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LINC00339 long intergenic non-protein coding RNA 339 [ Homo sapiens (human) ]

Gene ID: 29092, updated on 8-Oct-2024

Summary

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Official Symbol
LINC00339provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 339provided by HGNC
Primary source
HGNC:HGNC:25011
See related
Ensembl:ENSG00000218510 AllianceGenome:HGNC:25011
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HSPC157; NCRNA00339
Expression
Ubiquitous expression in pancreas (RPKM 12.3), ovary (RPKM 9.6) and 25 other tissues See more
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Genomic context

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See LINC00339 in Genome Data Viewer
Location:
1p36.12
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (22025191..22031224)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (21848994..21855007)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (22351684..22357717)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene chymotrypsin like elastase 3A Neighboring gene RNA, 7SL, cytoplasmic 186, pseudogene Neighboring gene RNA, U6 small nuclear 776, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 345 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 393 Neighboring gene Sharpr-MPRA regulatory region 3950 Neighboring gene long intergenic non-protein coding RNA 1635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 347 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 394 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:22379623-22380190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22380191-22380759 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22387820-22388320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22388321-22388821 Neighboring gene cell division cycle 42 Neighboring gene MPHOSPH6 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 348 Neighboring gene Sharpr-MPRA regulatory region 8542 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22446773-22447390 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22448010-22448627 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22457824-22458584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22458585-22459343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22459683-22460408 Neighboring gene Wnt family member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22462663-22463176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22465050-22466004 Neighboring gene uncharacterized LOC105376845 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 399

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. Functional mechanism and clinical implications of LINC00339 in delayed fracture healing. Li Y, et al. J Orthop Surg Res, 2024 Aug 27. PMID 39192334, Free PMC Article
  2. LINC00339 accelerates invasion and migration of colorectal cancer via mediating miRNA-30a-5p. Zhou P, et al. Cell Mol Biol (Noisy-le-grand), 2023 Dec 20. PMID 38279428
  3. LINC00339: An emerging major player in cancer and metabolic diseases. Wu Z, et al. Biomed Pharmacother, 2022 May. PMID 35276468
  4. Elucidating the role of long intergenic non-coding RNA 339 in human endometrium and endometriosis. Holdsworth-Carson SJ, et al. Mol Hum Reprod, 2021 Feb 27. PMID 33576410
  5. Avasimibe inhibits the proliferation, migration and invasion of glioma cells by suppressing linc00339. Luo Y, et al. Biomed Pharmacother, 2020 Oct. PMID 32682982

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Functional mechanism and clinical implications of LINC00339 in delayed fracture healing.
    Title: Functional mechanism and clinical implications of LINC00339 in delayed fracture healing.
  2. LINC00339 accelerates invasion and migration of colorectal cancer via mediating miRNA-30a-5p.
    Title: LINC00339 accelerates invasion and migration of colorectal cancer via mediating miRNA-30a-5p.
  3. LINC00339: An emerging major player in cancer and metabolic diseases.
    Title: LINC00339: An emerging major player in cancer and metabolic diseases.
  4. Elucidating the role of long intergenic non-coding RNA 339 in human endometrium and endometriosis.
    Title: Elucidating the role of long intergenic non-coding RNA 339 in human endometrium and endometriosis.
  5. CCL18-induced LINC00319 promotes proliferation and metastasis in oral squamous cell carcinoma via the miR-199a-5p/FZD4 axis.
    Title: CCL18-induced LINC00319 promotes proliferation and metastasis in oral squamous cell carcinoma via the miR-199a-5p/FZD4 axis.
  6. Avasimibe inhibits the proliferation, migration and invasion of glioma cells by suppressing linc00339.
    Title: Avasimibe inhibits the proliferation, migration and invasion of glioma cells by suppressing linc00339.
  7. LINC00339 regulates ROCK1 by miR-152 to promote cell proliferation and migration in hepatocellular carcinoma.
    Title: LINC00339 regulates ROCK1 by miR-152 to promote cell proliferation and migration in hepatocellular carcinoma.
  8. LINC00339 regulated ovarian cancer cell proliferation, migration, and invasion by targeting miR-148a-3p/ROCK1 pathway.
    Title: LINC00339 promotes cell proliferation, migration, and invasion of ovarian cancer cells via miR-148a-3p/ROCK1 axes.
  9. LINC00339 was markedly over-expressed in pancreatic cancer (PANC) tissues and cells and promoted cell proliferation, invasion, and migration via sponging miR-497-5p, thereby increasing IGF1R expression. Our study could provide a novel target for PANC diagnosis and biotherapy.
    Title: LINC00339 promotes cell proliferation and metastasis in pancreatic cancer via miR-497-5p/IGF1R axis.
  10. LINC00339 promotes proliferation, and suppresses apoptosis of colorectal cancer cells via downregulating miR-218
    Title: [The expression and functional mechanism of long non-coding RNA LINC00339 in colorectal cancer].
Submit: New GeneRIF Correction See all GeneRIFs (13)

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: CDC42

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_023918.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) contains an alternate 5'-terminal exon and lacks an internal exon, compared to variant 3.
    Source sequence(s)
    AL031281, BC071749, CA489192
    Related
    ENST00000434233.2

  2. NR_023919.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an internal exon, compared to variant 3.
    Source sequence(s)
    AF161506, AL031281, BX509008, CA489192
    Related
    ENST00000416769.2

  3. NR_109759.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in the 5' region and lacks an internal exon, compared to variant 3.
    Source sequence(s)
    AF161506, AL031281, BX509008, CA489192

  4. NR_109760.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an internal exon and uses an alternate splice site in the 3' region, compared to variant 3.
    Source sequence(s)
    AF161506, AL031281, BX509008, CA489192

  5. NR_109761.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' region, compared to variant 3.
    Source sequence(s)
    AL031281, BG432520, BX509008

  6. NR_109762.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents the longest transcript.
    Source sequence(s)
    AL031281, BG432520, BX509008, H87321

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    22025191..22031224
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    21848994..21855007
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_014179.1: Suppressed sequence

    Description
    NM_014179.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version

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