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LINC00649 long intergenic non-protein coding RNA 649 [ Homo sapiens (human) ]

Gene ID: 100506334, updated on 8-Mar-2024

Summary

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Official Symbol
LINC00649provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 649provided by HGNC
Primary source
HGNC:HGNC:44305
See related
Ensembl:ENSG00000237945 AllianceGenome:HGNC:44305
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
LINC00650; lnc-ITSN1-2
Annotation information
Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
Expression
Broad expression in lymph node (RPKM 1.8), placenta (RPKM 1.7) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
21q22.11
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (33931122..33971186)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (32312834..32352998)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (35303426..35343487)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:35285966-35287165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18384 Neighboring gene ATP synthase peripheral stalk subunit OSCP Neighboring gene RNA, 7SL, cytoplasmic 740, pseudogene Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:35303079-35303720 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:35319651-35320850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18386 Neighboring gene uncharacterized LOC124905013 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:35343981-35344670 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:35348180-35349379 Neighboring gene uncharacterized LOC101928126 Neighboring gene uncharacterized LOC105372790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18388 Neighboring gene uncharacterized LOC105372789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18390

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. Long noncoding RNA LINC00649 functions as a microRNA‑432‑5p sponge to facilitate tumourigenesis in colorectal cancer by upregulating HDGF. Bao J, et al. Mol Med Rep, 2022 Mar. PMID 35088877, Free PMC Article
  2. LINC00649 underexpression is an adverse prognostic marker in acute myeloid leukemia. Guo C, et al. BMC Cancer, 2020 Sep 3. PMID 32883226, Free PMC Article
  3. Lnc-ITSN1-2, Derived From RNA Sequencing, Correlates With Increased Disease Risk, Activity and Promotes CD4(+) T Cell Activation, Proliferation and Th1/Th17 Cell Differentiation by Serving as a ceRNA for IL-23R via Sponging miR-125a in Inflammatory Bowel Disease. Nie J, et al. Front Immunol, 2020. PMID 32547537, Free PMC Article
  4. LncRNA LINC00649 aggravates the progression of cervical cancer through sponging miR-216a-3p. Si C, et al. J Obstet Gynaecol Res, 2022 Nov. PMID 36054700
  5. LncRNA LINC00649 recruits TAF15 and enhances MAPK6 expression to promote the development of lung squamous cell carcinoma via activating MAPK signaling pathway. Zhu H, et al. Cancer Gene Ther, 2022 Aug. PMID 35228660

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LncRNA LINC00649 aggravates the progression of cervical cancer through sponging miR-216a-3p.
    Title: LncRNA LINC00649 aggravates the progression of cervical cancer through sponging miR-216a-3p.
  2. LncRNA LINC00649 recruits TAF15 and enhances MAPK6 expression to promote the development of lung squamous cell carcinoma via activating MAPK signaling pathway.
    Title: LncRNA LINC00649 recruits TAF15 and enhances MAPK6 expression to promote the development of lung squamous cell carcinoma via activating MAPK signaling pathway.
  3. LncRNA LINC00649 promotes the growth and metastasis of triple-negative breast cancer by maintaining the stability of HIF-1alpha through the NF90/NF45 complex.
    Title: LncRNA LINC00649 promotes the growth and metastasis of triple-negative breast cancer by maintaining the stability of HIF-1α through the NF90/NF45 complex.
  4. Long noncoding RNA LINC00649 functions as a microRNA4325p sponge to facilitate tumourigenesis in colorectal cancer by upregulating HDGF.
    Title: Long noncoding RNA LINC00649 functions as a microRNA‑432‑5p sponge to facilitate tumourigenesis in colorectal cancer by upregulating HDGF.
  5. LINC00649 Facilitates the Cellular Process of Bladder Cancer Cells via Signaling Axis miR-16-5p/JARID2.
    Title: LINC00649 Facilitates the Cellular Process of Bladder Cancer Cells via Signaling Axis miR-16-5p/JARID2.
  6. Long non-coding RNA LINC00649 regulates YES-associated protein 1 (YAP1)/Hippo pathway to accelerate gastric cancer (GC) progression via sequestering miR-16-5p.
    Title: Long non-coding RNA LINC00649 regulates YES-associated protein 1 (YAP1)/Hippo pathway to accelerate gastric cancer (GC) progression via sequestering miR-16-5p.
  7. LINC00649 underexpression is an adverse prognostic marker in acute myeloid leukemia.
    Title: LINC00649 underexpression is an adverse prognostic marker in acute myeloid leukemia.
  8. Lnc-ITSN1-2, Derived From RNA Sequencing, Correlates With Increased Disease Risk, Activity and Promotes CD4(+) T Cell Activation, Proliferation and Th1/Th17 Cell Differentiation by Serving as a ceRNA for IL-23R via Sponging miR-125a in Inflammatory Bowel Disease.
    Title: Lnc-ITSN1-2, Derived From RNA Sequencing, Correlates With Increased Disease Risk, Activity and Promotes CD4(+) T Cell Activation, Proliferation and Th1/Th17 Cell Differentiation by Serving as a ceRNA for IL-23R via Sponging miR-125a in Inflammatory Bowel Disease.
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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

Homology

Other Names

  • TCONS_00028768
  • long intergenic non-protein coding RNA 650

Clone Names

  • FLJ46020

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_038883.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AK311545, AP000569, DA374118

  2. NR_134558.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon, compared to variant 1.
    Source sequence(s)
    AP000569, CD699867
    Related
    ENST00000400353.6

  3. NR_134559.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two 3' exons but instead contains an alternate 3' terminal exon, compared to variant 1.
    Source sequence(s)
    AK311545, AP000314, BX102617, DA374118
    Related
    ENST00000599421.1

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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    33931122..33971186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    32312834..32352998
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001288961.1: Suppressed sequence

    Description
    NM_001288961.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.

  2. NM_207472.1: Suppressed sequence

    Description
    NM_207472.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version

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