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

Gene ID: 102724508, updated on 22-Oct-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (47303443..47323901, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48165810..48186280, complement)
RS_2024_09 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 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
    Related
    ENST00000783725.1

  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_2024_08

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

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