Aliases for THUMPD2 Gene

Aliases for THUMPD2 Gene

  • THUMP Domain Containing 2 2 3 5
  • THUMP Domain-Containing Protein 2 3 4
  • C2orf8 3 4
  • Epididymis Secretory Sperm Binding Protein 3
  • Chromosome 2 Open Reading Frame 8 2
  • SAM-Dependent Methyltransferase 3

External Ids for THUMPD2 Gene

Previous HGNC Symbols for THUMPD2 Gene

  • C2orf8

Previous GeneCards Identifiers for THUMPD2 Gene

  • GC02M039938
  • GC02M039875

Summaries for THUMPD2 Gene

GeneCards Summary for THUMPD2 Gene

THUMPD2 (THUMP Domain Containing 2) is a Protein Coding gene. Diseases associated with THUMPD2 include Retinitis Pigmentosa 11. Gene Ontology (GO) annotations related to this gene include RNA binding and methyltransferase activity. An important paralog of this gene is THUMPD3.

Additional gene information for THUMPD2 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for THUMPD2 Gene

Genomics for THUMPD2 Gene

GeneHancer (GH) Regulatory Elements for THUMPD2 Gene

Promoters and enhancers for THUMPD2 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
GH02J039777 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 779.5 +0.7 675 3.6 ZBTB40 MLX RBPJ POLR2A USF2 MYC NFYC ELF1 L3MBTL2 MAX THUMPD2 lnc-SLC8A1-4 MAP4K3 SOS1 DHX57 SLC8A1-AS1
GH02J039780 Promoter 0.9 Ensembl 765.3 -1.9 -1925 1.2 RBPJ ZNF148 GTF2F1 ZNF316 ZNF24 MAFK MGA CTBP1 ZBTB17 GATAD2A THUMPD2 lnc-SLC8A1-4 SLC8A1-AS1 piR-32214-369
GH02J039118 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 41.5 +656.4 656352 9.8 SIN3A SP1 ZBTB40 CTCF ZBTB6 FOXA1 MLX RBPJ SMARCE1 POLR2A SOS1 THUMPD2 HNRNPLL DHX57 ARHGEF33 SRSF7 TMEM178A RPLP0P6 MAP4K3 CDKL4
GH02J039133 Enhancer 1.3 Ensembl ENCODE dbSUPER 53.1 +640.2 640175 12.2 GATA3 MLX RBPJ SMARCE1 NR2F1 NR2F6 CREB1 MIXL1 CC2D1A HLF THUMPD2 SRSF7 SOS1 DHX57 MAP4K3 ARHGEF33 ASS1P2 ENSG00000273035 hsa-miR-5095-291 ENSG00000202309
GH02J039432 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 26 +342.7 342664 7.6 MLX RBPJ SMARCE1 POLR2A USF2 MIXL1 ZNF133 CC2D1A ELF1 HLF MAP4K3 THUMPD2 DHX57 HNRNPLL RPLP0P6 SRSF7 SOS1 ASS1P2 MAP4K3-DT TMEM178A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around THUMPD2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the THUMPD2 gene promoter:
  • COMP1
  • FOXJ2
  • FOXJ2 (long isoform)
  • FOXL1
  • Lmo2
  • NF-1/L
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • Sox9

Genomic Locations for THUMPD2 Gene

Genomic Locations for THUMPD2 Gene
chr2:39,736,060-39,779,276
(GRCh38/hg38)
Size:
43,217 bases
Orientation:
Minus strand
chr2:39,963,200-40,006,416
(GRCh37/hg19)
Size:
43,217 bases
Orientation:
Minus strand

Genomic View for THUMPD2 Gene

Genes around THUMPD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
THUMPD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for THUMPD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for THUMPD2 Gene

Proteins for THUMPD2 Gene

  • Protein details for THUMPD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BTF0-THUM2_HUMAN
    Recommended name:
    THUMP domain-containing protein 2
    Protein Accession:
    Q9BTF0
    Secondary Accessions:
    • A8K7I7
    • Q53TT8
    • Q53TV0

    Protein attributes for THUMPD2 Gene

    Size:
    503 amino acids
    Molecular mass:
    56433 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH04163.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH13299.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAL26317.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAY14769.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for THUMPD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for THUMPD2 Gene

Post-translational modifications for THUMPD2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for THUMPD2 Gene

Domains & Families for THUMPD2 Gene

Gene Families for THUMPD2 Gene

Protein Domains for THUMPD2 Gene

Suggested Antigen Peptide Sequences for THUMPD2 Gene

GenScript: Design optimal peptide antigens:
  • THUMP domain containing 2, isoform CRA_b (D6W593_HUMAN)
  • THUMP domain-containing protein 2 (THUM2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BTF0

UniProtKB/Swiss-Prot:

THUM2_HUMAN :
  • Belongs to the methyltransferase superfamily.
Family:
  • Belongs to the methyltransferase superfamily.
genes like me logo Genes that share domains with THUMPD2: view

