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    Thumpd3 THUMP domain containing 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500288, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Thumpd3provided by RGD
    Official Full Name
    THUMP domain containing 3provided by RGD
    Primary source
    RGD:1560852
    See related
    EnsemblRapid:ENSRNOG00000006941 AllianceGenome:RGD:1560852
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1560852
    Summary
    Predicted to enable tRNA (guanine(6)-N2)-methyltransferase activity and tRNA (guanine(7)-N2)-methyltransferase activity. Predicted to be involved in tRNA methylation. Predicted to be located in cytosol and nucleolus. Orthologous to human THUMPD3 (THUMP domain containing 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 170.2), Thymus (RPKM 114.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Thumpd3 in Genome Data Viewer
    Location:
    4q42
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (147741288..147764254)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (146185422..146209802)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (144985850..145010164)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U3 Neighboring gene uncharacterized LOC102548337 Neighboring gene uncharacterized LOC134486622 Neighboring gene U6 spliceosomal RNA Neighboring gene THUMPD3 antisense RNA 1 Neighboring gene SET domain containing 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables tRNA (guanine(6)-N2)-methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables tRNA (guanine(7)-N2)-methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables tRNA (guanine) methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in tRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA methylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    tRNA (guanine(6)-N2)-methyltransferase THUMP3
    Names
    THUMP domain-containing protein 3
    NP_001164017.1
    NP_001164018.1
    NP_001164019.1
    XP_006237111.1
    XP_063142639.1

    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.

    mRNA and Protein(s)

    1. NM_001170546.1 → NP_001164017.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3

      See identical proteins and their annotated locations for NP_001164017.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript. Variants 1-3 encoded the same protein.
      Source sequence(s)
      BC166466, CB800288
      UniProtKB/TrEMBL
      A0A8I6A2Z6, A6IBN8, D3ZSV7
      Related
      ENSRNOP00000089723.2, ENSRNOT00000111842.2
      Conserved Domains (2) summary
      smart00981
      Location:219 → 284
      THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
      pfam01170
      Location:294 → 479
      UPF0020; Putative RNA methylase family UPF0020

    2. NM_001170547.1 → NP_001164018.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3

      See identical proteins and their annotated locations for NP_001164018.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs at the 5' end compared to variant 1. Variants 1-3 encoded the same protein.
      Source sequence(s)
      BC166466, FM092153
      UniProtKB/TrEMBL
      A0A8I6A2Z6, A6IBN8, D3ZSV7
      Related
      ENSRNOP00000086777.2, ENSRNOT00000105716.2
      Conserved Domains (2) summary
      smart00981
      Location:219 → 284
      THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
      pfam01170
      Location:294 → 479
      UPF0020; Putative RNA methylase family UPF0020

    3. NM_001170548.1 → NP_001164019.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3

      See identical proteins and their annotated locations for NP_001164019.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs at the 5' end compared to variant 1. Variants 1-3 encoded the same protein.
      Source sequence(s)
      BC166466, FM120112
      UniProtKB/TrEMBL
      A0A8I6A2Z6, A6IBN8, D3ZSV7
      Conserved Domains (2) summary
      smart00981
      Location:219 → 284
      THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
      pfam01170
      Location:294 → 479
      UPF0020; Putative RNA methylase family UPF0020

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      147741288..147764254
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063286569.1 → XP_063142639.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

      UniProtKB/TrEMBL
      A0A8I6A8S0

    2. XM_006237049.5 → XP_006237111.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      See identical proteins and their annotated locations for XP_006237111.1

      UniProtKB/TrEMBL
      A0A8I6A2Z6, A6IBN8, D3ZSV7
      Conserved Domains (2) summary
      smart00981
      Location:219 → 284
      THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
      pfam01170
      Location:294 → 479
      UPF0020; Putative RNA methylase family UPF0020
    Nucleotide Protein Strain
    Heading Accession and Version

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