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

    Gene ID: 101927043, updated on 17-Sep-2024

    Summary

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    Official Symbol
    EPCAM-DTprovided by HGNC
    Official Full Name
    EPCAM divergent transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:52639
    See related
    Ensembl:ENSG00000234690 AllianceGenome:HGNC:52639
    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
    Low expression observed in reference dataset See more
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    Genomic context

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    See EPCAM-DT in Genome Data Viewer
    Location:
    2p21
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (47192405..47345074, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (47197516..47350113, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (47419544..47572213, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:47316060-47317259 Neighboring gene sperm-tail PG-rich repeat containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15722 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:47402112-47402778 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:47402802-47402952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15725 Neighboring gene calmodulin 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47419971-47420492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47420493-47421014 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:47434831-47435330 Neighboring gene uncharacterized LOC105374588 Neighboring gene uncharacterized LOC124907763 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47465802-47466556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:47471001-47471501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:47476213-47476714 Neighboring gene uncharacterized LOC107985882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15727 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:47501342-47501842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:47501843-47502343 Neighboring gene MPRA-validated peak3693 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr2:47519444-47519732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15729 Neighboring gene Sharpr-MPRA regulatory regions 1090 and 15339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15731 Neighboring gene Sharpr-MPRA regulatory region 12385 Neighboring gene Sharpr-MPRA regulatory region 1814 Neighboring gene brain cytoplasmic RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47596083-47596759 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47596760-47597435 Neighboring gene RN7SK pseudogene 119 Neighboring gene epithelial cell adhesion molecule Neighboring gene microRNA 559

    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
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    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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    Clone Names

    • AC073283.4

    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_110207.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC079775, AK094343
      Related
      ENST00000419035.1

    2. NR_110208.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two exons and contains four alternate 3' exons, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC073283, AC079775

    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
      47192405..47345074 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      47197516..47350113 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    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.

    Molecular Biology Databases
    Research Materials