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TRMT10A Gene

protein-coding   GIFtS: 40
GCID: GC04M100468

TRNA Methyltransferase 10 Homolog A (S. Cerevisiae)

(Previous name: RNA (guanine-9-) methyltransferase domain containing 2)
(Previous symbol: RG9MTD2)
  See related diseases
at  

(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
TRNA Methyltransferase 10 Homolog A (S. Cerevisiae)1 2     TRM102
RG9MTD21 2 3     Epididymis Secretory Protein Li 882
RNA (Guanine-9-) Methyltransferase Domain Containing 21 2     TRNA Methyltransferase 10 Homolog A2
RNA (Guanine-9-)-Methyltransferase Domain-Containing Protein 22 3     EC 2.1.1.-3
HEL-S-882     

External Ids:    HGNC: 284031   Entrez Gene: 935872   Ensembl: ENSG000001453317   UniProtKB: Q8TBZ63   

Export aliases for TRMT10A gene to outside databases


(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 TRMT10A Gene:
TRMT10A (tRNA methyltransferase 10 homolog A (S. cerevisiae)) is a protein-coding gene. Diseases associated with TRMT10A include primary microcephaly-mild intellectual disability-young-onset diabetes syndrome, and breast and colorectal cancer. GO annotations related to this gene include methyltransferase activity. An important paralog of this gene is TRMT10C.

UniProtKB/Swiss-Prot: TM10A_HUMAN, Q8TBZ6
Function: Probable RNA methyltransferase (By similarity)




(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:
NC_000004.12  NT_016354.20  NC_018915.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for TRMT10A
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTRMT10A promoter sequence
   Search Chromatin IP Primers for TRMT10A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TRMT10A


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

Entrez Gene cytogenetic band: 4q23   Ensembl cytogenetic band:  4q23   HGNC cytogenetic band: 4q23

TRMT10A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRMT10A gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M100468:  view genomic region     (about GC identifiers)

Start:
100,467,864 bp from pter      End:
100,485,189 bp from pter
Size:
17,326 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., 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: TM10A_HUMAN, Q8TBZ6 (See protein sequence)
Recommended Name: tRNA methyltransferase 10 homolog A  
Size: 339 amino acids; 39719 Da
1 PDB 3D structure from and Proteopedia for TRMT10A:
4FMW (3D)    
Secondary accessions: B2R8X7 Q9Y2T9

Explore the universe of human proteins at neXtProt for TRMT10A: NX_Q8TBZ6

Explore proteomics data for TRMT10A at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See TRMT10A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001128137.1  NP_001128138.1  NP_689505.1  

    ENSEMBL proteins: 
     ENSP00000378343   ENSP00000273962   ENSP00000378342   ENSP00000397551   ENSP00000423628  

    TRMT10A Human Recombinant Protein Products:

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    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR028564 MT_TRM10-typ
     IPR016009 tRNA_MeTrfase
     IPR007356 tRNA_m1G_MeTrfase_euk
     IPR016653 tRNA_MeTfrase_TRM10

    Graphical View of Domain Structure for InterPro Entry Q8TBZ6

    ProtoNet protein and cluster: Q8TBZ6

    UniProtKB/Swiss-Prot: TM10A_HUMAN, Q8TBZ6
    Similarity: Belongs to the class IV-like SAM-binding methyltransferase superfamily. TRM10 family
    Similarity: Contains 1 SAM-dependent MTase TRM10-type domain


    TRMT10A for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TM10A_HUMAN, Q8TBZ6
    Function: Probable RNA methyltransferase (By similarity)

         Enzyme Number (IUBMB): EC 2.1.1.-1

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0008168methyltransferase activity IEA--
    GO:0044822poly(A) RNA binding IDA--
         
    TRMT10A for ontologies           About GeneDecksing


    Phenotypes:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Trmt10a):
     homeostasis/metabolism 

    TRMT10A for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TRMT10A
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for TRMT10A
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for TRMT10A

    miRNA
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    miRTarBase miRNAs that target TRMT10A:
    hsa-mir-375 (MIRT019687)

