Human Gene TRMT10A (uc003hva.4)
  Description: Homo sapiens tRNA methyltransferase 10 homolog A (S. cerevisiae) (TRMT10A), transcript variant 3, mRNA.
RefSeq Summary (NM_001134666): This gene encodes a protein that belongs to the tRNA (Guanine-1)-methyltransferase family. A similar gene in yeast modifies several different tRNA species. Mutations in this gene are associated with microcephaly, short stature, and impaired glucose metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014].
Transcript (Including UTRs)
   Position: hg19 chr4:100,467,864-100,485,189 Size: 17,326 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr4:100,470,245-100,480,495 Size: 10,251 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:100,467,864-100,485,189)mRNA (may differ from genome)Protein (339 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TM10A_HUMAN
DESCRIPTION: RecName: Full=tRNA methyltransferase 10 homolog A; EC=2.1.1.-; AltName: Full=RNA (guanine-9-)-methyltransferase domain-containing protein 2;
FUNCTION: Probable RNA methyltransferase (By similarity).
SIMILARITY: Belongs to the RNA methyltransferase TrmD family. TRM10 subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: TRMT10A
Diseases sorted by gene-association score: microcephaly, short stature, and impaired glucose metabolism 1* (1230), primary microcephaly-mild intellectual disability-young-onset diabetes syndrome* (350), microcephaly (10)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.36 RPKM in Testis
Total median expression: 68.10 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -42.20132-0.320 Picture PostScript Text
3' UTR -556.432381-0.234 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016009 - tRNA_m1G_MeTrfase
IPR007356 - tRNA_m1G_MeTrfase_euk
IPR016653 - tRNA_MeTfrase_TRM10

Pfam Domains:
PF01746 - tRNA (Guanine-1)-methyltransferase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
4FMW - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8TBZ6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0009019 tRNA (guanine-N1-)-methyltransferase activity
GO:0016740 transferase activity
GO:0052905 tRNA (guanine(9)-N(1))-methyltransferase activity

Biological Process:
GO:0030488 tRNA methylation
GO:0032259 methylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0015629 actin cytoskeleton
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF206350 - JP 2014500723-A/13853: Polycomb-Associated Non-Coding RNAs.
BC028373 - Homo sapiens RNA (guanine-9-) methyltransferase domain containing 2, mRNA (cDNA clone MGC:27034 IMAGE:4838346), complete cds.
EU668342 - Homo sapiens epididymis secretory protein Li 88 (HEL-S-88) mRNA, complete cds.
JD386442 - Sequence 367466 from Patent EP1572962.
JD348061 - Sequence 329085 from Patent EP1572962.
JD546067 - Sequence 527091 from Patent EP1572962.
JD362764 - Sequence 343788 from Patent EP1572962.
JD137346 - Sequence 118370 from Patent EP1572962.
JD314645 - Sequence 295669 from Patent EP1572962.
JD082843 - Sequence 63867 from Patent EP1572962.
JD152916 - Sequence 133940 from Patent EP1572962.
JD208339 - Sequence 189363 from Patent EP1572962.
LF353459 - JP 2014500723-A/160962: Polycomb-Associated Non-Coding RNAs.
AK000332 - Homo sapiens cDNA FLJ20325 fis, clone HEP09891, highly similar to AF106046 Homo sapiens unknown mRNA.
JD376968 - Sequence 357992 from Patent EP1572962.
JD305421 - Sequence 286445 from Patent EP1572962.
JD110774 - Sequence 91798 from Patent EP1572962.
JD299610 - Sequence 280634 from Patent EP1572962.
AF106046 - Homo sapiens unknown mRNA.
JD202529 - Sequence 183553 from Patent EP1572962.
AK313548 - Homo sapiens cDNA, FLJ94108.
LF353458 - JP 2014500723-A/160961: Polycomb-Associated Non-Coding RNAs.
LF353457 - JP 2014500723-A/160960: Polycomb-Associated Non-Coding RNAs.
LF353456 - JP 2014500723-A/160959: Polycomb-Associated Non-Coding RNAs.
LF353455 - JP 2014500723-A/160958: Polycomb-Associated Non-Coding RNAs.
MA441927 - JP 2018138019-A/13853: Polycomb-Associated Non-Coding RNAs.
MA589036 - JP 2018138019-A/160962: Polycomb-Associated Non-Coding RNAs.
MA589035 - JP 2018138019-A/160961: Polycomb-Associated Non-Coding RNAs.
MA589034 - JP 2018138019-A/160960: Polycomb-Associated Non-Coding RNAs.
MA589033 - JP 2018138019-A/160959: Polycomb-Associated Non-Coding RNAs.
MA589032 - JP 2018138019-A/160958: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8TBZ6 (Reactome details) participates in the following event(s):

R-HSA-6786621 TRMT10A methylates guanosine-9 in tRNA
R-HSA-6782315 tRNA modification in the nucleus and cytosol
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B2R8X7, NM_001134666, NP_689505, Q8TBZ6, Q9Y2T9, RG9MTD2, TM10A_HUMAN
UCSC ID: uc003hva.4
RefSeq Accession: NM_001134666
Protein: Q8TBZ6 (aka TM10A_HUMAN)
CCDS: CCDS3650.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001134666.1
exon count: 8CDS single in 3' UTR: no RNA size: 3541
ORF size: 1020CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2240.00frame shift in genome: no % Coverage: 99.77
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.