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CHROMR cholesterol induced regulator of metabolism RNA [ Homo sapiens (human) ]

Gene ID: 101927027, updated on 10-Oct-2023

Summary

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Official Symbol
CHROMRprovided by HGNC
Official Full Name
cholesterol induced regulator of metabolism RNAprovided by HGNC
Primary source
HGNC:HGNC:54059
See related
Ensembl:ENSG00000223960 AllianceGenome:HGNC:54059
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
CHROME; PRKRA-AS1
Expression
Ubiquitous expression in testis (RPKM 3.8), endometrium (RPKM 3.8) and 25 other tissues See more
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Genomic context

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Location:
2q31.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (178413659..178440243)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (178896451..178923035)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (179278386..179304970)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:179018955-179019456 Neighboring gene RNA, U5E small nuclear 9, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12148 Neighboring gene Sharpr-MPRA regulatory region 8011 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:179075951-179076528 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:179076529-179077106 Neighboring gene oxysterol binding protein like 6 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:179142162-179142662 Neighboring gene Sharpr-MPRA regulatory region 7285 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:179217195-179217695 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:179228225-179228383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16802 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:179278150-179278725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:179279303-179279877 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:179315058-179315632 Neighboring gene protein activator of interferon induced protein kinase EIF2AK2 Neighboring gene uncharacterized LOC124906102 Neighboring gene nuclear distribution C pseudogene 2 Neighboring gene pejvakin Neighboring gene FKBP prolyl isomerase 7

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. Long noncoding RNA CHROMR regulates antiviral immunity in humans. van Solingen C, et al. Proc Natl Acad Sci U S A, 2022 Sep 13. PMID 36001732, Free PMC Article
  2. The long noncoding RNA CHROME regulates cholesterol homeostasis in primate. Hennessy EJ, et al. Nat Metab, 2019 Jan. PMID 31410392, Free PMC Article
  3. Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles. Mero IL, et al. PLoS One, 2013. PMID 23472185, Free PMC Article
  4. Gene expression profile of the human trabecular meshwork: NEIBank sequence tag analysis. Tomarev SI, et al. Invest Ophthalmol Vis Sci, 2003 Jun. PMID 12766061
  5. Identification of genes related to Parkinson's disease using expressed sequence tags. Kim JM, et al. DNA Res, 2006 Dec 31. PMID 17213182

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Long noncoding RNA CHROMR regulates antiviral immunity in humans.
    Title: Long noncoding RNA CHROMR regulates antiviral immunity in humans.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles.
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

General gene information

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Other Names

  • PRKRA antisense RNA 1
  • cholesterol homeostasis regulator of miRNA expression

Clone Names

  • AC009948.5, DKFZp686G1498

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_110204.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AL520497, BX371397, CD676753, CN415424, DA520566, DT216517
    Related
    ENST00000453026.7

  2. NR_110205.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains multiple differences, compared to variant 1, resulting in a shorter transcript.
    Source sequence(s)
    BI915242, BM996025, DA520566, DT216517
    Related
    ENST00000691078.2

  3. NR_110206.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains multiple differences, compared to variant 1, resulting in a shorter transcript.
    Source sequence(s)
    BI915242, BM996025, DA520566, DT216517
    Related
    ENST00000436616.4

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    178413659..178440243
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    178896451..178923035
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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