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    POU2AF3 POU class 2 homeobox associating factor 3 [ Homo sapiens (human) ]

    Gene ID: 120376, updated on 17-Jun-2024

    Summary

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    Official Symbol
    POU2AF3provided by HGNC
    Official Full Name
    POU class 2 homeobox associating factor 3provided by HGNC
    Primary source
    HGNC:HGNC:26978
    See related
    Ensembl:ENSG00000214290 MIM:615694; AllianceGenome:HGNC:26978
    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
    CASC13; COLCA2; OCA-T2; C11orf93; LOH11CR1G
    Summary
    Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in stomach (RPKM 2.9), duodenum (RPKM 2.1) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See POU2AF3 in Genome Data Viewer
    Location:
    11q23.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (111298546..111308735)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (111308735..111318916)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (111169271..111179460)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723966 Neighboring gene ribosomal protein S17 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5504 Neighboring gene POU class 2 homeobox associating factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3894 Neighboring gene colorectal cancer associated 1 Neighboring gene uncharacterized LOC105369491 Neighboring gene uncharacterized LOC124902755

    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. rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis. Hitomi Y, et al. Sci Rep, 2021 Feb 25. PMID 33633225, Free PMC Article
    2. Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants. Peltekova VD, et al. Int J Cancer, 2014 May 15. PMID 24154973, Free PMC Article
    3. Refinement of the basis and impact of common 11q23.1 variation to the risk of developing colorectal cancer. Pittman AM, et al. Hum Mol Genet, 2008 Dec 1. PMID 18753146
    4. OCA-T1 and OCA-T2 are coactivators of POU2F3 in the tuft cell lineage. Wu XS, et al. Nature, 2022 Jul. PMID 35576971, Free PMC Article
    5. Genetic association of PLCE1, C11orf92-C11orf93, and NOC3L with colorectal cancer risk in the Han population. Duan X, et al. Tumour Biol, 2014 Mar. PMID 24146276

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. COLCA2 (POU2AF3) and likely C11orf53 (POU2AF2) function as transcriptional co-activators of POU2F3 in tuft cell-like small cell lung cancer.
      Title: Selective regulation of tuft cell-like small cell lung cancer by novel transcriptional co-activators C11orf53 and COLCA2.
    2. OCA-T1 and OCA-T2 are coactivators of POU2F3 in the tuft cell lineage.
      Title: OCA-T1 and OCA-T2 are coactivators of POU2F3 in the tuft cell lineage.
    3. rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis.
      Title: rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis.
    4. We found PLCE1, C11orf92-C11orf93, and NOC3L associated with colorectal cancer susceptibility
      Title: Genetic association of PLCE1, C11orf92-C11orf93, and NOC3L with colorectal cancer risk in the Han population.
    5. Data implicate COLCA1 and COLCA2 in the pathogenesis of colon cancer.
      Title: Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Generalizability and epidemiologic characterization of eleven colorectal cancer GWAS hits in multiple populations.
    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 scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21.
    EBI GWAS Catalog
    Identification of Genetic Susceptibility Loci for Colorectal Tumors in a Genome-Wide Meta-analysis.
    EBI GWAS Catalog
    Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk.
    EBI GWAS Catalog
    Meta-analysis of new genome-wide association studies of colorectal cancer risk.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables POU domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    POU class 2 homeobox associating factor 3
    Names
    cancer susceptibility candidate 13
    cancer susceptibility candidate protein 13
    colorectal cancer associated 2
    colorectal cancer associated two
    colorectal cancer-associated protein 2

    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_001136105.3 → NP_001129577.1  POU class 2 homeobox associating factor 3 isoform 2

      See identical proteins and their annotated locations for NP_001129577.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents an alternate 5' UTR exon. Variants 2 and 3 encode the same protein which is N-terminally truncated compared to isoform 1.
      Source sequence(s)
      AK292195, AP002448, BC042557, DA307321
      Consensus CDS
      CCDS44728.1
      UniProtKB/Swiss-Prot
      A8K830
      Related
      ENSP00000381115.2, ENST00000398035.6

    2. NM_001271457.2 → NP_001258386.1  POU class 2 homeobox associating factor 3 isoform 2

      See identical proteins and their annotated locations for NP_001258386.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents an alternate 5' UTR exon. Variants 2 and 3 encode the same protein which is N-terminally truncated compared to isoform 1.
      Source sequence(s)
      AP002448, BC042557, BQ893717
      Consensus CDS
      CCDS44728.1
      UniProtKB/Swiss-Prot
      A8K830
      Related
      ENSP00000481028.2, ENST00000614153.4

    3. NM_001271458.2 → NP_001258387.1  POU class 2 homeobox associating factor 3 isoform 1

      See identical proteins and their annotated locations for NP_001258387.1

      Status: VALIDATED

      Source sequence(s)
      AP002448
      Consensus CDS
      CCDS73378.1
      UniProtKB/Swiss-Prot
      A8K830, E9PMJ8, Q2TBJ3, V5LD62, V5LDI3, V5LDV1, V5LE09, V5LEU3
      Related
      ENSP00000484135.1, ENST00000610738.6

    4. NM_001370484.1 → NP_001357413.1  POU class 2 homeobox associating factor 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variants 2 and 3, encodes isoform 2.
      Source sequence(s)
      AP002448
      Consensus CDS
      CCDS44728.1
      Related
      ENSP00000434519.1, ENST00000526216.1

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      111298546..111308735
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017017196.3 → XP_016872685.1  POU class 2 homeobox associating factor 3 isoform X1

    2. XM_017017199.2 → XP_016872688.1  POU class 2 homeobox associating factor 3 isoform X3

      UniProtKB/Swiss-Prot
      A8K830

    3. XM_047426365.1 → XP_047282321.1  POU class 2 homeobox associating factor 3 isoform X3

    4. XM_017017200.2 → XP_016872689.1  POU class 2 homeobox associating factor 3 isoform X3

      UniProtKB/Swiss-Prot
      A8K830

    5. XM_047426364.1 → XP_047282320.1  POU class 2 homeobox associating factor 3 isoform X3

    6. XM_017017197.2 → XP_016872686.2  POU class 2 homeobox associating factor 3 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      111308735..111318916
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367657.1 → XP_054223632.1  POU class 2 homeobox associating factor 3 isoform X1

    2. XM_054367660.1 → XP_054223635.1  POU class 2 homeobox associating factor 3 isoform X3

    3. XM_054367661.1 → XP_054223636.1  POU class 2 homeobox associating factor 3 isoform X3

    4. XM_054367659.1 → XP_054223634.1  POU class 2 homeobox associating factor 3 isoform X3

    5. XM_054367662.1 → XP_054223637.1  POU class 2 homeobox associating factor 3 isoform X3

    6. XM_054367658.1 → XP_054223633.1  POU class 2 homeobox associating factor 3 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A8K830.2 GenPept UniProtKB/Swiss-Prot:A8K830

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