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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TRMT13 Gene

protein-coding   GIFtS: 39
GCID: GC01P100599

tRNA methyltransferase 13 homolog (S. cerevisiae)

(Previous name: coiled-coil domain containing 76 )
(Previous symbol: CCDC76)
 Explore 1 disease affiliated with
TRMT13 via our new
 Human Malady Compendium 
Biological research products
for TRMT13
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
TRNA Methyltransferase 13 Homolog (S. Cerevisiae)1 2     FLJ112191
CCDC761 2 3     TRNA [Gm4] Methyltransferase2
Coiled-Coil Domain Containing 761 2     TRNA Guanosine-2'-O-Methyltransferase TRM13 Homolog2
Coiled-Coil Domain-Containing Protein 762 3     EC 2.1.1.2253
FLJ102871     

External Ids:    HGNC: 255021   Entrez Gene: 544822   Ensembl: ENSG000001224357   UniProtKB: Q9NUP73   

Export aliases for TRMT13 gene to outside databases


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: TRM13_HUMAN, Q9NUP7
Function: tRNA methylase which 2'-O-methylates cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in
tRNA(His) (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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for TRMT13
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTRMT13 promoter sequence
   Search SABiosciences Chromatin IP Primers for TRMT13

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TRMT13


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

Entrez Gene cytogenetic band: 1p21.2   Ensembl cytogenetic band:  1p21.2   HGNC cytogenetic band: 1p21.2

TRMT13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRMT13 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P100599:  view genomic region     (about GC identifiers)

Start:
100,598,706 bp from pter      End:
100,616,054 bp from pter
Size:
17,349 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: TRM13_HUMAN, Q9NUP7 (See protein sequence)
Recommended Name: tRNA:m(4)X modification enzyme TRM13 homolog  
Size: 481 amino acids; 54247 Da
Secondary accessions: Q5VVL0 Q9NW65
Alternative splicing: 2 isoforms:  Q9NUP7-1   Q9NUP7-2   

Explore the universe of human proteins at neXtProt for TRMT13: NX_Q9NUP7

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NUP7

  • TRMT13 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_061956.2  
    ENSEMBL proteins: 
     ENSP00000359162   ENSP00000359160   ENSP00000432616   ENSP00000359158  

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    Uscn Proteins for TRMT13


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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    TRMT13 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR007871 Methyltransferase_TRM13
     IPR021721 Znf_CCCH-type_TRM13
     IPR022776 TRM13/UPF0224_CHHC_Znf_dom

    Graphical View of Domain Structure for InterPro Entry Q9NUP7

    ProtoNet protein and cluster: Q9NUP7

    UniProtKB/Swiss-Prot: TRM13_HUMAN, Q9NUP7
    Similarity: Belongs to the TRM13 family
    Similarity: Contains 1 CHHC-type zinc finger


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: TRM13_HUMAN, Q9NUP7
    Function: tRNA methylase which 2'-O-methylates cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in
    tRNA(His) (By similarity)
    Catalytic activity: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methyluridine
    Catalytic activity: S-adenosyl-L-methionine + cytidine(4) in tRNA(Pro) = S-adenosyl-L-homocysteine +
    2'-O-methylcytidine(4) in tRNA(Pro)
    Catalytic activity: S-adenosyl-L-methionine + cytidine(4) in tRNA(Gly)(GCC) = S-adenosyl-L-homocysteine +
    2'-O-methylcytidine(4) in tRNA(Gly)(GCC)
    Catalytic activity: S-adenosyl-L-methionine + adenosine(4) in tRNA(His) = S-adenosyl-L-homocysteine +
    2'-O-methyladenosine(4) in tRNA(His)

    Enzyme Number (IUBMB): EC 2.1.1.2251

    miRNA
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    Inhib. RNA
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRMT13

    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008168methyltransferase activity IEA--
    GO:0046872metal ion binding IEA--


    TRMT13 for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TRMT13

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for TRMT13 (ENSP000003591604) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008033tRNA processing IEA--


    TRMT13 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TRMT13
    Search CenterWatch for drugs/clinical trials and news about TRMT13 / TRM13 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for TRMT13 gene: 
    NM_019083.2  

    Unigene Cluster for TRMT13:

    TRNA methyltransferase 13 homolog (S. cerevisiae)
    Hs.729095  [show with all ESTs]
    Unigene Representative Sequence: BC075811
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000370143 ENST00000370141(uc001dsv.3 uc010ouf.2 uc009wea.3)
    ENST00000482437 ENST00000370139 ENST00000493651

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    SwitchGear 3'UTR luciferase reporter plasmidTRMT13 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for TRMT13 (see all 7)
    OriGene shRNA RFP: TRMT13
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat TRMT13
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    Additional cDNA sequence: 

    AK001149.1 AK002081.1 AK289404.1 AK294738.1 AK295828.1 AK298941.1 BC057226.1 BC075811.1 

    10 DOTS entries:

    DT.97820384  DT.212706  DT.307267  DT.97783625  DT.95263903  DT.100637842  DT.75188916  DT.91807726 
    DT.97817538  DT.91977190 

    24/85 AceView cDNA sequences (see all 85):

