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    THUMPD3 THUMP domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 25917, updated on 10-Dec-2024

    Summary

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    Official Symbol
    THUMPD3provided by HGNC
    Official Full Name
    THUMP domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:24493
    See related
    Ensembl:ENSG00000134077 AllianceGenome:HGNC:24493
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables tRNA (guanine(6)-N2)-methyltransferase activity and tRNA (guanine(7)-N2)-methyltransferase activity. Involved in tRNA methylation. Located in cytosol and nucleolus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in testis (RPKM 18.1), thyroid (RPKM 8.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See THUMPD3 in Genome Data Viewer
    Location:
    3p25.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9363054..9386791)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9354825..9378730)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9404738..9428475)

    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 THUMPD3 antisense RNA 1 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 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: 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. THUMPD3-TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates. Yang WQ, et al. Nucleic Acids Res, 2021 Nov 18. PMID 34669960, Free PMC Article
    2. Human TRMT112-Methyltransferase Network Consists of Seven Partners Interacting with a Common Co-Factor. Brūmele B, et al. Int J Mol Sci, 2021 Dec 18. PMID 34948388, Free PMC Article
    3. Proteomic Analysis Reveals a Role for RSK in p120-catenin Phosphorylation and Melanoma Cell-Cell Adhesion. Méant A, et al. Mol Cell Proteomics, 2020 Jan. PMID 31678930, Free PMC Article
    4. Proteomic and Biochemical Comparison of the Cellular Interaction Partners of Human VPS33A and VPS33B. Hunter MR, et al. J Mol Biol, 2018 Jul 6. PMID 29778605, Free PMC Article
    5. A protein interaction framework for human mRNA degradation. Lehner B, et al. Genome Res, 2004 Jul. PMID 15231747, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. THUMPD3-TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates.
      Title: THUMPD3-TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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

    Clone Names

    • DKFZp434F091

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA (guanine(6)-N2)-methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables tRNA (guanine(7)-N2)-methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    tRNA (guanine(6)-N2)-methyltransferase THUMP3
    Names
    THUMP domain-containing protein 3
    NP_001107564.1
    NP_056268.2
    XP_005265078.1
    XP_005265079.1
    XP_005265080.1
    XP_006713149.1
    XP_011531872.1
    XP_016861602.1
    XP_016861603.1
    XP_016861604.1
    XP_016861605.1
    XP_047303885.1
    XP_054202066.1
    XP_054202067.1
    XP_054202068.1
    XP_054202069.1
    XP_054202070.1
    XP_054202071.1
    XP_054202072.1
    XP_054202073.1
    XP_054202074.1
    XP_054202075.1

    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_001114092.2 → NP_001107564.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3

      See identical proteins and their annotated locations for NP_001107564.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC018506, AK001680, AL117483, DA713744
      Consensus CDS
      CCDS2573.1
      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3
      Related
      ENSP00000395893.2, ENST00000452837.7
      Conserved Domains (2) summary
      cd11715
      Location:40 → 286
      THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
      pfam01170
      Location:293 → 478
      UPF0020; Putative RNA methylase family UPF0020

    2. NM_015453.3 → NP_056268.2  tRNA (guanine(6)-N2)-methyltransferase THUMP3

      See identical proteins and their annotated locations for NP_056268.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC018506, AK001680, AL117483, DA713744
      Consensus CDS
      CCDS2573.1
      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3
      Related
      ENSP00000339532.3, ENST00000345094.7
      Conserved Domains (2) summary
      cd11715
      Location:40 → 286
      THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
      pfam01170
      Location:293 → 478
      UPF0020; Putative RNA methylase family UPF0020

    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
      9363054..9386791
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011533570.3 → XP_011531872.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      See identical proteins and their annotated locations for XP_011531872.1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3
      Conserved Domains (2) summary
      cd11715
      Location:40 → 286
      THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
      pfam01170
      Location:293 → 478
      UPF0020; Putative RNA methylase family UPF0020

    2. XM_006713086.4 → XP_006713149.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      See identical proteins and their annotated locations for XP_006713149.1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3
      Conserved Domains (2) summary
      cd11715
      Location:40 → 286
      THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
      pfam01170
      Location:293 → 478
      UPF0020; Putative RNA methylase family UPF0020

    3. XM_017006114.2 → XP_016861603.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    4. XM_005265022.5 → XP_005265079.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      See identical proteins and their annotated locations for XP_005265079.1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3
      Related
      ENSP00000424064.1, ENST00000515662.6
      Conserved Domains (2) summary
      cd11715
      Location:40 → 286
      THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
      pfam01170
      Location:293 → 478
      UPF0020; Putative RNA methylase family UPF0020

    5. XM_005265021.5 → XP_005265078.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      See identical proteins and their annotated locations for XP_005265078.1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3
      Conserved Domains (2) summary
      cd11715
      Location:40 → 286
      THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
      pfam01170
      Location:293 → 478
      UPF0020; Putative RNA methylase family UPF0020

    6. XM_017006113.2 → XP_016861602.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    7. XM_017006115.3 → XP_016861604.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    8. XM_005265023.4 → XP_005265080.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      See identical proteins and their annotated locations for XP_005265080.1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3
      Conserved Domains (2) summary
      cd11715
      Location:40 → 286
      THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
      pfam01170
      Location:293 → 478
      UPF0020; Putative RNA methylase family UPF0020

    9. XM_047447929.1 → XP_047303885.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    10. XM_017006116.3 → XP_016861605.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      9354825..9378730
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346091.1 → XP_054202066.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3

    2. XM_054346094.1 → XP_054202069.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3

    3. XM_054346093.1 → XP_054202068.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3

    4. XM_054346092.1 → XP_054202067.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3

    5. XM_054346098.1 → XP_054202073.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    6. XM_054346099.1 → XP_054202074.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    7. XM_054346100.1 → XP_054202075.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    8. XM_054346097.1 → XP_054202072.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    9. XM_054346096.1 → XP_054202071.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X2

    10. XM_054346095.1 → XP_054202070.1  tRNA (guanine(6)-N2)-methyltransferase THUMP3 isoform X1

      UniProtKB/Swiss-Prot
      Q9BV44, Q9H8V6, Q9NVC1, Q9UFS3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BV44.1 GenPept UniProtKB/Swiss-Prot:Q9BV44

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