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    PRDM16-DT PRDM16 divergent transcript [ Homo sapiens (human) ]

    Gene ID: 440556, updated on 22-Oct-2024

    Summary

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    Official Symbol
    PRDM16-DTprovided by HGNC
    Official Full Name
    PRDM16 divergent transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:48664
    See related
    Ensembl:ENSG00000177133 AllianceGenome:HGNC:48664
    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
    LINC00982; lnc-dPrdm16
    Expression
    Biased expression in kidney (RPKM 17.6), stomach (RPKM 7.0) and 5 other tissues See more
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    Genomic context

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    See PRDM16-DT in Genome Data Viewer
    Location:
    1p36.32
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3059617..3067725, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (2561659..2569767, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2976181..2984289, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903826 Neighboring gene uncharacterized LOC124903825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2766741-2767242 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:2824551-2825750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2837727-2838286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 57 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2931349-2932112 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6546 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6552 Neighboring gene translation initiation factor IF-2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2976872-2977417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2984086-2984660 Neighboring gene opioid growth factor receptor pseudogene Neighboring gene actin related protein T2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2989243-2990091 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:3008649-3008795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3011815-3012660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3023590-3024149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3030215-3030791 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3030792-3031367 Neighboring gene PR/SET domain 16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3041525-3042136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3042749-3043359 Neighboring gene microRNA 4251

    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. LINC00982 Inhibits the Proliferation, Migration, and Invasion of Breast Cancer Cells Through the miR-765/DPF3 Axis. Chi F, et al. DNA Cell Biol, 2022 Apr. PMID 35325570
    2. Upregulation of LINC00982 inhibits cell proliferation and promotes cell apoptosis by regulating the activity of PI3K/AKT signaling pathway in renal cancer. Zhang C, et al. Eur Rev Med Pharmacol Sci, 2019 Feb. PMID 30840265
    3. Upregulated expression of long non-coding RNA LINC00982 regulates cell proliferation and its clinical relevance in patients with gastric cancer. Fei ZH, et al. Tumour Biol, 2016 Feb. PMID 26334618
    4. LINC00982-encoded protein PRDM16-DT regulates CHEK2 splicing to suppress colorectal cancer metastasis and chemoresistance. Hu HF, et al. Theranostics, 2024. PMID 38855188, Free PMC Article
    5. Low expression of LINC00982 and PRDM16 is associated with altered gene expression, damaged pathways and poor survival in lung adenocarcinoma. Lv W, et al. Oncol Rep, 2018 Nov. PMID 30132554

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LINC00982-encoded protein PRDM16-DT regulates CHEK2 splicing to suppress colorectal cancer metastasis and chemoresistance.
      Title: LINC00982-encoded protein PRDM16-DT regulates CHEK2 splicing to suppress colorectal cancer metastasis and chemoresistance.
    2. LncRNA PVT1 is increased in renal cell carcinoma and affects viability and migration in vitro.
      Title: LncRNA PVT1 is increased in renal cell carcinoma and affects viability and migration in vitro.
    3. LINC00982 Inhibits the Proliferation, Migration, and Invasion of Breast Cancer Cells Through the miR-765/DPF3 Axis.
      Title: LINC00982 Inhibits the Proliferation, Migration, and Invasion of Breast Cancer Cells Through the miR-765/DPF3 Axis.
    4. Overexpression of LINC00982 inhibited proliferation and promoted apoptosis and regulate the activity of PI3K/AKT signaling pathway.
      Title: Upregulation of LINC00982 inhibits cell proliferation and promotes cell apoptosis by regulating the activity of PI3K/AKT signaling pathway in renal cancer.
    5. Study revealed that LINC00982 and PRDM16 may serve as biomarkers or potential drug targets for the diagnosis and therapy of lung adenocarcinoma.
      Title: Low expression of LINC00982 and PRDM16 is associated with altered gene expression, damaged pathways and poor survival in lung adenocarcinoma.
    6. Our findings present that decreased lncRNA LINC00982 could be identified as a poor prognostic biomarker in gastric cancer and regulate cell proliferation.
      Title: Upregulated expression of long non-coding RNA LINC00982 regulates cell proliferation and its clinical relevance in patients with gastric cancer.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Other Names

    • long intergenic non-protein coding RNA 982

    Clone Names

    • FLJ42875, MGC35434, DKFZp761G0122

    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_015440.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AL713743, AL832943, BC029785, BM931404
      Related
      ENST00000445317.1

    2. NR_024371.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' end compared to variant 1.
      Source sequence(s)
      BC029785, BM931404

    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
      3059617..3067725 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      2561659..2569767 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001004337.1: Suppressed sequence

      Description
      NM_001004337.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.

    2. NM_198543.1: Suppressed sequence

      Description
      NM_198543.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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