Free for academic non-profit institutions. Other users need a Commercial license

Aliases for LCMT2 Gene

Aliases for LCMT2 Gene

  • Leucine Carboxyl Methyltransferase 2 2 3 4 5
  • TRNA(Phe) (7-(3-Amino-3-(Methoxycarbonyl)Propyl)Wyosine(37)-N)-Methoxycarbonyltransferase 3 4
  • TRNA(Phe) (7-(3-Amino-3-Carboxypropyl)Wyosine(37)-O)-Methyltransferase 3 4
  • TRNA YW-Synthesizing Protein 4 3 4
  • TYW4 3 4
  • P21WAF1/CIP1 Promoter-Interacting Protein 3
  • TRNA Wybutosine-Synthesizing Protein 4 3
  • TRNA-Wybutosine-Synthesizing Protein 4 3
  • TRNA-YW Synthesizing Protein 4 2
  • EC 2.1.1.290 4
  • EC 2.3.1.231 4
  • KIAA0547 4
  • PPM2 3

External Ids for LCMT2 Gene

Previous GeneCards Identifiers for LCMT2 Gene

  • GC15M036514
  • GC15M041199
  • GC15M041336
  • GC15M041407
  • GC15M043619
  • GC15M020468

Summaries for LCMT2 Gene

Entrez Gene Summary for LCMT2 Gene

  • 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]

GeneCards Summary for LCMT2 Gene

LCMT2 (Leucine Carboxyl Methyltransferase 2) is a Protein Coding gene. Among its related pathways are Gene Expression and tRNA processing. GO annotations related to this gene include methyltransferase activity. An important paralog of this gene is LCMT1.

UniProtKB/Swiss-Prot for LCMT2 Gene

  • 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.

Gene Wiki entry for LCMT2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LCMT2 Gene

Genomics for LCMT2 Gene

Regulatory Elements for LCMT2 Gene

Enhancers for LCMT2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15G042497 1.5 Ensembl ENCODE dbSUPER 10.8 +831.0 831015 4.3 HDGF PKNOX1 CREB3L1 ARNT FEZF1 TCF12 GTF3C2 FOS MEF2D SMARCA4 LRRC57 GANC HAUS2 TUBGCP4 LOC105370795 RPAP1 CDAN1 LCMT2 RPS3AP47 MAPKBP1
GH15G043823 1.2 ENCODE 10.8 -495.4 -495407 5.7 CREB3L1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC TBX21 SSRP1 GLIS1 ENSG00000249839 CTDSPL2 TUBGCP4 MFAP1 ADAL RPS3AP47 ELL3 ENSG00000259563 EIF3J-AS1 HNRNPMP1
GH15G044286 1.1 ENCODE 10.8 -958.2 -958172 3.7 HDGF PKNOX1 CREB3L1 SIN3A FEZF1 DMAP1 YY1 ZNF143 ZNF207 KLF13 CTDSPL2 ENSG00000259563 TUBGCP4 ENSG00000249839 ELL3 MFAP1 WDR76 LCMT2 ENSG00000259659 ADAL
GH15G042574 1.1 ENCODE 10.2 +755.0 755042 2.2 HDGF HNRNPUL1 PKNOX1 MLX CREB3L1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZSCAN29 ENSG00000260814 CDAN1 LRRC57 GANC TP53BP1 RPS3AP47 STARD9 UBR1 LCMT2
GH15G043285 0.9 ENCODE 11.4 +44.9 44885 0.2 HDAC1 ATF1 FOXA2 RB1 ZSCAN4 ZNF2 RAD21 CHAMP1 RFX5 GATA2 CCNDBP1 LCMT2 ADAL ENSG00000260406 ATP5HP1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LCMT2 on UCSC Golden Path with GeneCards custom track

Promoters for LCMT2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000075833 122 1801 PKNOX1 CREB3L1 ARNT AGO1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 ZNF2

Genomic Location for LCMT2 Gene

Chromosome:
15
Start:
43,323,649 bp from pter
End:
43,330,622 bp from pter
Size:
6,974 bases
Orientation:
Minus strand

Genomic View for LCMT2 Gene

Genes around LCMT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCMT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCMT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCMT2 Gene

Proteins for LCMT2 Gene

  • Protein details for LCMT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60294-TYW4_HUMAN
    Recommended name:
    tRNA wybutosine-synthesizing protein 4
    Protein Accession:
    O60294
    Secondary Accessions:
    • Q4JFT6
    • Q96B55
    • Q9NR10

    Protein attributes for LCMT2 Gene

    Size:
    686 amino acids
    Molecular mass:
    75602 Da
    Quaternary structure:
    • Interacts with RNF144B/IBRDC2.
    SequenceCaution:
    • Sequence=BAA25473.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for LCMT2 Gene

Post-translational modifications for LCMT2 Gene

  • Ubiquitination at posLast=2424, isoforms=356, and isoforms=401
  • Modification sites at PhosphoSitePlus

Other Protein References for LCMT2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LCMT2 Gene

Domains & Families for LCMT2 Gene

Protein Domains for LCMT2 Gene

Graphical View of Domain Structure for InterPro Entry

O60294

UniProtKB/Swiss-Prot:

