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

    Gene ID: 10141, updated on 2-Nov-2024

    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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    See LINC01587 in Genome Data Viewer
    Location:
    4p16.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (5524569..5527801)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (5494009..5497241)
    RS_2024_09 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)

    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
      Related
      ENST00000818287.1

    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
      Related
      ENST00000818285.1

    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_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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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