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LINC01516 long intergenic non-protein coding RNA 1516 [ Homo sapiens (human) ]

Gene ID: 101929025, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01516provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1516provided by HGNC
Primary source
HGNC:HGNC:51211
See related
Ensembl:ENSG00000231422 AllianceGenome:HGNC:51211
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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Location:
10p12.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (25113058..25161233)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (25131287..25179465)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (25401987..25450162)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene phosphoribosyl transferase domain containing 1 Neighboring gene NFE2L2 motif-containing MPRA enhancer 245 Neighboring gene RN7SK pseudogene 241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2230 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:25305216-25305978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3161 Neighboring gene threonine synthase like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3162 Neighboring gene enkurin, TRPC channel interacting protein Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:25348855-25350054 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:25350646-25351845 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:25356859-25358058 Neighboring gene NANOG hESC enhancer GRCh37_chr10:25394727-25395330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2233 Neighboring gene GPR158 antisense RNA 1 Neighboring gene G protein-coupled receptor 158 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:25542036-25542637 Neighboring gene RN7SK pseudogene 220 Neighboring gene Sharpr-MPRA regulatory region 12818 Neighboring gene MPRA-validated peak912 silencer Neighboring gene GPN-loop GTPase 3 pseudogene 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. 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
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

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

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_120649.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL139821, BC042983
    Related
    ENST00000436140.2

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    25113058..25161233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    25131287..25179465
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
Molecular Biology Databases