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    EFCAB13-DT EFCAB13 divergent transcript [ Homo sapiens (human) ]

    Gene ID: 102724508, updated on 21-Feb-2024

    Summary

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    Official Symbol
    EFCAB13-DTprovided by HGNC
    Official Full Name
    EFCAB13 divergent transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:55338
    See related
    Ensembl:ENSG00000263293 AllianceGenome:HGNC:55338
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    THCAT158
    Expression
    Biased expression in testis (RPKM 2.3), thyroid (RPKM 1.2) and 8 other tissues See more
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    Genomic context

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    See EFCAB13-DT in Genome Data Viewer
    Location:
    17q21.32
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (47303443..47323901, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48165810..48186280, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (45380809..45401267, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RNA, U7 small nuclear 186 pseudogene Neighboring gene integrin subunit beta 3 Neighboring gene Sharpr-MPRA regulatory region 629 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45353259-45353806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12306 Neighboring gene uncharacterized LOC107985029 Neighboring gene Sharpr-MPRA regulatory region 4923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12309 Neighboring gene Sharpr-MPRA regulatory region 4395 Neighboring gene VISTA enhancer hs2033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45369753-45370253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8625 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12311 Neighboring gene EF-hand calcium binding domain 13 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:45416653-45417154 Neighboring gene Sharpr-MPRA regulatory region 1659 Neighboring gene UDP-N-acetylglucosamine pyrophosphorylase 1 pseudogene Neighboring gene MPRA-validated peak2872 silencer Neighboring gene MPRA-validated peak2873 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8626 Neighboring gene nuclear factor, erythroid 2 like 3 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. The landscape of long noncoding RNAs in the human transcriptome. Iyer MK, et al. Nat Genet, 2015 Mar. PMID 25599403, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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

    General gene information

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    Other Names

    • thyroid cancer-associated transcript 158

    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_110880.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AA609236, AW293117, HY036509

    2. NR_110881.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' terminal exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC068234
      Related
      ENST00000575039.1

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      47303443..47323901 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      48165810..48186280 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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