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LINC01563 long intergenic non-protein coding RNA 1563 [ Homo sapiens (human) ]

Gene ID: 101060544, updated on 17-Sep-2024

Summary

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Official Symbol
LINC01563provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1563provided by HGNC
Primary source
HGNC:HGNC:51343
See related
Ensembl:ENSG00000236819 AllianceGenome:HGNC:51343
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
HP08942
Expression
Biased expression in brain (RPKM 1.8), prostate (RPKM 0.5) and 2 other tissues See more
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Genomic context

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Location:
17p11.2
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (21075556..21090613)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (21024412..21039464)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (20978869..20993926)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900389 Neighboring gene uncharacterized LOC339260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11876 Neighboring gene SPECC1 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:20901079-20901896 Neighboring gene ubiquitin specific peptidase 22 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:20937215-20937716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8311 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:20946145-20947094 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:20947095-20948042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:20954728-20955314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11877 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:20970211-20970711 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:20978550-20979050 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:20987896-20989095 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:21002173-21002789 and GRCh37_chr17:21002790-21003407 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:21011664-21012527 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11879 Neighboring gene dehydrogenase/reductase 7B Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:21102215-21103012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:21108419-21109051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11880 Neighboring gene transmembrane protein 11

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. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. Oshikawa M, et al. Invest Ophthalmol Vis Sci, 2011 Aug 22. PMID 21697133

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)

General gene information

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Clone Names

  • AC087393.1

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_110895.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AC087393
    Related
    ENST00000668335.1

  2. NR_110896.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate internal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC087393
    Related
    ENST00000456235.1

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
    21075556..21090613
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    21024412..21039464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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