Human Gene TRMT5 (uc001xff.4) Description and Page Index
  Description: Homo sapiens tRNA methyltransferase 5 homolog (S. cerevisiae) (TRMT5), mRNA.
RefSeq Summary (NM_020810): tRNAs contain as many as 13 or 14 nucleotides that are modified posttranscriptionally by enzymes that are highly specific for particular nucleotides in the tRNA structure. TRMT5 methylates the N1 position of guanosine-37 (G37) in selected tRNAs using S-adenosyl methionine (Brule et al., 2004 [PubMed 15248782]).[supplied by OMIM, Mar 2008].
Transcript (Including UTRs)
   Position: hg19 chr14:61,438,167-61,447,782 Size: 9,616 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr14:61,441,827-61,447,691 Size: 5,865 Coding Exon Count: 5 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:61,438,167-61,447,782)mRNA (may differ from genome)Protein (509 aa)
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UniProtKB

-  Comments and Description Text from UniProtKB
  ID: TRM5_HUMAN
DESCRIPTION: RecName: Full=tRNA (guanine(37)-N1)-methyltransferase; EC=2.1.1.228; AltName: Full=M1G-methyltransferase; AltName: Full=tRNA [GM37] methyltransferase; AltName: Full=tRNA methyltransferase 5 homolog;
FUNCTION: Specifically methylates the N1 position of guanosine-37 in various cytoplasmic and mitochondrial tRNAs. Methylation is not dependent on the nature of the nucleoside 5' of the target nucleoside. This is the first step in the biosynthesis of wybutosine (yW), a modified base adjacent to the anticodon of tRNAs and required for accurate decoding.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA.
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Mitochondrion matrix (By similarity). Nucleus (By similarity). Cytoplasm (By similarity). Note=Predominantly in the mitochondria and in the nucleus (By similarity).
SIMILARITY: Belongs to the TRM5 / TYW2 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TRMT5
CDC HuGE Published Literature: TRMT5
Positive Disease Associations: Body Mass Index
Related Studies:
  1. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.

-  MalaCards Disease Associations
  MalaCards Gene Search: TRMT5
Diseases sorted by gene-association score: combined oxidative phosphorylation deficiency 26* (1580)
* = 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: 8.61 RPKM in Testis
Total median expression: 148.76 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 -36.8091-0.404 Picture PostScript Text
3' UTR -983.453660-0.269 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
IPR025792 - tRNA_Gua_MeTrfase_euk
IPR003402 - tRNA_Trfase_Trm5/Tyw2

Pfam Domains:
PF02475 - Met-10+ like-protein

SCOP Domains:
53335 - S-adenosyl-L-methionine-dependent methyltransferases

ModBase Predicted Comparative 3D Structure on Q32P41
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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:0008168 methyltransferase activity
GO:0009019 tRNA (guanine-N1-)-methyltransferase activity
GO:0016740 transferase activity
GO:0052906 tRNA (guanine(37)-N(1))-methyltransferase activity

