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LINC01587 long intergenic non-protein coding RNA 1587 [ Homo sapiens (human) ]

Gene ID: 10141, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01587provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1587provided by HGNC
Primary source
HGNC:HGNC:13716
See related
Ensembl:ENSG00000082929 AllianceGenome:HGNC:13716
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
aC1; C4orf6
Summary
This gene is expressed in neuroblastoma; however, the function of this gene is not yet determined. [provided by RefSeq, Jul 2008]
Expression
Low expression observed in reference dataset See more
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Genomic context

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Location:
4p16.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (5524569..5527801)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (5494009..5497241)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (5526296..5529528)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:5044739-5045239 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5053909-5054447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21237 Neighboring gene serine/threonine kinase 32B Neighboring gene Sharpr-MPRA regulatory region 6927 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:5135748-5136346 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:5155881-5156382 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:5167073-5168272 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:5200564-5201064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5206884-5207384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5207385-5207885 Neighboring gene Sharpr-MPRA regulatory region 9083 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:5367115-5368314 Neighboring gene RN7SK pseudogene 275 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:5526681-5527880 Neighboring gene uncharacterized LOC124900166 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:5593995-5594527 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5595819-5596318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5595317-5595818 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:5610365-5610542 Neighboring gene NANOG hESC enhancer GRCh37_chr4:5613379-5613880 Neighboring gene EvC ciliary complex subunit 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:5641443-5642642 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:5666069-5667268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21241 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5710226-5710845 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:5754671-5755626 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:5760129-5761328 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:5774235-5774978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:5774979-5775720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21246 Neighboring gene EvC ciliary complex subunit 1 Neighboring gene collapsin response mediator protein 1

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. Fluorescent differential display analysis of gene expression in differentiating neuroblastoma cells. Kito K, et al. Gene, 1997 Jan 3. PMID 9016955
  2. Long interspersed nuclear element-1 (LINE1)-mediated deletion of EVC, EVC2, C4orf6, and STK32B in Ellis-van Creveld syndrome with borderline intelligence. Temtamy SA, et al. Hum Mutat, 2008 Jul. PMID 18454448
  3. Systematic identification of pathological lamin A interactors. Dittmer TA, et al. Mol Biol Cell, 2014 May. PMID 24623722, Free PMC Article
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  5. Architecture of the human interactome defines protein communities and disease networks. Huttlin EL, et al. Nature, 2017 May 25. PMID 28514442, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. In a consanguineous pedigree diagnosed with EvC and borderline intelligence, a 520-kb homozygous deletion comprising EVC, EVC2, C4orf6, and STK32B, caused by recombination between LINE-1 elements, was detected
    Title: Long interspersed nuclear element-1 (LINE1)-mediated deletion of EVC, EVC2, C4orf6, and STK32B in Ellis-van Creveld syndrome with borderline intelligence.
Submit: New GeneRIF Correction

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Other Names

  • expressed in neuroblastoma

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in nervous system development TAS
Traceable Author Statement
more info
 PubMed 

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_126517.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AA281699, AI590573, BU743146, D82070

  2. NR_126518.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1.
    Source sequence(s)
    AI590573, BU743146, D82070
    Related
    ENST00000623565.3

  3. NR_126519.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains alternate 5' exon structure and uses an alternate splice site in an internal exon, compared to variant 1.
    Source sequence(s)
    AI590573, BU743146, DB043858

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    5524569..5527801
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    5494009..5497241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_005750.2: Suppressed sequence

    Description
    NM_005750.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99440.1 GenPept UniProtKB/Swiss-Prot:Q99440

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