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

Gene ID: 25917, updated on 6-Sep-2022

Summary

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

See THUMPD3 in Genome Data Viewer
Location:
3p25.3
Exon count:
10
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9363054..9386791)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9355000..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 phosphoglycerate mutase 1 pseudogene 4 Neighboring gene THUMPD3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 11896 Neighboring gene SET domain containing 5 Neighboring gene Sharpr-MPRA regulatory region 15302 Neighboring gene LHFPL tetraspan subfamily member 4

Genomic regions, transcripts, and products

Expression

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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) methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables tRNA (guanine-N2-)-methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables tRNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in tRNA N2-guanine methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in tRNA methylation IBA
Inferred from Biological aspect of Ancestor
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

Preferred Names
tRNA (guanine(6)-N2)-methyltransferase THUMP3; 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

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_001114092.2NP_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, Q9UFS3
    UniProtKB/TrEMBL
    A0A024R2D3, A0A024R2F4
    Related
    ENSP00000395893.2, ENST00000452837.7
    Conserved Domains (2) summary
    cd11715
    Location:40286
    THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
    pfam01170
    Location:293478
    UPF0020; Putative RNA methylase family UPF0020
  2. NM_015453.3NP_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, Q9UFS3
    UniProtKB/TrEMBL
    A0A024R2D3, A0A024R2F4
    Related
    ENSP00000339532.3, ENST00000345094.7
    Conserved Domains (2) summary
    cd11715
    Location:40286
    THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
    pfam01170
    Location:293478
    UPF0020; Putative RNA methylase family UPF0020

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_011533570.3XP_011531872.1  THUMP domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011531872.1

    UniProtKB/Swiss-Prot
    Q9BV44, Q9UFS3
    UniProtKB/TrEMBL
    A0A024R2D3, A0A024R2F4
    Conserved Domains (2) summary
    cd11715
    Location:40286
    THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
    pfam01170
    Location:293478
    UPF0020; Putative RNA methylase family UPF0020
  2. XM_006713086.4XP_006713149.1  THUMP domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006713149.1

    UniProtKB/Swiss-Prot
    Q9BV44, Q9UFS3
    UniProtKB/TrEMBL
    A0A024R2D3, A0A024R2F4
    Conserved Domains (2) summary
    cd11715
    Location:40286
    THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
    pfam01170
    Location:293478
    UPF0020; Putative RNA methylase family UPF0020
  3. XM_017006114.2XP_016861603.1  THUMP domain-containing protein 3 isoform X2

  4. XM_005265022.5XP_005265079.1  THUMP domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_005265079.1

    UniProtKB/Swiss-Prot
    Q9BV44, Q9UFS3
    UniProtKB/TrEMBL
    A0A024R2D3, A0A024R2F4
    Related
    ENSP00000424064.1, ENST00000515662.6
    Conserved Domains (2) summary
    cd11715
    Location:40286
    THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
    pfam01170
    Location:293478
    UPF0020; Putative RNA methylase family UPF0020
  5. XM_005265021.5XP_005265078.1  THUMP domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_005265078.1

    UniProtKB/Swiss-Prot
    Q9BV44, Q9UFS3
    UniProtKB/TrEMBL
    A0A024R2D3, A0A024R2F4
    Conserved Domains (2) summary
    cd11715
    Location:40286
    THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
    pfam01170
    Location:293478
    UPF0020; Putative RNA methylase family UPF0020
  6. XM_017006113.2XP_016861602.1  THUMP domain-containing protein 3 isoform X2

  7. XM_017006115.3XP_016861604.1  THUMP domain-containing protein 3 isoform X2

  8. XM_005265023.4XP_005265080.1  THUMP domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_005265080.1

    UniProtKB/Swiss-Prot
    Q9BV44, Q9UFS3
    UniProtKB/TrEMBL
    A0A024R2D3, A0A024R2F4
    Conserved Domains (2) summary
    cd11715
    Location:40286
    THUMP_AdoMetMT; THUMP domain associated with S-adenosylmethionine-dependent methyltransferases
    pfam01170
    Location:293478
    UPF0020; Putative RNA methylase family UPF0020
  9. XM_047447929.1XP_047303885.1  THUMP domain-containing protein 3 isoform X2

  10. XM_017006116.3XP_016861605.1  THUMP domain-containing protein 3 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    9355000..9378730
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)