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

Gene ID: 441108, updated on 5-Mar-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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Location:
5q31.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132410929..132476044)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132930840..132995864)
105.20220307 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
  • 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. 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
  2. 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
  3. Genome-wide association study to identify genetic determinants of severe asthma. Wan YI, et al. Thorax, 2012 Sep. PMID 22561531
  4. 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
  5. Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. McGovern DP, et al. Hum Mol Genet, 2010 Sep 1. PMID 20570966, Free PMC Article

See all (14) 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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

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_2023_10

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
Protein Accession Links
GenPept Link UniProtKB Link
Q8N8D9.2 GenPept UniProtKB/Swiss-Prot:Q8N8D9

Gene LinkOut

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

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