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Aliases for THUMPD1 Gene

Aliases for THUMPD1 Gene

  • THUMP Domain Containing 1 2 3 5
  • THUMP Domain-Containing Protein 1 3
  • TAN1 3

External Ids for THUMPD1 Gene

Previous GeneCards Identifiers for THUMPD1 Gene

  • GC16M020711
  • GC16M020652
  • GC16M020744
  • GC16M019280

Summaries for THUMPD1 Gene

GeneCards Summary for THUMPD1 Gene

THUMPD1 (THUMP Domain Containing 1) is a Protein Coding gene. Among its related pathways are Gene Expression and rRNA processing in the nucleus and cytosol. Gene Ontology (GO) annotations related to this gene include RNA binding.

UniProtKB/Swiss-Prot for THUMPD1 Gene

  • Functions as a tRNA-binding adapter to mediate NAT10-dependent tRNA acetylation (PubMed:25653167).

Additional gene information for THUMPD1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for THUMPD1 Gene

Genomics for THUMPD1 Gene

GeneHancer (GH) Regulatory Elements for THUMPD1 Gene

Promoters and enhancers for THUMPD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I020739 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 +1.0 1027 2.8 PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 THUMPD1 ACSM3 ACSM1 PIR32517
GH16I020896 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 24.9 -160.6 -160572 11.5 CLOCK DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC MEF2D GLIS1 DCUN1D3 LYRM1 THUMPD1 ACSM3 SMG1P3 ACSM1 CRYM ERI2 PIR35456 GC16P020829
GH16I021517 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 33.9 -778.1 -778145 4.7 HDGF PKNOX1 CLOCK FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 SMG1P3 SLC7A5P2 THUMPD1 RRN3P1 NPIPB4 NPIPB3 NPIPB5 C16orf52 SMG1P1 ENSG00000260635
GH16I020743 Enhancer 1.4 Ensembl ENCODE dbSUPER 26.8 -4.0 -4000 4.3 HDGF PKNOX1 SMAD1 FOXA2 ARNT ZNF766 CBX5 ZNF143 FOS ZC3H11A THUMPD1 ACSM3 NPIPB3 SMG1P3 REXO5 ERI2 GC16P020744 ENSG00000260510
GH16I020762 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 17 -23.0 -22982 4.5 HDGF PKNOX1 SMAD1 ARID4B SIN3A YBX1 IRF4 YY1 ZNF280A SLC30A9 ACSM3 ENSG00000260510 THUMPD1 SMG1P3 NPIPB3 REXO5 GC16P020744
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around THUMPD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the THUMPD1 gene promoter:

Genomic Locations for THUMPD1 Gene

Genomic Locations for THUMPD1 Gene
chr16:20,702,816-20,742,084
(GRCh38/hg38)
Size:
39,269 bases
Orientation:
Minus strand
chr16:20,744,986-20,753,406
(GRCh37/hg19)

Genomic View for THUMPD1 Gene

Genes around THUMPD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
THUMPD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for THUMPD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for THUMPD1 Gene

Proteins for THUMPD1 Gene

  • Protein details for THUMPD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NXG2-THUM1_HUMAN
    Recommended name:
    THUMP domain-containing protein 1
    Protein Accession:
    Q9NXG2
    Secondary Accessions:
    • Q9BWC3

    Protein attributes for THUMPD1 Gene

    Size:
    353 amino acids
    Molecular mass:
    39315 Da
    Quaternary structure:
    • Interacts with NAT10 (PubMed:25653167).

    Three dimensional structures from OCA and Proteopedia for THUMPD1 Gene

neXtProt entry for THUMPD1 Gene

Post-translational modifications for THUMPD1 Gene

  • Ubiquitination at posLast=1515, posLast=178178, isoforms=189, and isoforms=254
  • Modification sites at PhosphoSitePlus

Other Protein References for THUMPD1 Gene

No data available for DME Specific Peptides for THUMPD1 Gene

Domains & Families for THUMPD1 Gene

Gene Families for THUMPD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for THUMPD1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for THUMPD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NXG2

UniProtKB/Swiss-Prot:

THUM1_HUMAN :
  • Belongs to the THUMPD1 family.
Family:
  • Belongs to the THUMPD1 family.
genes like me logo Genes that share domains with THUMPD1: view

Function for THUMPD1 Gene

Molecular function for THUMPD1 Gene

UniProtKB/Swiss-Prot Function:
Functions as a tRNA-binding adapter to mediate NAT10-dependent tRNA acetylation (PubMed:25653167).

