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    CCDC140 CCDC140 long non-coding RNA [ Homo sapiens (human) ]

    Gene ID: 151278, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CCDC140provided by HGNC
    Official Full Name
    CCDC140 long non-coding RNAprovided by HGNC
    Primary source
    HGNC:HGNC:26514
    See related
    Ensembl:ENSG00000163081 AllianceGenome:HGNC:26514
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes a protein that appears to be restricted to select higher primate species. This protein contains a C-terminal coiled-coil domain, which is a versatile structural motif consisting of multiple amphipathic alpha-helices that twist around each other to form a supercoil. [provided by RefSeq, Aug 2011]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See CCDC140 in Genome Data Viewer
    Location:
    2q36.1
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (222298147..222305217)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (222783273..222790336)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223162866..223169936)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:222917569-222918330 Neighboring gene ribosomal protein L23a pseudogene 28 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223072996-223073618 Neighboring gene uncharacterized LOC107985991 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:223084735-223085934 Neighboring gene paired box 3 Neighboring gene NANOG hESC enhancer GRCh37_chr2:223137199-223137802 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:223154577-223155490 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:223155491-223156404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:223158467-223159003 Neighboring gene PAX3 promoter region Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171419-223171954 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171955-223172489 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223182883-223183478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12368 Neighboring gene ring finger protein 228 Neighboring gene cancer/testis associated transcript 75 Neighboring gene NANOG hESC enhancer GRCh37_chr2:223258471-223259068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17166 Neighboring gene sphingosine-1-phosphate phosphatase 2 Neighboring gene Nanog homeobox pseudogene 2

    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. Coiled coil domains: stability, specificity, and biological implications. Mason JM, et al. Chembiochem, 2004 Feb 6. PMID 14760737
    2. Alpha-helical coiled-coil oligomerization domains in extracellular proteins. Kammerer RA. Matrix Biol, 1997 Mar. PMID 9138288
    3. Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Tsumagari K, et al. Epigenetics, 2013 Mar. PMID 23417056, Free PMC Article
    4. Coiled coils: a highly versatile protein folding motif. Burkhard P, et al. Trends Cell Biol, 2001 Feb. PMID 11166216
    5. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. Aregger M, et al. Nat Metab, 2020 Jun. PMID 32694731, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Other Names

    • CCDC140 lncRNA
    • coiled-coil domain containing 140
    • coiled-coil domain-containing protein 140

    Clone Names

    • FLJ32447, MGC133159

    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.

    Genomic

    1. NG_021186.1 RefSeqGene

      Range
      5001..12071
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. NR_161172.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC010980
      Related
      ENST00000647762.1

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      222298147..222305217
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      222783273..222790336
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_153038.1: Suppressed sequence

      Description
      NM_153038.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96MF4.1 GenPept UniProtKB/Swiss-Prot:Q96MF4

    Gene LinkOut

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

    Chemical Information
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