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LINC02140 long intergenic non-protein coding RNA 2140 [ Homo sapiens (human) ]

Gene ID: 100996345, updated on 17-Sep-2024

Summary

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Official Symbol
LINC02140provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 2140provided by HGNC
Primary source
HGNC:HGNC:53000
See related
Ensembl:ENSG00000261803 AllianceGenome:HGNC:53000
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
Restricted expression toward testis (RPKM 8.5) See more
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Genomic context

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See LINC02140 in Genome Data Viewer
Location:
16q12.2
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (54366007..54370699, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (60164020..60168716, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (54399919..54404611, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2169 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54318795-54319714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54319715-54320634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:54320768-54321268 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:54321269-54321769 Neighboring gene VISTA enhancer hs51 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54325084-54325965 Neighboring gene iroquois homeobox 3 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54364959-54365668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54396413-54396916 Neighboring gene uncharacterized LOC105371272 Neighboring gene NANOG hESC enhancer GRCh37_chr16:54459786-54460294 Neighboring gene NANOG hESC enhancer GRCh37_chr16:54464241-54464805 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:54523058-54523261 Neighboring gene VISTA enhancer hs43 Neighboring gene long intergenic non-protein coding RNA 2183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54616376-54617284 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:54618909-54619453 Neighboring gene VISTA enhancer hs37 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:54658831-54659077 Neighboring gene uncharacterized LOC105371274

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 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. 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

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_134922.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AC018553, AK057319
    Related
    ENST00000566649.1

  2. NR_134923.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon and is shorter, compared to variant 1.
    Source sequence(s)
    AC018553, AK057319, DB447763

  3. NR_134924.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' terminal exon and is shorter, compared to variant 1.
    Source sequence(s)
    AC018553, AK057319, HY020479

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    54366007..54370699 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    60164020..60168716 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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