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LINC00486 long intergenic non-protein coding RNA 486 [ Homo sapiens (human) ]

Gene ID: 285045, updated on 10-Oct-2023

Summary

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Official Symbol
LINC00486provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 486provided by HGNC
Primary source
HGNC:HGNC:42946
See related
Ensembl:ENSG00000230876 AllianceGenome:HGNC:42946
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
Low expression observed in reference dataset See more
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Genomic context

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See LINC00486 in Genome Data Viewer
Location:
2p22.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (32825441..32842597)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (32874202..32891358)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (33050500..33171203)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905985 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:32852317-32852978 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:32852979-32853638 Neighboring gene microRNA 4765 Neighboring gene tetratricopeptide repeat domain 27 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:32962230-32963429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15561 Neighboring gene Sharpr-MPRA regulatory region 12694 Neighboring gene Sharpr-MPRA regulatory region 6729 Neighboring gene uncharacterized LOC105374453 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:33111152-33111352 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_58246 Neighboring gene uncharacterized LOC100271832

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. A nuclear NKRF interacting long noncoding RNA controls EBV eradication and suppresses tumor progression in natural killer/T-cell lymphoma. Wang WF, et al. Biochim Biophys Acta Mol Basis Dis, 2023 Aug. PMID 37084822
  2. Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis. Bunyavanich S, et al. BMC Med Genomics, 2014 Aug 2. PMID 25085501, Free PMC Article
  3. Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. Kennedy RB, et al. Hum Genet, 2012 Sep. PMID 22610502, 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. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

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
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
EBI GWAS Catalog
Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis.
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

Clone Names

  • AL121656.4, AL121656.5

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_183190.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL121656
    Related
    ENST00000648808.2

  2. NR_183192.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL121656

  3. NR_183193.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL121656
    Related
    ENST00000657199.1

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    32825441..32842597
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    32874202..32891358
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_027098.2: Suppressed sequence

    Description
    NR_027098.2: This RefSeq was removed because currently there is insufficient support for the transcript.

  2. NR_027099.2: Suppressed sequence

    Description
    NR_027099.2: This RefSeq was removed because currently there is insufficient support for the transcript.

  3. NR_027100.1: Suppressed sequence

    Description
    NR_027100.1: This RefSeq was removed because it is thought to represent a partial transcript.
Nucleotide Protein
Heading Accession and Version

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