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

Gene ID: 151278, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (222298147..222305217)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (222783273..222790336)
105.20220307 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: 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. 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)

Genotypes

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_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
    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.

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