Human Gene LCMT2 (uc001zrg.3)
  Description: Homo sapiens leucine carboxyl methyltransferase 2 (LCMT2), mRNA.
RefSeq Summary (NM_014793): The protein encoded by this intronless gene belongs to the highly variable methyltransferase superfamily. This gene is the inferred homolog of the Saccharomyces cerevisiae carboxymethyltransferase gene PPM2 that is essential for the synthesis of the hypermodified guanosine Wybutosine (yW). [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr15:43,619,974-43,622,820 Size: 2,847 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr15:43,620,627-43,622,687 Size: 2,061 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:43,619,974-43,622,820)mRNA (may differ from genome)Protein (686 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LCMT2_HUMAN
DESCRIPTION: RecName: Full=Leucine carboxyl methyltransferase 2; EC=2.1.1.-; AltName: Full=p21WAF1/CIP1 promoter-interacting protein; AltName: Full=tRNA wybutosine-synthesizing protein 4 homolog; Short=tRNA yW-synthesizing protein 4 homolog;
FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA (By similarity). May methylate the carboxyl group of leucine residues to form alpha- leucine ester residues.
PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
SUBUNIT: Interacts with RNF144B/IBRDC2.
SIMILARITY: Belongs to the methyltransferase superfamily. LCMT family.
SEQUENCE CAUTION: Sequence=BAA25473.2; Type=Erroneous initiation;
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/lcmt2/";

-  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
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.36 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 153.33 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -45.40133-0.341 Picture PostScript Text
3' UTR -156.78653-0.240 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
IPR015915 - Kelch-typ_b-propeller
IPR007213 - LCM_MeTrfase
IPR021121 - LCM_MeTrfase_euk

Pfam Domains:
PF04072 - Leucine carboxyl methyltransferase
PF13964 - Kelch motif

SCOP Domains:
50965 - Galactose oxidase, central domain
53335 - S-adenosyl-L-methionine-dependent methyltransferases

ModBase Predicted Comparative 3D Structure on O60294
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-  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 orthologGenome BrowserGenome BrowserNo orthologNo orthologGenome Browser
Gene DetailsGene Details   Gene Details
Gene SorterGene Sorter   Gene Sorter
 RGDEnsembl  SGD
 Protein SequenceProtein Sequence  Protein Sequence
 AlignmentAlignment  Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008175 tRNA methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0016740 transferase activity

Biological Process:
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0031591 wybutosine biosynthetic process
GO:0032259 methylation

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AB011119 - Homo sapiens KIAA0547 mRNA for KIAA0547 protein.
KJ892862 - Synthetic construct Homo sapiens clone ccsbBroadEn_02256 LCMT2 gene, encodes complete protein.
AF265443 - Homo sapiens p21WAF1/CIP1 promoter-interacting protein mRNA, partial cds.
BC015949 - Homo sapiens leucine carboxyl methyltransferase 2, mRNA (cDNA clone MGC:9534 IMAGE:3922888), complete cds.
AK292587 - Homo sapiens cDNA FLJ76457 complete cds, highly similar to Homo sapiens leucine carboxyl methyltransferase 2 (LCMT2), mRNA.
JD349583 - Sequence 330607 from Patent EP1572962.
JD256284 - Sequence 237308 from Patent EP1572962.
JD303917 - Sequence 284941 from Patent EP1572962.
JD488537 - Sequence 469561 from Patent EP1572962.
AK300820 - Homo sapiens cDNA FLJ51321 complete cds, highly similar to Leucine carboxyl methyltransferase 2 (EC 2.1.1.-).
AB383903 - Synthetic construct DNA, clone: pF1KSDA0547, Homo sapiens LCMT2 gene for leucine carboxyl methyltransferase 2, complete cds, without stop codon, in Flexi system.
CU677535 - Synthetic construct Homo sapiens gateway clone IMAGE:100017455 5' read LCMT2 mRNA.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00340 - Histidine metabolism
hsa00350 - Tyrosine metabolism
hsa00450 - Selenoamino acid metabolism

Reactome (by CSHL, EBI, and GO)

Protein O60294 (Reactome details) participates in the following event(s):

R-HSA-6782881 LCMT2 methylates yW-72 yielding yW-58 at nucleotide 37 of tRNA(Phe)
R-HSA-6782890 LCMT2 methoxycarbonylates yW-58 yielding yW (wybutosine) at nucleotide 37 of tRNA(Phe)
R-HSA-6783473 LCMT2 methoxycarbonylates OHyW-72 yielding OHyW (hydroxywybutosine) 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: KIAA0547, LCMT2_HUMAN, NM_014793, NP_055608, O60294, Q4JFT6, Q96B55, Q9NR10, TYW4
UCSC ID: uc001zrg.3
RefSeq Accession: NM_014793
Protein: O60294 (aka LCMT2_HUMAN or LCM2_HUMAN)
CCDS: CCDS10094.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014793.4
exon count: 1CDS single in 3' UTR: no RNA size: 2860
ORF size: 2061CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4221.00frame shift in genome: no % Coverage: 99.55
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.