    Block miRNA regulation of human, mouse, rat TRMT10A using miScript Target Protectors
    Search for qRT-PCR Assays for microRNAs that regulate TRMT10A
    SwitchGear 3'UTR luciferase reporter plasmidTRMT10A 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat TRMT10A

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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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    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0070062extracellular vesicular exosome IDA19056867

    TRMT10A for ontologies           About GeneDecksing


    (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 TRMT10A
    Interactions:

        Search GeneGlobe Interaction Network for TRMT10A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 22)

    Selected Interacting proteins for TRMT10A (Q8TBZ63 ENSP000002739624) via UniProtKB, MINT, STRING, and/or I2D (see all 38)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ADAT2Q7Z6V53, ENSP000002372834I2D: score=1 STRING: ENSP00000237283
    PUS1Q9Y6063, ENSP000003658374I2D: score=1 STRING: ENSP00000365837
    XPOTO435923, ENSP000003278214I2D: score=1 STRING: ENSP00000327821
    METTL1Q9UBP63, ENSP000003144414I2D: score=2 STRING: ENSP00000314441
    TRMT1Q9NXH93, ENSP000003503524I2D: score=1 STRING: ENSP00000350352
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    TRMT10A for ontologies           About GeneDecksing



    (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 TRMT10A (TM10A)



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for TRMT10A gene (3 alternative transcripts): 
    NM_001134665.1  NM_001134666.1  NM_152292.4  

    Unigene Cluster for TRMT10A:

    TRNA methyltransferase 10 homolog A (S. cerevisiae)
    Hs.380412  [show with all ESTs]
    Unigene Representative Sequence: NM_152292
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000394877(uc003huz.4 uc003hva.4) ENST00000273962(uc003huy.3)
    ENST00000394876 ENST00000455368 ENST00000514547 ENST00000515831 ENST00000507394

    miRNA
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    Block miRNA regulation of human, mouse, rat TRMT10A using miScript Target Protectors
    Search for qRT-PCR Assays for microRNAs that regulate TRMT10A
    SwitchGear 3'UTR luciferase reporter plasmidTRMT10A 3' UTR sequence
    Inhib. RNA
    Products:
         
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    Predesigned siRNA for gene silencing in human, mouse, rat TRMT10A
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    Primer
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    OriGene qPCR primer pairs and template standards for TRMT10A
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      QuantiTect SYBR Green Assays in human, mouse, rat TRMT10A
      QuantiFast Probe-based Assays in human, mouse, rat TRMT10A

    Additional mRNA sequence: 

    AF106046.1 AK000332.1 AK313548.1 BC028373.2 

    7 DOTS entries:

    DT.102825271  DT.108302  DT.92424319  DT.92032782  DT.97818017  DT.100702267  DT.86836828 

    Selected AceView cDNA sequences (see all 93):

    AA330454 AI627530 BQ721850 AA983872 AA305933 AW594250 BF433159 BM464705 
    CR598836 AA329639 AI372956 AA987337 BC028373 NM_152292 CR623954 BE671949 
    AI167459 BQ000156 AA434121 AA252654 CR598027 BX432957 AW500761 AL556159 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for TRMT10A    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8
    SP1:                                                                                          
    SP2:                                                                                          
    SP3:                    -                                                                     
    SP4:                    -     -                                                               
    SP5:                          -                                                               


    ECgene alternative splicing isoforms for TRMT10A

    (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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    TRMT10A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    TRMT10A Expression
    About this image

    TRMT10A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TRMT10A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.380412
        Custom PCR Arrays for TRMT10A
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRMT10A

    (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 and fungi.

