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

    Gene ID: 728264, updated on 10-Dec-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. Predicted to be part of RISC complex. Biomarker of atherosclerosis. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in endometrium (RPKM 8.6), prostate (RPKM 5.7) and 18 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (149406845..149432836)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (149941690..149967678)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Post-transcriptional regulation of tumor suppressor gene lncRNA CARMN via m(6)A modification and miRNA regulation in cervical cancer. Yu B, et al. J Cancer Res Clin Oncol, 2023 Sep. PMID 37273106
    2. Negative feedback circuitry between MIR143HG and RBM24 in Hirschsprung disease. Du C, et al. Biochim Biophys Acta, 2016 Nov. PMID 27565737
    3. MiR-143HG Gene Polymorphisms as Risk Factors for Gastric Cancer in Chinese Han Population. Liu J, et al. Curr Mol Med, 2020. PMID 31880258
    4. Genetic variations of CARMN affect risk of esophageal cancer in northwest China. Jia A, et al. Gene, 2020 Jul 20. PMID 32305636
    5. LncRNA miR143HG inhibits the proliferation of glioblastoma cells by sponging miR-504. Wang P, et al. Int J Neurosci, 2022 Nov. PMID 33461388

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA CARMN facilitates odontogenic differentiation of dental pulp cells by impairing EZH2.
      Title: LncRNA CARMN facilitates odontogenic differentiation of dental pulp cells by impairing EZH2.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice.
      Title: CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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)

    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_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
      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

    Gene LinkOut

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

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    Research Materials