    AI922312 AK002081 AA377262 CF272221 NM_019083 AK001149 AI922321 AA804788 
    AA292064 AA287558 BQ187089 BC075811 AA430376 BF514089 AA286765 AL040239 
    AA853970 AA476706 AA971154 AI028617 AU120776 AA292164 BU741542 AI276467 

    GeneLoc Exon Structure

    5/9 Alternative Splicing Database (ASD) splice patterns (SP) for TRMT13 (see all 9)    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^ 11 ^ 12
    SP1:                                                                                            -                                             
    SP2:                                                              -                             -                                             
    SP3:                                                  -           -     -                       -                                             
    SP4:                                                  -                                                                                       
    SP5:                                                              -     -                                                                     


    ECgene alternative splicing isoforms for TRMT13

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section
    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --


    TRMT13 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Intermediate limb mesenchymal cells (ILM cells) (Primary Cell)Bone, Cartilage, Limb
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See TRMT13 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TRMT13

    SOURCE GeneReport for Unigene cluster: Hs.729095
        SABiosciences Custom PCR Arrays for TRMT13
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    In Situ
    Assay Products:
     

     
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    (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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for TRMT13 gene from 10/31 species (see all 31)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Trmt131 , 5 coiled-coil domain containing 765
    tRNA methyltransferase 131
    86.74(n)1
    86.53(a)1
      3 (50.40 cM)5
    2297801  NM_030016.21  NP_084292.11 
     1165810935 
    chicken
    (Gallus gallus)
    Aves CCDC761 coiled-coil domain containing 76 69.04(n)
    65.95(a)
      424470  XM_422313.2  XP_422313.2 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC766
    --
    64(a)
    1 ↔ 1
    4(87758643-87771335)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.310502 Xenopus laevis transcribed sequence with weak similarity more 74.66(n)    BU906768.1 
    zebrafish
    (Danio rerio)
    Actinopterygii trmt131 tRNA methyltransferase 13 homolog (S. cerevisiae) 63.01(n)
    61.42(a)
      541496  NM_001014309.1  NP_001014331.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG180481 CG18048 46.35(n)
    36.52(a)
      40782  NM_141389.3  NP_649646.3 
    worm
    (Caenorhabditis elegans)
    Secernentea Y49A3A.31 Protein Y49A3A.3 46.43(n)
    33.24(a)
      3565972  NM_074159.3  NP_506560.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes TRM13(YOL125W)4
    TRM131
    2'-O-methyltransferase responsible for modification more4
    Trm13p1
    47.81(n)1
    36.5(a)1
      15(83834-85264)4
    8539951, 4  NP_014516.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G018801 methyltransferase 48.58(n)
    38(a)
      828223  NM_116418.2  NP_192097.2 
    rice
    (Oryza sativa)
    Liliopsida Os03g08332001 hypothetical protein 44.62(n)
    33.33(a)
      9267457  NM_001186771.1  NP_001173700.1 


    ENSEMBL Gene Tree for TRMT13 (if available)
    TreeFam Gene Tree for TRMT13 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/308 NCBI SNPs in TRMT13 are shown (see all 308    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1404397171,2
    C,--100596810(+) GGCAC-/AAATAG 2 -- int1 us2k10--------
    rs1840410661,2
    --100596840(+) GCTTAC/GGCTCA 2 -- us2k1 int10--------
    rs111664041,2
    C,F,A,H,--100596890(+) ACGGGT/CGTGAG 2 -- int1 us2k12Minor allele frequency- C:0.05NA 124
    rs1168175361,2
    F,--100596896(+) GTGAGC/TCACCA 2 -- int1 us2k11Minor allele frequency- T:0.02WA 118
    rs727281341,2
    C,--100596929(+) TCTAGA/TAGTCA 2 -- int1 us2k12Minor allele frequency- T:0.32NA 122
    rs1873097501,2
    --100596962(+) GCAGGC/TGAAAT 2 -- int1 us2k10--------
    rs1920798741,2
    --100596976(+) TTTTAA/GTAATA 2 -- us2k1 int10--------
    rs1853614921,2
    --100597088(+) CAACGG/TGCATT 2 -- int1 us2k10--------
    rs1481710261,2
    --100597378(+) ACATAC/TGATTT 2 -- int1 us2k10--------
    rs1460529771,2
    --100597408(+) AAACAC/TGTGAA 2 -- us2k1 int10--------

    HapMap Linkage Disequilibrium report for TRMT13 (100598706 - 100616054 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for TRMT13: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TRMT13
    DNA2.0 Custom Variant and Variant Library Synthesis for TRMT13

    (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.)
    About This Section

    TRMT13 for disorders           About GeneDecksing

    1 disease for TRMT13:    About MalaCards
    homocysteine


    Export disorders for TRMT13 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)
    About This Section

    PubMed articles for TRMT13 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with TRMT13)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    2. 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. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. (PubMed id 11799066)1, 3 Weinmann A.S....Farnham P.J. (2002)
    5. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    6. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    7. A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes. (PubMed id 18703587)2 Andreeva A. and Tidow H. (2008)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (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)
    About This Section
    Entrez Gene: 54482 HGNC: 25502 AceView: FLJ10287 Ensembl:ENSG00000122435 euGenes: HUgn54482
    ECgene: TRMT13 H-InvDB: TRMT13

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for TRMT13 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for TRMT13 gene:
    Search GeneIP for patents involving TRMT13

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



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