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    DUBR DPPA2 upstream binding RNA [ Homo sapiens (human) ]

    Gene ID: 344595, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DUBRprovided by HGNC
    Official Full Name
    DPPA2 upstream binding RNAprovided by HGNC
    Primary source
    HGNC:HGNC:48569
    See related
    Ensembl:ENSG00000243701 MIM:616619; AllianceGenome:HGNC:48569
    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
    DUM; LINC0883; LINC00883
    Summary
    Predicted to act upstream of or within negative regulation of gene expression via chromosomal CpG island methylation; negative regulation of transcription by RNA polymerase II; and positive regulation of myoblast differentiation. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in ovary (RPKM 6.4), testis (RPKM 4.8) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DUBR in Genome Data Viewer
    Location:
    3q13.12
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (107240692..107326964)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (109960376..110046666)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (106959539..107045811)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene PTPN11 pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 882 Neighboring gene NANOG hESC enhancer GRCh37_chr3:106861597-106862136 Neighboring gene uncharacterized LOC124909404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14585 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:107003277-107004086 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:107004087-107004896 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:107027390-107028318 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:107034942-107035442 Neighboring gene CS pseudogene 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:107085622-107086821 Neighboring gene coiled-coil domain containing 54

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Linc00883 affects colorectal cancer through miR-577/FKBP14 axis: a novel mechanism for regulating colorectal cancer cell proliferation, invasion, and migration. Bai Y, et al. Cell Cycle, 2022 Nov. PMID 35833665, Free PMC Article
    2. DUBR suppresses migration and invasion of human lung adenocarcinoma cells via ZBTB11-mediated inhibition of oxidative phosphorylation. Nie W, et al. Acta Pharmacol Sin, 2022 Jan. PMID 33758355, Free PMC Article
    3. Role of non-coding RNAs in maintaining primary airway smooth muscle cells. Perry MM, et al. Respir Res, 2014 May 16. PMID 24886442, Free PMC Article
    4. LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration. Wang L, et al. Cell Res, 2015 Mar. PMID 25686699, Free PMC Article
    5. 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

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Linc00883 affects colorectal cancer through miR-577/FKBP14 axis: a novel mechanism for regulating colorectal cancer cell proliferation, invasion, and migration.
      Title: Linc00883 affects colorectal cancer through miR-577/FKBP14 axis: a novel mechanism for regulating colorectal cancer cell proliferation, invasion, and migration.
    2. DUBR suppresses migration and invasion of human lung adenocarcinoma cells via ZBTB11-mediated inhibition of oxidative phosphorylation.
      Title: DUBR suppresses migration and invasion of human lung adenocarcinoma cells via ZBTB11-mediated inhibition of oxidative phosphorylation.
    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)

    See Variation Viewer (GRCh38)

    General gene information

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    Markers

    Homology

    Other Names

    • long intergenic non-protein coding RNA 883

    Clone Names

    • FLJ31372

    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_028301.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC074043, BC039550, BU618315, DA339707
      Related
      ENST00000466734.6

    2. NR_028302.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses the same first exon as variant 1, but has a distinct 3' splice pattern.
      Source sequence(s)
      AC063944, AK309100
      Related
      ENST00000490441.1

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      107240692..107326964
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      109960376..110046666
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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