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

Gene ID: 25917, updated on 5-Mar-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
Predicted to enable tRNA (guanine) methyltransferase activity. Predicted to be involved in tRNA methylation. Located in cytosol and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 18.1), thyroid (RPKM 8.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3p25.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9363054..9386791)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9354825..9378730)
105.20220307 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: 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. 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 (35) 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)

Genotypes

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_2023_10

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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