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LINC00680 long intergenic non-protein coding RNA 680 [ Homo sapiens (human) ]

Gene ID: 106660612, updated on 10-Oct-2023

Summary

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Official Symbol
LINC00680provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 680provided by HGNC
Primary source
HGNC:HGNC:44417
See related
Ensembl:ENSG00000290555 AllianceGenome:HGNC:44417
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
Ubiquitous expression in endometrium (RPKM 2.1), brain (RPKM 2.1) and 25 other tissues See more
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Genomic context

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Location:
6p11.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (57945834..57961446, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (57784624..57800233, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (58272112..58287724, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927268 Neighboring gene tRNA-Ala (anticodon AGC) 12-3 Neighboring gene LINC00680-GUSBP4 readthrough, transcribed pseudogene Neighboring gene GUSB pseudogene 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:58263882-58264790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24711 Neighboring gene uncharacterized LOC101927293 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 15 Neighboring gene uncharacterized LOC124901336

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. LINC00680 modulates docetaxel resistance in breast cancer via the miR-320b/CDKL5 axis. Li J, et al. Int J Immunopathol Pharmacol, 2022 Jan-Dec. PMID 35667653, Free PMC Article
  2. LncRNA LINC00680 promotes lung adenocarcinoma growth via binding to GATA6 and canceling GATA6-mediated suppression of SOX12 expression. Sun X, et al. Exp Cell Res, 2021 Aug 1. PMID 34029572
  3. Long non-coding RNA LINC00680 functions as a ceRNA to promote esophageal squamous cell carcinoma progression through the miR-423-5p/PAK6 axis. Xue ST, et al. Mol Cancer, 2022 Mar 7. PMID 35255921, Free PMC Article
  4. LINC00680 enhances hepatocellular carcinoma stemness behavior and chemoresistance by sponging miR-568 to upregulate AKT3. Shu G, et al. J Exp Clin Cancer Res, 2021 Jan 26. PMID 33499874, Free PMC Article
  5. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Liu SJ, et al. Science, 2017 Jan 6. PMID 27980086, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LINC00680 modulates docetaxel resistance in breast cancer via the miR-320b/CDKL5 axis.
    Title: LINC00680 modulates docetaxel resistance in breast cancer via the miR-320b/CDKL5 axis.
  2. Long non-coding RNA LINC00680 functions as a ceRNA to promote esophageal squamous cell carcinoma progression through the miR-423-5p/PAK6 axis.
    Title: Long non-coding RNA LINC00680 functions as a ceRNA to promote esophageal squamous cell carcinoma progression through the miR-423-5p/PAK6 axis.
  3. LncRNA LINC00680 promotes lung adenocarcinoma growth via binding to GATA6 and canceling GATA6-mediated suppression of SOX12 expression.
    Title: LncRNA LINC00680 promotes lung adenocarcinoma growth via binding to GATA6 and canceling GATA6-mediated suppression of SOX12 expression.
  4. LINC00680 enhances hepatocellular carcinoma stemness behavior and chemoresistance by sponging miR-568 to upregulate AKT3.
    Title: LINC00680 enhances hepatocellular carcinoma stemness behavior and chemoresistance by sponging miR-568 to upregulate AKT3.
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)

Genotypes

General gene information

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Readthrough LINC00680-GUSBP4

Readthrough gene: LINC00680-GUSBP4, Included gene: GUSBP4

Clone Names

  • FLJ13549, DKFZp761D0811

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_125727.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the reference transcript.
    Source sequence(s)
    AL021368, AL162041, BC011838, BI756196, CA334877
    Related
    ENST00000418368.1

  2. NR_125728.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate internal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AL021368, AL162041, AL541195, BC011838, CA334877, DA613065

  3. NR_125729.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate internal exon and uses an alternate splice site, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AL021368, AL162041, BC011838, BC017330, CA334877
    Related
    ENST00000450081.5

  4. NR_132994.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate internal splice site, resulting in a longer transcript, compared to variant 1.
    Source sequence(s)
    AK023611, AL021368, AL162041, BC065547

  5. NR_132995.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate internal splice site, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AL021368, AL162041, BC011838
    Related
    ENST00000399751.6

  6. NR_132996.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks two alternate internal exons, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AK023611, AL021368, AL162041, BE885753

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
    57945834..57961446 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    57784624..57800233 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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