Human Gene TRMT2A (ENST00000252136.12_9) from GENCODE V47lift37
  Description: tRNA methyltransferase 2 homolog A, transcript variant 2 (from RefSeq NM_182984.5)
Gencode Transcript: ENST00000252136.12_9
Gencode Gene: ENSG00000099899.16_17
Transcript (Including UTRs)
   Position: hg19 chr22:20,099,398-20,104,749 Size: 5,352 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr22:20,100,086-20,104,429 Size: 4,344 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:20,099,398-20,104,749)mRNA (may differ from genome)Protein (625 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TRM2A_HUMAN
DESCRIPTION: RecName: Full=tRNA (uracil-5-)-methyltransferase homolog A; AltName: Full=HpaII tiny fragments locus 9c protein;
FUNCTION: May be involved in nucleic acid metabolism and/or modifications.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  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


-  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: 29.31 RPKM in Testis
Total median expression: 684.81 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 -168.20320-0.526 Picture PostScript Text
3' UTR -296.70688-0.431 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom
IPR010280 - U5_MeTrfase

Pfam Domains:
PF01135 - Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
PF01209 - ubiE/COQ5 methyltransferase family
PF02390 - Putative methyltransferase
PF03602 - Conserved hypothetical protein 95
PF05175 - Methyltransferase small domain
PF05958 - tRNA (Uracil-5-)-methyltransferase
PF08241 - Methyltransferase domain
PF13649 - Methyltransferase domain
PF13847 - Methyltransferase domain

SCOP Domains:
51735 - NAD(P)-binding Rossmann-fold domains
53335 - S-adenosyl-L-methionine-dependent methyltransferases
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q8IZ69
FrontTopSide
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0016740 transferase activity

Biological Process:
GO:0001510 RNA methylation
GO:0006396 RNA processing
GO:0032259 methylation


-  Descriptions from all associated GenBank mRNAs
  LF210538 - JP 2014500723-A/18041: Polycomb-Associated Non-Coding RNAs.
BC017184 - Homo sapiens TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:3087 IMAGE:3347641), complete cds.
AK025106 - Homo sapiens cDNA: FLJ21453 fis, clone COL04585.
BC013352 - Homo sapiens TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:14943 IMAGE:4054100), complete cds.
BC108251 - Homo sapiens TRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:102728 IMAGE:3852106), complete cds.
AK057029 - Homo sapiens cDNA FLJ32467 fis, clone SKNMC2000097, moderately similar to M.musculus mRNA for protein Htf9C.
JD282093 - Sequence 263117 from Patent EP1572962.
JD446260 - Sequence 427284 from Patent EP1572962.
CR456354 - Homo sapiens Em:AC006547.2 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.Em:AC006547.2).
JD170575 - Sequence 151599 from Patent EP1572962.
JD389121 - Sequence 370145 from Patent EP1572962.
JD389120 - Sequence 370144 from Patent EP1572962.
CU013064 - Homo sapiens Em:AC006547.C22.2, mRNA (cDNA clone IMAGE:100000323), complete cds, with stop codon, in Gateway system.
KJ898653 - Synthetic construct Homo sapiens clone ccsbBroadEn_08047 TRMT2A gene, encodes complete protein.
AB527162 - Synthetic construct DNA, clone: pF1KE0342, Homo sapiens HTF9C gene for TRM2 tRNA methyltransferase 2 homolog A, without stop codon, in Flexi system.
CU013352 - Homo sapiens Em:AC006547.C22.2, mRNA (cDNA clone IMAGE:100000227), complete cds, without stop codon, in Gateway system.
JD123180 - Sequence 104204 from Patent EP1572962.
LF338627 - JP 2014500723-A/146130: Polycomb-Associated Non-Coding RNAs.
AK304068 - Homo sapiens cDNA FLJ61051 complete cds, highly similar to HpaII tiny fragments locus 9c protein.
CU680570 - Synthetic construct Homo sapiens gateway clone IMAGE:100019959 5' read HTF9C mRNA.
BC060318 - Homo sapiens cDNA clone IMAGE:4944653, **** WARNING: chimeric clone ****.
JD495309 - Sequence 476333 from Patent EP1572962.
JD390727 - Sequence 371751 from Patent EP1572962.
JD531956 - Sequence 512980 from Patent EP1572962.
JD460540 - Sequence 441564 from Patent EP1572962.
MA446115 - JP 2018138019-A/18041: Polycomb-Associated Non-Coding RNAs.
MA574204 - JP 2018138019-A/146130: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DX25, ENST00000252136.1, ENST00000252136.10, ENST00000252136.11, ENST00000252136.2, ENST00000252136.3, ENST00000252136.4, ENST00000252136.5, ENST00000252136.6, ENST00000252136.7, ENST00000252136.8, ENST00000252136.9, NM_182984, Q32P57, Q8IZ69, Q96ME6, Q9H732, TRM2A_HUMAN, TRMT2A , uc317fgf.1, uc317fgf.2
UCSC ID: ENST00000252136.12_9
RefSeq Accession: NM_022727.6
Protein: Q8IZ69 (aka TRM2A_HUMAN)

-  Gene Model Information
  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.