cl11960
    Location:341 → 404
    Ig; Immunoglobulin domain

  2. NM_020789.4 → NP_065840.2  protein turtle homolog A isoform b precursor

    See identical proteins and their annotated locations for NP_065840.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AB037776, AI758999, AL513485, BC030141, CK299326
    Consensus CDS
    CCDS1190.1
    UniProtKB/Swiss-Prot
    Q9P2J2
    Related
    ENSP00000355049.3, ENST00000361509.7
    Conserved Domains (7) summary
    cd00096
    Location:154 → 220
    Ig; Immunoglobulin domain
    smart00410
    Location:233 → 319
    IG_like; Immunoglobulin like
    cd00063
    Location:609 → 699
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:136 → 223
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:495 → 580
    fn3; Fibronectin type III domain
    pfam13927
    Location:226 → 305
    Ig_3; Immunoglobulin domain
    cl11960
    Location:325 → 388
    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
    159927041..159945613 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    159064110..159082679 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P2J2.2 GenPept UniProtKB/Swiss-Prot:Q9P2J2

Gene LinkOut

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

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