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LINC00578 long intergenic non-protein coding RNA 578 [ Homo sapiens (human) ]

Gene ID: 100505566, updated on 10-Oct-2023

Summary

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Official Symbol
LINC00578provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 578provided by HGNC
Primary source
HGNC:HGNC:43807
See related
Ensembl:ENSG00000228221 AllianceGenome:HGNC:43807
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
Biased expression in prostate (RPKM 1.5), esophagus (RPKM 1.4) and 10 other tissues See more
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Genomic context

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See LINC00578 in Genome Data Viewer
Location:
3q26.32
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (177441921..177752704)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (180245069..180555603)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (177159709..177470492)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986053 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:177001817-177002549 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:177006212-177006426 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:177011460-177012659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20838 Neighboring gene MPRA-validated peak4933 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14906 Neighboring gene long intergenic non-protein coding RNA 501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20839 Neighboring gene Sharpr-MPRA regulatory region 4767 Neighboring gene Sharpr-MPRA regulatory region 10654 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:177062319-177062838 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:177063359-177063876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20841 Neighboring gene argininosuccinate synthetase 1 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20842 Neighboring gene Sharpr-MPRA regulatory region 9868 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:177077317-177078158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177083633-177084134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20846 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20847 Neighboring gene MPRA-validated peak4934 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:177174687-177175886 Neighboring gene NANOG hESC enhancer GRCh37_chr3:177205476-177205977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177234333-177235097 Neighboring gene RN7SK pseudogene 52 Neighboring gene uncharacterized LOC124906306 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:177301340-177301507 Neighboring gene MPRA-validated peak4935 silencer Neighboring gene MPRA-validated peak4936 silencer Neighboring gene Sharpr-MPRA regulatory region 14869 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:177324712-177324912 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:177327959-177328599 Neighboring gene small nucleolar RNA SNORA18 Neighboring gene Sharpr-MPRA regulatory region 5391 Neighboring gene NANOG hESC enhancer GRCh37_chr3:177383662-177384200 Neighboring gene fibroblast growth factor receptor 3 pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177543728-177544228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177544229-177544729 Neighboring gene long intergenic non-protein coding RNA 2015 Neighboring gene uncharacterized LOC107986154

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. Intergenic variants may predispose to major depression disorder through regulation of long non-coding RNA expression. Ye N, et al. Gene, 2017 Feb 15. PMID 27940106
  2. A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks. Kapoor M, et al. Hum Genet, 2013 Oct. PMID 23743675, Free PMC Article
  3. Genome-wide and gene-based association studies of anxiety disorders in European and African American samples. Otowa T, et al. PLoS One, 2014. PMID 25390645, Free PMC Article
  4. Novel loci for major depression identified by genome-wide association study of Sequenced Treatment Alternatives to Relieve Depression and meta-analysis of three studies. Shyn SI, et al. Mol Psychiatry, 2011 Feb. PMID 20038947, Free PMC Article
  5. Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. Lu Y, et al. Nat Genet, 2013 Feb. PMID 23291589, Free PMC Article

See all (6) citations in PubMed

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
A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.
EBI GWAS Catalog
Genome-wide and gene-based association studies of anxiety disorders in European and african american samples.
EBI GWAS Catalog
Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus.
EBI GWAS Catalog
Novel loci for major depression identified by genome-wide association study of Sequenced Treatment Alternatives to Relieve Depression and meta-analysis of three studies.
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)

Genotypes

General gene information

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Markers

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_047568.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC026325, AC026355, AC112136, BX101293
    Related
    ENST00000442937.6

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    177441921..177752704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    180245069..180555603
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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