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    COPB2-DT COPB2 divergent transcript [ Homo sapiens (human) ]

    Gene ID: 100507291, updated on 22-Oct-2024

    Summary

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    Official Symbol
    COPB2-DTprovided by HGNC
    Official Full Name
    COPB2 divergent transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:55579
    See related
    Ensembl:ENSG00000248932 AllianceGenome:HGNC:55579
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Expression
    Broad expression in testis (RPKM 5.5), thyroid (RPKM 1.5) and 23 other tissues See more
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    Genomic context

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    See COPB2-DT in Genome Data Viewer
    Location:
    3q23
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (139389803..139583319)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (142137362..142330749)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (139108645..139302161)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 3993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20611 Neighboring gene mitochondrial ribosomal protein S22 Neighboring gene uncharacterized LOC124906339 Neighboring gene COPI coat complex subunit beta 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:139108213-139108774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:139108775-139109337 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:139191689-139192888 Neighboring gene retinol binding protein 2 Neighboring gene actin gamma 1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 7279 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:139252819-139253320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:139253967-139254614 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:139256460-139257659 Neighboring gene retinol binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20615 Neighboring gene nicotinamide nucleotide adenylyltransferase 3 Neighboring gene RN7SK pseudogene 124 Neighboring gene DTWD1 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:139326683-139327202 Neighboring gene RNA, 7SL, cytoplasmic 724, pseudogene

    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. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. Deng X, et al. PLoS One, 2013. PMID 24324551, Free PMC Article
    2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    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)

    General gene information

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    Markers

    Other Names

    • RP11-319G6.1

    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_121608.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC097103, BX098847, DB446595

    2. NR_121609.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon and contains two alternate 3' exons, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      DA364121, DB034152, DB446595
      Related
      ENST00000515247.5

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      139389803..139583319
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      142137362..142330749
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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