Phenotypes From GWAS Catalog for THUMPD1 Gene

Gene Ontology (GO) - Molecular Function for THUMPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA --
GO:0005515 protein binding IPI 25653167
genes like me logo Genes that share ontologies with THUMPD1: view
genes like me logo Genes that share phenotypes with THUMPD1: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for THUMPD1 Gene

Localization for THUMPD1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for THUMPD1 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for THUMPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with THUMPD1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for THUMPD1 Gene

Pathways & Interactions for THUMPD1 Gene

genes like me logo Genes that share pathways with THUMPD1: view

Pathways by source for THUMPD1 Gene

Gene Ontology (GO) - Biological Process for THUMPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000154 rRNA modification TAS --
GO:0006400 tRNA modification IBA --
genes like me logo Genes that share ontologies with THUMPD1: view

No data available for SIGNOR curated interactions for THUMPD1 Gene

Drugs & Compounds for THUMPD1 Gene

No Compound Related Data Available

Transcripts for THUMPD1 Gene

Unigene Clusters for THUMPD1 Gene

THUMP domain containing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for THUMPD1 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b · 5c · 5d ^ 6
SP1: - - - -
SP2: - - -
SP3: -
SP4:
SP5:
SP6:
SP7: -

Relevant External Links for THUMPD1 Gene

GeneLoc Exon Structure for
THUMPD1
ECgene alternative splicing isoforms for
THUMPD1

Expression for THUMPD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for THUMPD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for THUMPD1 Gene

This gene is overexpressed in Nasal epithelium (16.5) and Heart (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for THUMPD1 Gene



Protein tissue co-expression partners for THUMPD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of THUMPD1 Gene:

THUMPD1

SOURCE GeneReport for Unigene cluster for THUMPD1 Gene:

Hs.700004

Evidence on tissue expression from TISSUES for THUMPD1 Gene

  • Lung(4.5)
  • Liver(4.3)
  • Nervous system(4.3)
  • Blood(4.1)
  • Kidney(2)
genes like me logo Genes that share expression patterns with THUMPD1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for THUMPD1 Gene

Orthologs for THUMPD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for THUMPD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia THUMPD1 33 34
  • 99.53 (n)
cow
(Bos Taurus)
Mammalia THUMPD1 33 34
  • 90.34 (n)
dog
(Canis familiaris)
Mammalia THUMPD1 33 34
  • 90.22 (n)
mouse
(Mus musculus)
Mammalia Thumpd1 33 16 34
  • 85.62 (n)
rat
(Rattus norvegicus)
Mammalia Thumpd1 33
  • 85.23 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 74 (a)
OneToMany
-- 34
  • 74 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia THUMPD1 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves THUMPD1 33 34
  • 72.47 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 64 (a)
OneToMany
-- 34
  • 61 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia thumpd1 33
  • 70.11 (n)
MGC75804 33
zebrafish
(Danio rerio)
Actinopterygii thumpd1 33 34
  • 55.84 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007705 33
  • 49.73 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG15014 33 34
  • 48.53 (n)
worm
(Caenorhabditis elegans)
Secernentea W02G9.3 34
  • 17 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TAN1 34 36
  • 28 (a)
OneToOne
Species where no ortholog for THUMPD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for THUMPD1 Gene

ENSEMBL:
Gene Tree for THUMPD1 (if available)
TreeFam:
Gene Tree for THUMPD1 (if available)

Paralogs for THUMPD1 Gene

(1) SIMAP similar genes for THUMPD1 Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for THUMPD1 Gene

genes like me logo Genes that share paralogs with THUMPD1: view

No data available for Paralogs for THUMPD1 Gene

Variants for THUMPD1 Gene

Sequence variations from dbSNP and Humsavar for THUMPD1 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000186685 -- 20,732,465(-) G/T genic_downstream_transcript_variant, intron_variant
rs1000689950 -- 20,741,796(-) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, upstream_transcript_variant
rs1000993929 -- 20,741,027(-) G/C intron_variant
rs1001526043 -- 20,740,787(-) AAAA/AA intron_variant
rs1001570022 -- 20,741,435(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for THUMPD1 Gene

Variant ID Type Subtype PubMed ID
nsv1047581 CNV loss 25217958
nsv436835 CNV insertion 17901297
nsv833165 CNV loss 17160897

Variation tolerance for THUMPD1 Gene

Residual Variation Intolerance Score: 66.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.83; 67.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for THUMPD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
THUMPD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for THUMPD1 Gene

Disorders for THUMPD1 Gene

Additional Disease Information for THUMPD1

No disorders were found for THUMPD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for THUMPD1 Gene

Publications for THUMPD1 Gene

  1. Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. (PMID: 25653167) Sharma S … Lafontaine DL (Nucleic acids research 2015) 2 3 4 58
  2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PMID: 10493829) Loftus BJ … Adams MD (Genomics 1999) 3 4 58

Products for THUMPD1 Gene

Sources for THUMPD1 Gene

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