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LINC02563 long intergenic non-protein coding RNA 2563 [ Homo sapiens (human) ]

Gene ID: 105827617, updated on 10-Oct-2023

Summary

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Official Symbol
LINC02563provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 2563provided by HGNC
Primary source
HGNC:HGNC:52923
See related
Ensembl:ENSG00000263520 AllianceGenome:HGNC:52923
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
CRAT40
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Genomic context

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See LINC02563 in Genome Data Viewer
Location:
17q24.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (65457541..65458408)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (66327285..66328152)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (63453659..63454526)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100507002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8860 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:63118742-63119273 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:63119274-63119804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8862 Neighboring gene VISTA enhancer hs1517 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63169068-63169861 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63179933-63180469 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63179396-63179932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63181573-63182096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63182097-63182620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63220448-63221252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63221253-63222057 Neighboring gene zinc finger protein 848, pseudogene Neighboring gene MPRA-validated peak2941 silencer Neighboring gene regulator of G protein signaling 9 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:63358670-63359869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63434615-63435115 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:63451995-63452494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63456111-63456744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63456745-63457378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63457379-63458011 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:63491028-63491660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63492294-63492926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63519932-63520432 Neighboring gene Sharpr-MPRA regulatory region 3713 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63526146-63526660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63526661-63527173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63527688-63528200 Neighboring gene MPRA-validated peak2942 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63550543-63551315 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63551316-63552089 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12611 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63568601-63569439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63579618-63580152 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63589757-63590572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63625333-63625832 Neighboring gene axin 2 Neighboring gene chloride intracellular channel 1 pseudogene Neighboring gene centrosomal protein 112

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. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Dias Neto E, et al. Proc Natl Acad Sci U S A, 2000 Mar 28. PMID 10737800, 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)

Genotypes

General gene information

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Other Names

  • CTD-2535L24.3
  • cervical cancer-associated transcript 40

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_131984.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC115994, BF757519
    Related
    ENST00000579474.1

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
    65457541..65458408
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    66327285..66328152
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases