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THUMPD2 Gene

protein-coding   GIFtS: 49
GCID: GC02M039875

THUMP Domain Containing 2

(Previous name: chromosome 2 open reading frame 8)
(Previous symbol: C2orf8)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
THUMP Domain Containing 21 2
C2orf81 2 3 5
Chromosome 2 Open Reading Frame 81
SAM-Dependent Methyltransferase2
THUMP Domain-Containing Protein 22

External Ids:    HGNC: 148901   Entrez Gene: 807452   Ensembl: ENSG000001380507   OMIM: 6117515   UniProtKB: Q9BTF03   

Export aliases for THUMPD2 gene to outside databases

Previous GC identifers: GC02M039938 GC02M039702


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for THUMPD2 Gene:
THUMPD2 (THUMP domain containing 2) is a protein-coding gene. GO annotations related to this gene include methyltransferase activity and RNA binding. An important paralog of this gene is THUMPD3.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_022184.16  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the THUMPD2 gene promoter:
         NF-1/L   Lmo2   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   FOXL1   COMP1   FOXJ2 (long isoform)   Sox9   FOXJ2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTHUMPD2 promoter sequence
   Search Chromatin IP Primers for THUMPD2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat THUMPD2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2p22.1|2p22-p21   Ensembl cytogenetic band:  2p22.1   HGNC cytogenetic band: 2p22.2

THUMPD2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
THUMPD2 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M039875:  view genomic region     (about GC identifiers)

Start:
39,963,200 bp from pter      End:
40,006,416 bp from pter
Size:
43,217 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: THUM2_HUMAN, Q9BTF0 (See protein sequence)
Recommended Name: THUMP domain-containing protein 2  
Size: 503 amino acids; 56433 Da
Sequence caution: Sequence=AAH04163.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAH13299.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAL26317.1;
Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAY14769.1; Type=Erroneous
initiation; Note=Translation N-terminally extended;
Secondary accessions: A8K7I7 Q53TT8 Q53TV0
Alternative splicing: 2 isoforms:  Q9BTF0-1   Q9BTF0-2   

Explore the universe of human proteins at neXtProt for THUMPD2: NX_Q9BTF0

Explore proteomics data for THUMPD2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See THUMPD2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_079540.2  
    ENSEMBL proteins: 
     ENSP00000423933   ENSP00000368001   ENSP00000434844   ENSP00000426202   ENSP00000260619  
     ENSP00000392122  

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    Cloud-Clone Corp. Proteins for THUMPD2

     
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR004114 THUMP
     IPR000241 RNA_methylase_dom

    Graphical View of Domain Structure for InterPro Entry Q9BTF0

    ProtoNet protein and cluster: Q9BTF0

    1 Blocks protein domain: IPB000241 Putative RNA methylase

    UniProtKB/Swiss-Prot: THUM2_HUMAN, Q9BTF0
    Similarity: Belongs to the methyltransferase superfamily
    Similarity: Contains 1 THUMP domain


    Find genes that share domains with THUMPD2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding IEA--
    GO:0008168methyltransferase activity IEA--
         
    Find genes that share ontologies with THUMPD2           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for THUMPD2:
     Decreased viability of wild-ty 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for THUMPD2
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    hsa-miR-587 hsa-miR-889 hsa-miR-3647-3p
    SwitchGear 3'UTR luciferase reporter plasmidTHUMPD2 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    mitochondrion1
    peroxisome1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for THUMPD2
    Interactions:

        Search GeneGlobe Interaction Network for THUMPD2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 14)

    Selected Interacting proteins for THUMPD2 (ENSP000002606194) via UniProtKB, MINT, STRING, and/or I2D (see all 14)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TRMT112ENSP000003094334STRING: ENSP00000309433
    GET4ENSP000002658574STRING: ENSP00000265857
    ALKBH8ENSP000003742194STRING: ENSP00000374219
    NSUN2ENSP000002646704STRING: ENSP00000264670
    NSUN3ENSP000003189864STRING: ENSP00000318986
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008152metabolic process ----

    Find genes that share ontologies with THUMPD2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for THUMPD2 (THUM2)

    1 Novoseek inferred chemical compound relationship for THUMPD2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    s-adenosylmethionine 80 11 19815105 (2), 12837779 (2), 14556746 (2), 20196537 (1) (see all 6)



    Find genes that share compounds with THUMPD2           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for THUMPD2 gene: 
    NM_025264.4  

    Unigene Cluster for THUMPD2:

    THUMP domain containing 2
    Hs.468254  [show with all ESTs]
    Unigene Representative Sequence: AF380578
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000460072 ENST00000505747(uc002rru.2 uc010ynt.1) ENST00000378727(uc002rrv.2)
    ENST00000530522 ENST00000530095 ENST00000510781 ENST00000527689 ENST00000403537
    ENST00000531687 ENST00000260619 ENST00000454352(uc010ynu.1)
    miRNA
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    3 qRT-PCR Assays for microRNAs that regulate THUMPD2:
    hsa-miR-587 hsa-miR-889 hsa-miR-3647-3p
    SwitchGear 3'UTR luciferase reporter plasmidTHUMPD2 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat THUMPD2
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      QuantiTect SYBR Green Assays in human, mouse, rat THUMPD2
      QuantiFast Probe-based Assays in human, mouse, rat THUMPD2

    Additional mRNA sequence: 

    AF380577.1 AF380578.1 AF380579.1 AK057801.1 AK093580.1 AK226034.1 AK292002.1 AK298178.1 
    AK301353.1 AK307754.1 AL832115.1 BC004163.2 BC013299.2 NR_028102.1 

    7 DOTS entries:

    DT.120962574  DT.120962513  DT.97779810  DT.454131  DT.100754250  DT.40130652  DT.95271775 

    Selected AceView cDNA sequences (see all 96):

    C06360 AA708774 CB130552 BM711553 AA708517 AA689584 BM665468 AA088201 
    BC013299 AF380578 AI694271 NM_025264 AX748213 BC004163 CA848676 AK093580 
    BX644806 AA496778 AA496721 AI193198 AF380577 BQ016108 AA258999 AI278104 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for THUMPD2    About this scheme

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


    ECgene alternative splicing isoforms for THUMPD2

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    THUMPD2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTTGGTAAGA
    THUMPD2 Expression
    About this image

    THUMPD2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    THUMPD2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.468254

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

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for THUMPD2

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for THUMPD2 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Thumpd21 , 5 THUMP domain containing 21, 5 77(n)1
    69.2(a)1
      17 (51.04 cM)5
    721671  NM_028138.11  NP_082414.11 
     810263275 
    chicken
    (Gallus gallus)
    Aves THUMPD21 THUMP domain containing 2 63.69(n)
    56.13(a)
      421310  XM_004935287.1  XP_004935344.1 
    lizard
    (Anolis carolinensis)
    Reptilia THUMPD26
    THUMP domain containing 2
    48(a)
    1 ↔ 1
    1(253711497-253740258)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.70662 Xenopus laevis transcribed sequence with weak similarity more 72.88(n)    BJ057674.1 
    zebrafish
    (Danio rerio)
    Actinopterygii thumpd21 THUMP domain containing 2 53.18(n)
    42.35(a)
      562797  XM_686171.4  XP_691263.4 
    worm
    (Caenorhabditis elegans)
    Secernentea M04B2.26
    Protein M04B2.2 (M04B2.2) mRNA, complete cds
    22(a)
    1 → many
    IV(11528056-11530632) WBGene00010846


    ENSEMBL Gene Tree for THUMPD2 (if available)
    TreeFam Gene Tree for THUMPD2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for THUMPD2 gene
    THUMPD32  

    Find genes that share paralogs with THUMPD2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for THUMPD2 (see all 998)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1444096911,2
    C--39962723(+) AGTAAC/TGAATT 2 -- ds50010--------
    rs170242781,2
    C,F,H--39962778(+) TCTCCA/GTTATC 2 -- ds500119Minor allele frequency- G:0.06NA NS EA WA 1882
    rs1889039721,2
    --39962963(+) AAGATC/TGCTTT 2 -- ds50010--------
    rs1487148421,2
    C--39962964(+) AGATCA/GCTTTG 2 -- ds50010--------
    rs1422982991,2
    --39963069(+) TGACTC/TCTGCT 2 -- ds50010--------
    rs46709551,2
    C,F,A,H--39963122(+) CAAAGT/CTGTTC 2 -- ds500120Minor allele frequency- C:0.44NA NS EA WA CSA 2346
    rs1931028241,2
    --39963185(+) AACATC/TAAACC 2 -- ds50010--------
    rs170242821,2
    C,F,H--39963273(+) AAATAA/CGGGCG 2 -- ut31 nc-transcript-variant9Minor allele frequency- C:0.04NA NS EA WA 682
    rs1508386301,2
    --39963277(+) AAGGGC/TGAGGT 2 -- ut31 nc-transcript-variant0--------
    rs1399877721,2
    C--39963293(+) TGTATC/GAATGC 2 -- ut31 nc-transcript-variant0--------

    HapMap Linkage Disequilibrium report for THUMPD2 (39963200 - 40006416 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for THUMPD2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv2696CNV Loss18451855
    nsv833881CNV Loss17160897
    nsv873890CNV Gain21882294
    nsv833870CNV Gain17160897

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing THUMPD2
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 611751    OMIM disorders: --

    1 disease from the University of Copenhagen DISEASES database for THUMPD2:
    Vitamin B12 deficiency

    Find genes that share disorders with THUMPD2           About GenesLikeMe

    Genetic Association Database (GAD): THUMPD2

    Export disorders for THUMPD2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for THUMPD2 gene, integrated from 10 sources (see all 19):
    (articles sorted by number of sources associating them with THUMPD2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Localization, genomic organization, and alternative transcription of a novel human SAM-dependent methyltransferase gene on chromosome 2p22-->p21. (PubMed id 12063391)1, 2, 3, 9 Zhang Y.... Hart T.C. (Cytogenet. Cell Genet. 2001)
    2. Genome-wide association scan for five major dimensions of personality. (PubMed id 18957941)1, 4 Terracciano A....Costa P.T. (Mol. Psychiatry 2010)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    6. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    7. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
    8. Genome-wide association with select biomarker traits in the Framingham Heart Study. (PubMed id 17903293)4 Benjamin E.J....Vasan R.S. (BMC Med. Genet. 2007)
    9. Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. (PubMed id 17903301)4 Vasan R.S....Benjamin E.J. (BMC Med. Genet. 2007)
    10. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W.... Wilson R.K. (Nature 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 80745 HGNC: 14890 AceView: THUMPD2 Ensembl:ENSG00000138050 euGenes: HUgn80745
    ECgene: THUMPD2 H-InvDB: THUMPD2

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for THUMPD2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for THUMPD2 gene:
    Search GeneIP for patents involving THUMPD2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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