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

Gene ID: 100507291, updated on 10-Oct-2023

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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (139389803..139583319)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (142137362..142330749)
105.20220307 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)

Genotypes

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
    Related
    ENST00000690901.1

  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_2023_10

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

Gene LinkOut

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Molecular Biology Databases