    Orthologs for TRMT10A gene from Selected species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Trmt10a1 , 5 RNA (guanine-9-) methyltransferase domain containing more5
    tRNA methyltransferase 10A1
    81.22(n)1
    78.64(a)1
      3 (64.09 cM)5
    1089431  NM_175389.41  NP_780598.21 
     1381434485 
    chicken
    (Gallus gallus)
    Aves TRMT10A1 tRNA methyltransferase 10 homolog A (S. cerevisiae) 75.69(n)
    78.82(a)
      422708  XM_001234300.3  XP_001234301.2 
    lizard
    (Anolis carolinensis)
    Reptilia TRMT10A6
    tRNA methyltransferase 10 homolog A (S. cerevisiae...
    63(a)
    1 ↔ 1
    GL343323.1(1194141-1205815)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.150282 Xenopus laevis transcribed sequence with weak similarity more 77.41(n)    BJ078621.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5602221 RNA (guanine-9-)-methyltransferase domain-containing more 64.58(n)
    66.55(a)
      560222  XM_683615.3  XP_688707.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG146181 CG14618 43.51(n)
    37.66(a)
      33134  NM_134620.4  NP_608464.1 
    worm
    (Caenorhabditis elegans)
    Secernentea F25H8.11 F25H8.1 53.48(n)
    42.78(a)
      177847  NM_001129301.2  NP_001122773.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes TRM10(YOL093W)4
    TRM101
    tRNA methyltransferase, methylates the N-1 position more4
    TRM101
    45.16(n)1
    33.96(a)1
      15(142815-143696)4
    8540601, 4  NP_014548.11, 4 


    ENSEMBL Gene Tree for TRMT10A (if available)
    TreeFam Gene Tree for TRMT10A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TRMT10A gene
    TRMT10C2  TRMT10B2  

    TRMT10A for paralogs           About GeneDecksing



    (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 TRMT10A (see all 300)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0372224
    A breast cancer sample4--see VAR_0372222 P Q mis40--------
    rs800994091,2
    C,F--100467462(+) AAATCT/CCTACC 3 -- int11Minor allele frequency- C:0.03WA 118
    rs105546161,2
    C--100467474(+) TTCTC-/CTTT  
            
    CTTTC
    3 -- int10--------
    rs1827985651,2
    --100467550(+) TTTTAC/TCTACA 3 -- int10--------
    rs65328201,2
    C,F,A,H--100467622(+) CCAGTC/TACTGC 3 -- int133Minor allele frequency- T:0.40NA NS EA WA CSA 3262
    rs1427580681,2
    --100467641(+) ATCATC/TGTTCA 3 -- int10--------
    rs1878822971,2
    --100467743(+) CAACAA/GCACCA 3 -- int10--------
    rs1923525421,2
    --100467785(+) TTCTCC/TTAAGA 3 -- int10--------
    rs1829460221,2
    --100467807(+) TTATGA/TTCACT 3 -- int10--------
    rs110976671,2
    C,F,H--100467808(+) TATGAT/ACACTG 3 -- int129Minor allele frequency- A:0.26NS EA NA WA CSA 2908

    HapMap Linkage Disequilibrium report for TRMT10A (100467864 - 100485189 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for TRMT10A: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing TRMT10A
    DNA2.0 Custom Variant and Variant Library Synthesis for TRMT10A

    (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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    4 diseases for TRMT10A:    
    About MalaCards
    primary microcephaly-mild intellectual disability-young-onset diabetes syndrome    breast and colorectal cancer    malaria    colorectal cancer


    TRMT10A for disorders           About GeneDecksing


    Export disorders for TRMT10A 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 TRMT10A gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TRMT10A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    2. A high-throughput approach for measuring temporal changes in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (Nat. Methods 2012)
    3. Large-scale proteomics and phosphoproteomics of urinary exosomes. (PubMed id 19056867)1 Gonzales P.A....Knepper M.A. (J. Am. Soc. Nephrol. 2009)
    4. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (Science 2006)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
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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: 93587 HGNC: 28403 AceView: RG9MTD2 Ensembl:ENSG00000145331 euGenes: HUgn93587
    ECgene: TRMT10A H-InvDB: TRMT10A

    (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 TRMT10A 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 TRMT10A gene:
    Search GeneIP for patents involving TRMT10A

    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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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