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LINC01010 long intergenic non-protein coding RNA 1010 [ Homo sapiens (human) ]

Gene ID: 154092, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01010provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1010provided by HGNC
Primary source
HGNC:HGNC:48978
See related
Ensembl:ENSG00000236700 AllianceGenome:HGNC:48978
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 testis (RPKM 1.9), brain (RPKM 0.3) and 3 other tissues See more
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Genomic context

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See LINC01010 in Genome Data Viewer
Location:
6q23.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (134437716..134504020)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (135625962..135692270)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (134758854..134825158)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378009 Neighboring gene SGK1-CHCHD2P4 intergenic CAGE-defined mid-level expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17559 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 2 pseudogene 4 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:134757040-134758239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25090 Neighboring gene cancer/testis associated transcript 69 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:134808766-134808977 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:134855294-134856493 Neighboring gene long intergenic non-protein coding RNA 3002 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:134858047-134859246 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:134905935-134906540 Neighboring gene family with sequence similarity 8 member A6, pseudogene

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. HBV HBx-Downregulated lncRNA LINC01010 Attenuates Cell Proliferation by Interacting with Vimentin. Gan L, et al. Int J Mol Sci, 2021 Nov 19. PMID 34830378, Free PMC Article
  2. Genome-wide association study for serum urate concentrations and gout among African Americans identifies genomic risk loci and a novel URAT1 loss-of-function allele. Tin A, et al. Hum Mol Genet, 2011 Oct 15. PMID 21768215, Free PMC Article
  3. 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
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. HBV HBx-Downregulated lncRNA LINC01010 Attenuates Cell Proliferation by Interacting with Vimentin.
    Title: HBV HBx-Downregulated lncRNA LINC01010 Attenuates Cell Proliferation by Interacting with Vimentin.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study for serum urate concentrations and gout among African Americans identifies genomic risk loci and a novel URAT1 loss-of-function allele.
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_038216.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AA952986, AL078590, BC041589, DA420003

  2. NR_038217.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AA952986, AL078590, BC041589, DA419376

  3. NR_038218.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' exon and uses an alternate splice site, compared to variant 1.
    Source sequence(s)
    AA952986, AL078590, BC041589, DA244667, DA265202

  4. NR_038219.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate 5' exon and two additional internal exons, and uses an alternate splice site, compared to variant 1.
    Source sequence(s)
    AA952986, AL078590, BC041589, DA265202, DA291077
    Related
    ENST00000653261.1

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    134437716..134504020
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    135625962..135692270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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