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CARMN cardiac mesoderm enhancer-associated non-coding RNA [ Homo sapiens (human) ]

Gene ID: 728264, updated on 5-Mar-2024

Summary

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Official Symbol
CARMNprovided by HGNC
Official Full Name
cardiac mesoderm enhancer-associated non-coding RNAprovided by HGNC
Primary source
HGNC:HGNC:42872
See related
AllianceGenome:HGNC:42872
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
CARMEN; MIR143HG
Summary
Predicted to be involved in regulation of gene expression. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in endometrium (RPKM 8.6), prostate (RPKM 5.7) and 18 other tissues See more
Orthologs
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Genomic context

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See CARMN in Genome Data Viewer
Location:
5q32
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (149406845..149432836)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (149941690..149967678)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (148786408..148812399)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16496 Neighboring gene Sharpr-MPRA regulatory region 12528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148746417-148747281 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148747282-148748145 Neighboring gene prenylcysteine oxidase 1 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148759103-148759637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148759990-148760702 Neighboring gene uncharacterized LOC101927046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148762129-148762840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148764726-148765226 Neighboring gene interleukin 17B Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148784456-148785046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148786897-148787897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148790014-148790554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148790555-148791094 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82102 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82107 Neighboring gene VISTA enhancer hs1752 Neighboring gene Sharpr-MPRA regulatory region 1487 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:148812860-148813360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148820757-148821574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148821575-148822392 Neighboring gene microRNA 143 Neighboring gene Sharpr-MPRA regulatory region 14097 Neighboring gene microRNA 145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148837126-148837626 Neighboring gene Sharpr-MPRA regulatory region 12996 Neighboring gene uncharacterized LOC124901105 Neighboring gene NANOG hESC enhancer GRCh37_chr5:148878477-148879023 Neighboring gene casein kinase 1 alpha 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82175 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82187 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:148920536-148920739 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148924456-148925365 Neighboring gene ribosomal protein L29 pseudogene 14

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. CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice. Vacante F, et al. Circ Res, 2021 Apr 30. PMID 33622045, Free PMC Article
  2. LncRNA miR143HG inhibits the proliferation of glioblastoma cells by sponging miR-504. Wang P, et al. Int J Neurosci, 2022 Nov. PMID 33461388
  3. Genetic variations of CARMN affect risk of esophageal cancer in northwest China. Jia A, et al. Gene, 2020 Jul 20. PMID 32305636
  4. MiR-143HG Gene Polymorphisms as Risk Factors for Gastric Cancer in Chinese Han Population. Liu J, et al. Curr Mol Med, 2020. PMID 31880258
  5. Negative feedback circuitry between MIR143HG and RBM24 in Hirschsprung disease. Du C, et al. Biochim Biophys Acta, 2016 Nov. PMID 27565737

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. MIR143HG promotes methylation of transcription factor HOXB7 promoter by recruiting methyltransferase DNMT1 to prevent the progression of colon cancer.
    Title: MIR143HG promotes methylation of transcription factor HOXB7 promoter by recruiting methyltransferase DNMT1 to prevent the progression of colon cancer.
  2. Post-transcriptional regulation of tumor suppressor gene lncRNA CARMN via m[6]A modification and miRNA regulation in cervical cancer.
    Title: Post-transcriptional regulation of tumor suppressor gene lncRNA CARMN via m(6)A modification and miRNA regulation in cervical cancer.
  3. The Long Noncoding RNA Cardiac Mesoderm Enhancer-Associated Noncoding RNA (Carmn) Is a Critical Regulator of Gastrointestinal Smooth Muscle Contractile Function and Motility.
    Title: The Long Noncoding RNA Cardiac Mesoderm Enhancer-Associated Noncoding RNA (Carmn) Is a Critical Regulator of Gastrointestinal Smooth Muscle Contractile Function and Motility.
  4. LncRNA CARMN inhibits cervical cancer cell growth via the miR-92a-3p/BTG2/Wnt/beta-catenin axis.
    Title: LncRNA CARMN inhibits cervical cancer cell growth via the miR-92a-3p/BTG2/Wnt/β-catenin axis.
  5. LncRNA miR143HG inhibits the proliferation of glioblastoma cells by sponging miR-504.
    Title: LncRNA miR143HG inhibits the proliferation of glioblastoma cells by sponging miR-504.
  6. LncRNA CARMN Affects Hepatocellular Carcinoma Prognosis by Regulating the miR-192-5p/LOXL2 Axis.
    Title: LncRNA CARMN Affects Hepatocellular Carcinoma Prognosis by Regulating the miR-192-5p/LOXL2 Axis.
  7. CARMN Is an Evolutionarily Conserved Smooth Muscle Cell-Specific LncRNA That Maintains Contractile Phenotype by Binding Myocardin.
    Title: CARMN Is an Evolutionarily Conserved Smooth Muscle Cell-Specific LncRNA That Maintains Contractile Phenotype by Binding Myocardin.
  8. CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice.
    Title: CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice.
  9. LncRNA CARMN overexpression promotes prognosis and chemosensitivity of triple negative breast cancer via acting as miR143-3p host gene and inhibiting DNA replication.
    Title: LncRNA CARMN overexpression promotes prognosis and chemosensitivity of triple negative breast cancer via acting as miR143-3p host gene and inhibiting DNA replication.
  10. MiR-143HG Gene Polymorphisms as Risk Factors for Gastric Cancer in Chinese Han Population.
    Title: MiR-143HG Gene Polymorphisms as Risk Factors for Gastric Cancer in Chinese Han Population.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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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

General gene information

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Markers

Homology

Other Names

  • MIR143 and MIR145 host
  • MIR143 host gene (non-protein coding)
  • cardiac mesoderm enhancer-associated noncoding RNA

Clone Names

  • FLJ36638, FLJ42808, FLJ44577, DKFZp781L018, DKFZp586C0721, DKFZp686L22126

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in miRNA-mediated post-transcriptional gene silencing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of RISC complex IEA
Inferred from Electronic Annotation
more info
  

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_105059.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AI674543, HQ848934

  2. NR_105060.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an internal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AI674543, HQ848935

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
    149406845..149432836
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    149941690..149967678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_027180.1: Suppressed sequence

    Description
    NR_027180.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version

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