Function for THUMPD2 Gene

Phenotypes From GWAS Catalog for THUMPD2 Gene

Gene Ontology (GO) - Molecular Function for THUMPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0008168 methyltransferase activity IEA --
GO:0016423 tRNA (guanine) methyltransferase activity IBA 21873635
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with THUMPD2: view
genes like me logo Genes that share phenotypes with THUMPD2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for THUMPD2

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for THUMPD2 Gene

Localization for THUMPD2 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 THUMPD2 gene
Compartment Confidence
nucleus 1
cytosol 1
mitochondrion 0
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for THUMPD2 Gene

Pathways & Interactions for THUMPD2 Gene

PathCards logo

SuperPathways for THUMPD2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for THUMPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030488 tRNA methylation IBA 21873635
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with THUMPD2: view

No data available for Pathways by source and SIGNOR curated interactions for THUMPD2 Gene

Drugs & Compounds for THUMPD2 Gene

(1) Additional Compounds for THUMPD2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with THUMPD2: view

Transcripts for THUMPD2 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for THUMPD2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for THUMPD2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c
SP1: -
SP2: - -
SP3: -
SP4:

Relevant External Links for THUMPD2 Gene

GeneLoc Exon Structure for
THUMPD2
ECgene alternative splicing isoforms for
THUMPD2

Expression for THUMPD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for THUMPD2 Gene

Protein differential expression in normal tissues from HIPED for THUMPD2 Gene

This gene is overexpressed in Prostate (24.7), CD4 Tcells (21.1), and Ovary (13.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for THUMPD2 Gene



NURSA nuclear receptor signaling pathways regulating expression of THUMPD2 Gene:

THUMPD2

SOURCE GeneReport for Unigene cluster for THUMPD2 Gene:

Hs.468254

mRNA Expression by UniProt/SwissProt for THUMPD2 Gene:

Q9BTF0-THUM2_HUMAN
Tissue specificity: Expressed in a variety of tissues including brain, colon, gingiva, heart, kidney, liver, lung, placenta, small intestine, spleen and thymus.

Evidence on tissue expression from TISSUES for THUMPD2 Gene

  • Intestine(4.2)
  • Muscle(4.2)
genes like me logo Genes that share expression patterns with THUMPD2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for THUMPD2 Gene

Orthologs for THUMPD2 Gene

This gene was present in the common ancestor of animals.

Orthologs for THUMPD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia THUMPD2 33 32
  • 99.47 (n)
OneToOne
dog
(Canis familiaris)
Mammalia THUMPD2 33 32
  • 87.56 (n)
OneToOne
cow
(Bos Taurus)
Mammalia THUMPD2 33 32
  • 83.8 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Thumpd2 17 33 32
  • 77 (n)
rat
(Rattus norvegicus)
Mammalia Thumpd2 32
  • 74.67 (n)
oppossum
(Monodelphis domestica)
Mammalia THUMPD2 33
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia THUMPD2 33
  • 59 (a)
OneToOne
chicken
(Gallus gallus)
Aves THUMPD2 33 32
  • 63.69 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia THUMPD2 33
  • 48 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia thumpd2 32
  • 56.54 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.7066 32
zebrafish
(Danio rerio)
Actinopterygii thumpd2 33 32
  • 53.18 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea M04B2.2 33
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 24 (a)
OneToMany
Species where no ortholog for THUMPD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 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 THUMPD2 Gene

ENSEMBL:
Gene Tree for THUMPD2 (if available)
TreeFam:
Gene Tree for THUMPD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for THUMPD2: view image

Paralogs for THUMPD2 Gene

Paralogs for THUMPD2 Gene

genes like me logo Genes that share paralogs with THUMPD2: view

Variants for THUMPD2 Gene

Sequence variations from dbSNP and Humsavar for THUMPD2 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000007173 -- 39,755,167(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000011613 -- 39,778,648(-) C/A/T intron_variant
rs1000116185 -- 39,773,738(-) T/C intron_variant
rs1000126630 -- 39,741,522(-) A/C genic_downstream_transcript_variant, intron_variant
rs1000134730 -- 39,761,155(-) T/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for THUMPD2 Gene

Variant ID Type Subtype PubMed ID
esv3590439 CNV loss 21293372
nsv2696 CNV deletion 18451855
nsv833870 CNV gain 17160897
nsv833881 CNV loss 17160897

Variation tolerance for THUMPD2 Gene

Residual Variation Intolerance Score: 26% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.32; 53.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for THUMPD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
THUMPD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for THUMPD2 Gene

Disorders for THUMPD2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for THUMPD2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 11
  • rp11
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for THUMPD2

genes like me logo Genes that share disorders with THUMPD2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for THUMPD2 Gene

Publications for THUMPD2 Gene

  1. Localization, genomic organization, and alternative transcription of a novel human SAM-dependent methyltransferase gene on chromosome 2p22-->p21. (PMID: 12063391) Zhang Y … Hart TC (Cytogenetics and cell genetics 2001) 2 3 4 23 56
  2. Genome-wide association scan for five major dimensions of personality. (PMID: 18957941) Terracciano A … Costa PT (Molecular psychiatry 2010) 3 43 56
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  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 56
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 56

Products for THUMPD2 Gene

Sources for THUMPD2 Gene