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    CARINH colitis associated IRF1 antisense regulator of intestinal homeostasis [ Homo sapiens (human) ]

    Gene ID: 441108, updated on 17-Sep-2024

    Summary

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    Official Symbol
    CARINHprovided by HGNC
    Official Full Name
    colitis associated IRF1 antisense regulator of intestinal homeostasisprovided by HGNC
    Primary source
    HGNC:HGNC:33838
    See related
    AllianceGenome:HGNC:33838
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C5orf56; IRF1-AS1
    Expression
    Ubiquitous expression in spleen (RPKM 7.3), lung (RPKM 5.1) and 24 other tissues See more
    Orthologs
    all
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    Genomic context

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    See CARINH in Genome Data Viewer
    Location:
    5q31.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132410929..132476044)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132930840..132995864)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131746621..131811736)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene MIR3936 host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131712295-131712796 Neighboring gene microRNA 3936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23070 Neighboring gene solute carrier family 22 member 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16319 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131751322-131751510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23075 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131763030-131763616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131763617-131764201 Neighboring gene long intergenic non-protein coding RNA 2863 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131780806-131781485 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:131786393-131787031 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131791634-131791826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131792105-131792775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131792776-131793445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131799668-131800632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131800633-131801597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131801783-131802284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23079 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23080 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:131821689-131822888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131825338-131825985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131827280-131827925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131832117-131833091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23085 Neighboring gene interferon regulatory factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131892292-131892952 Neighboring gene interleukin 5

    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. A lncRNA from an inflammatory bowel disease risk locus maintains intestinal host-commensal homeostasis. Ma H, et al. Cell Res, 2023 May. PMID 37055591, Free PMC Article
    2. An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation? Brandt M, et al. PLoS Genet, 2021 Jul. PMID 34314424, Free PMC Article
    3. Association of novel genetic Loci with circulating fibrinogen levels: a genome-wide association study in 6 population-based cohorts. Dehghan A, et al. Circ Cardiovasc Genet, 2009 Apr. PMID 20031576, Free PMC Article
    4. Genome-wide association study to identify genetic determinants of severe asthma. Wan YI, et al. Thorax, 2012 Sep. PMID 22561531
    5. Novel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women's Genome Health Study. Danik JS, et al. Circ Cardiovasc Genet, 2009 Apr. PMID 20031577, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation?
      Title: An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation?
    2. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Molecular reclassification of Crohn's disease by cluster analysis of genetic variants.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Analysis of 39 Crohn's disease risk loci in Swedish inflammatory bowel disease patients.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Association of novel genetic Loci with circulating fibrinogen levels: a genome-wide association study in 6 population-based cohorts.
    EBI GWAS Catalog
    Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease.
    EBI GWAS Catalog
    Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
    EBI GWAS Catalog
    Genome-wide association study to identify genetic determinants of severe asthma.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.
    EBI GWAS Catalog
    Novel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women's Genome Health Study.
    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

    Potential readthrough

    Included gene: RAD50

    Homology

    Other Names

    • IRF1 antisense RNA 1
    • uncharacterized protein C5orf56

    Clone Names

    • FLJ21568, FLJ26121

    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.

    RNA

    1. NR_161242.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC116366

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      132410929..132476044
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      132930840..132995864
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001013717.2: Suppressed sequence

      Description
      NM_001013717.2: This RefSeq was permanently suppressed because it is now thought that this gene does not encode a protein.

    2. NM_001207002.1: Suppressed sequence

      Description
      NM_001207002.1: This RefSeq was permanently suppressed because it is now thought that this gene does not encode a protein.

    3. NM_001207003.1: Suppressed sequence

      Description
      NM_001207003.1: This RefSeq was permanently suppressed because it is now thought that this gene does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version

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