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    THUMPD3-AS1 THUMPD3 antisense RNA 1 [ Homo sapiens (human) ]

    Gene ID: 440944, updated on 10-Dec-2024

    Summary

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    Official Symbol
    THUMPD3-AS1provided by HGNC
    Official Full Name
    THUMPD3 antisense RNA 1provided by HGNC
    Primary source
    HGNC:HGNC:44478
    See related
    Ensembl:ENSG00000206573 AllianceGenome:HGNC:44478
    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
    SETD5-AS1
    Expression
    Ubiquitous expression in thyroid (RPKM 8.8), prostate (RPKM 8.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See THUMPD3-AS1 in Genome Data Viewer
    Location:
    3p25.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9385264..9397494, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9377203..9389432, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9426948..9439178, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SLIT-ROBO Rho GTPase activating protein 3 Neighboring gene SRGAP3 antisense RNA 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19402 Neighboring gene phosphoglycerate mutase 1 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19403 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:9444537-9445037 Neighboring gene THUMP domain containing 3 Neighboring gene Sharpr-MPRA regulatory region 11896 Neighboring gene SET domain containing 5 Neighboring gene MPRA-validated peak4533 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9543010-9543735 Neighboring gene Sharpr-MPRA regulatory region 15302 Neighboring gene LHFPL tetraspan subfamily member 4

    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. LncRNA THUMPD3-AS1 enhances the proliferation and inflammatory response of chondrocytes in osteoarthritis. Wang Y, et al. Int Immunopharmacol, 2021 Nov. PMID 34509934
    2. Deletion of 3p25.3 in a patient with intellectual disability and dysmorphic features with further definition of a critical region. Kellogg G, et al. Am J Med Genet A, 2013 Jun. PMID 23613140
    3. Identification and targeting of the ROSA26 locus in human embryonic stem cells. Irion S, et al. Nat Biotechnol, 2007 Dec. PMID 18037879
    4. THUMPD3-AS1 facilitates cell growth and aggressiveness by the miR-218-5p/SKAP1 axis in colorectal cancer. Pu Y, et al. Cell Biochem Biophys, 2022 Sep. PMID 35538197
    5. Identification and Functional Characterization of Two Noncoding RNAs Transcribed from Putative Active Enhancers in Hepatocellular Carcinoma. Lee YE, et al. Mol Cells, 2021 Sep 30. PMID 34588321, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. THUMPD3-AS1 inhibits ovarian cancer cell apoptosis through the miR-320d/ARF1 axis.
      Title: THUMPD3-AS1 inhibits ovarian cancer cell apoptosis through the miR-320d/ARF1 axis.
    2. THUMPD3-AS1 Is Correlated with Gastric Cancer and Regulates Cell Function through miR-1252-3p and CXCL17.
      Title: THUMPD3-AS1 Is Correlated with Gastric Cancer and Regulates Cell Function through miR-1252-3p and CXCL17.
    3. THUMPD3-AS1 facilitates cell growth and aggressiveness by the miR-218-5p/SKAP1 axis in colorectal cancer.
      Title: THUMPD3-AS1 facilitates cell growth and aggressiveness by the miR-218-5p/SKAP1 axis in colorectal cancer.
    4. LncRNA THUMPD3-AS1 enhances the proliferation and inflammatory response of chondrocytes in osteoarthritis.
      Title: LncRNA THUMPD3-AS1 enhances the proliferation and inflammatory response of chondrocytes in osteoarthritis.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Other Names

    • SETD5 antisense RNA 1

    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_027007.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal exon compared to variant 1.
      Source sequence(s)
      AC018506, AI168488, AL110136
      Related
      ENST00000522525.6

    2. NR_132780.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AC018506, AI168488, BC052961, BX953112, HY142091
      Related
      ENST00000481221.8

    3. NR_132781.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses alternate exons at the 5' and 3' ends compared to variant 1.
      Source sequence(s)
      AC018506, AI248388, AW237468, BU621410

    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
      9385264..9397494 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      9377203..9389432 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001013713.1: Suppressed sequence

      Description
      NM_001013713.1: This RefSeq was permanently suppressed because currently support exists for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version

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