Biological Process:
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
GO:0070901 mitochondrial tRNA methylation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  BC029638 - Homo sapiens TRM5 tRNA methyltransferase 5 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4777228), with apparent retained intron.
BC063551 - Homo sapiens TRM5 tRNA methyltransferase 5 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4779792).
AB037814 - Homo sapiens mRNA for KIAA1393 protein, partial cds.
JD082361 - Sequence 63385 from Patent EP1572962.
JD229261 - Sequence 210285 from Patent EP1572962.
JD088890 - Sequence 69914 from Patent EP1572962.
JD436286 - Sequence 417310 from Patent EP1572962.
JD137222 - Sequence 118246 from Patent EP1572962.
JD553325 - Sequence 534349 from Patent EP1572962.
JD050698 - Sequence 31722 from Patent EP1572962.
JD209199 - Sequence 190223 from Patent EP1572962.
JD439938 - Sequence 420962 from Patent EP1572962.
JD208022 - Sequence 189046 from Patent EP1572962.
JD340325 - Sequence 321349 from Patent EP1572962.
JD442108 - Sequence 423132 from Patent EP1572962.
BC136606 - Homo sapiens TRM5 tRNA methyltransferase 5 homolog (S. cerevisiae), mRNA (cDNA clone MGC:168219 IMAGE:9020596), complete cds.
BC136607 - Homo sapiens TRM5 tRNA methyltransferase 5 homolog (S. cerevisiae), mRNA (cDNA clone MGC:168220 IMAGE:9020597), complete cds.
JD563698 - Sequence 544722 from Patent EP1572962.
JD170503 - Sequence 151527 from Patent EP1572962.
JD170504 - Sequence 151528 from Patent EP1572962.
JD440656 - Sequence 421680 from Patent EP1572962.
JD464671 - Sequence 445695 from Patent EP1572962.
JD490033 - Sequence 471057 from Patent EP1572962.
JD038437 - Sequence 19461 from Patent EP1572962.
JD331442 - Sequence 312466 from Patent EP1572962.
JD119446 - Sequence 100470 from Patent EP1572962.
JD458310 - Sequence 439334 from Patent EP1572962.
JD416360 - Sequence 397384 from Patent EP1572962.
JD111539 - Sequence 92563 from Patent EP1572962.
JD277157 - Sequence 258181 from Patent EP1572962.
JD196536 - Sequence 177560 from Patent EP1572962.
JD279451 - Sequence 260475 from Patent EP1572962.
JD302338 - Sequence 283362 from Patent EP1572962.
JD299534 - Sequence 280558 from Patent EP1572962.
JD049586 - Sequence 30610 from Patent EP1572962.
JD163912 - Sequence 144936 from Patent EP1572962.
JD163591 - Sequence 144615 from Patent EP1572962.
JD088450 - Sequence 69474 from Patent EP1572962.
JD252760 - Sequence 233784 from Patent EP1572962.
DQ581884 - Homo sapiens piRNA piR-49996, complete sequence.
JD250694 - Sequence 231718 from Patent EP1572962.
JD053087 - Sequence 34111 from Patent EP1572962.
JD507198 - Sequence 488222 from Patent EP1572962.
JD550713 - Sequence 531737 from Patent EP1572962.
JD080938 - Sequence 61962 from Patent EP1572962.
JD507091 - Sequence 488115 from Patent EP1572962.
JD379872 - Sequence 360896 from Patent EP1572962.
JD510468 - Sequence 491492 from Patent EP1572962.
JD490496 - Sequence 471520 from Patent EP1572962.
BC108284 - Homo sapiens TRM5 tRNA methyltransferase 5 homolog (S. cerevisiae), mRNA (cDNA clone MGC:111453 IMAGE:4371510), complete cds.
AK293158 - Homo sapiens cDNA FLJ54461 complete cds, highly similar to Homo sapiens TRM5 tRNA methyltransferase 5 homolog (TRMT5), mRNA.
JD168443 - Sequence 149467 from Patent EP1572962.
KJ899350 - Synthetic construct Homo sapiens clone ccsbBroadEn_08744 TRMT5 gene, encodes complete protein.
AB590562 - Synthetic construct DNA, clone: pFN21AE1953, Homo sapiens TRMT5 gene for TRM5 tRNA methyltransferase 5 homolog, without stop codon, in Flexi system.
JD227844 - Sequence 208868 from Patent EP1572962.
JD479024 - Sequence 460048 from Patent EP1572962.

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

Protein Q32P41 (Reactome details) participates in the following event(s):

R-HSA-6782859 TRMT5 methylates guanosine yielding 1-methylguanosine at nucleotide 37 of tRNA(Phe)
R-HSA-6782861 Synthesis of wybutosine at G37 of tRNA(Phe)
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: B2RN19, KIAA1393, NM_020810, NP_065861, Q32P41, Q9P2F4, TRM5, TRM5_HUMAN
UCSC ID: uc001xff.4
RefSeq Accession: NM_020810
Protein: Q32P41 (aka TRM5_HUMAN)
CCDS: CCDS32092.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020810.2
exon count: 5CDS single in 3' UTR: no RNA size: 5302
ORF size: 1530CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3260.00frame shift in genome: no % Coverage: 99.60
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.