TYW4_HUMAN :
  • Belongs to the methyltransferase superfamily. LCMT family.
Family:
  • Belongs to the methyltransferase superfamily. LCMT family.
genes like me logo Genes that share domains with LCMT2: view

Function for LCMT2 Gene

Molecular function for LCMT2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + 7-((3S)-3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) = S-adenosyl-L-homocysteine + 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe).
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe) + CO(2) = S-adenosyl-L-homocysteine + wybutosine(37) in tRNA(Phe).
UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for LCMT2 Gene

Gene Ontology (GO) - Molecular Function for LCMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12853982
GO:0008168 methyltransferase activity IEA --
GO:0008175 tRNA methyltransferase activity TAS --
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity IBA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with LCMT2: view

Phenotypes for LCMT2 Gene

genes like me logo Genes that share phenotypes with LCMT2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LCMT2 Gene

Localization for LCMT2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LCMT2 gene
Compartment Confidence
cytosol 4
nucleus 3
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for LCMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm TAS --
GO:0005829 cytosol IBA --
genes like me logo Genes that share ontologies with LCMT2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LCMT2 Gene

Pathways & Interactions for LCMT2 Gene

genes like me logo Genes that share pathways with LCMT2: view

Pathways by source for LCMT2 Gene

UniProtKB/Swiss-Prot O60294-TYW4_HUMAN

  • Pathway: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.

Gene Ontology (GO) - Biological Process for LCMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006400 tRNA modification TAS --
GO:0008033 tRNA processing IEA --
GO:0030488 tRNA methylation IBA --
GO:0031591 wybutosine biosynthetic process IBA --
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with LCMT2: view

No data available for SIGNOR curated interactions for LCMT2 Gene

Drugs & Compounds for LCMT2 Gene

(2) Drugs for LCMT2 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Leucine Approved Nutra Target 0
S-Adenosylmethionine Approved Nutra 0
genes like me logo Genes that share compounds with LCMT2: view

Transcripts for LCMT2 Gene

mRNA/cDNA for LCMT2 Gene

Unigene Clusters for LCMT2 Gene

Leucine carboxyl methyltransferase 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LCMT2 Gene

No ASD Table

Relevant External Links for LCMT2 Gene

GeneLoc Exon Structure for
LCMT2
ECgene alternative splicing isoforms for
LCMT2

Expression for LCMT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LCMT2 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LCMT2 Gene



NURSA nuclear receptor signaling pathways regulating expression of LCMT2 Gene:

LCMT2

SOURCE GeneReport for Unigene cluster for LCMT2 Gene:

Hs.200596

Evidence on tissue expression from TISSUES for LCMT2 Gene

  • Nervous system(4.2)
  • Skin(4.1)
  • Stomach(4.1)
genes like me logo Genes that share expression patterns with LCMT2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LCMT2 Gene

Orthologs for LCMT2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for LCMT2 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia LCMT2 34 35
  • 86.91 (n)
cow
(Bos Taurus)
Mammalia LCMT2 34 35
  • 85.74 (n)
chimpanzee
(Pan troglodytes)
Mammalia LCMT2 35
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lcmt2 34 16 35
  • 80.86 (n)
rat
(Rattus norvegicus)
Mammalia Lcmt2 34
  • 80.03 (n)
chicken
(Gallus gallus)
Aves LCMT2 34 35
  • 57.53 (n)
lizard
(Anolis carolinensis)
Reptilia LCMT2 35
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lcmt2 34
  • 53.98 (n)
zebrafish
(Danio rerio)
Actinopterygii lcmt2 34 35
  • 52.57 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL194W 34
  • 43.48 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PPM2 34 35 37
  • 41.63 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05392 34
  • 43.21 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC19C7.08c 34
  • 37.74 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10693 35
  • 29 (a)
OneToOne
Species where no ortholog for LCMT2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LCMT2 Gene

ENSEMBL:
Gene Tree for LCMT2 (if available)
TreeFam:
Gene Tree for LCMT2 (if available)

Paralogs for LCMT2 Gene

Paralogs for LCMT2 Gene

genes like me logo Genes that share paralogs with LCMT2: view

Variants for LCMT2 Gene

Sequence variations from dbSNP and Humsavar for LCMT2 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs1001536599 -- 43,329,894(+) CCGCG(A/G)CACTC upstream-variant-2KB, reference, missense
rs1001757263 -- 43,332,342(+) TTAAG(A/T)ACTGC intron-variant, upstream-variant-2KB
rs1001798952 -- 43,327,787(+) CATCA(A/G)AAGTT utr-variant-3-prime
rs1002134103 -- 43,329,239(+) TAAAG(C/G)CGTCC upstream-variant-2KB, reference, synonymous-codon
rs1002655249 -- 43,331,720(+) AGGGA(C/G)AGCAG intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for LCMT2 Gene

Variant ID Type Subtype PubMed ID
nsv1512 CNV deletion 18451855

Variation tolerance for LCMT2 Gene

Residual Variation Intolerance Score: 43.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.29; 53.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LCMT2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCMT2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCMT2 Gene

Disorders for LCMT2 Gene

Relevant External Links for LCMT2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LCMT2

No disorders were found for LCMT2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LCMT2 Gene

Publications for LCMT2 Gene

  1. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9628581) Nagase T. … Ohara O. (DNA Res. 1998) 2 3 4 64
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  3. p53RFP, a p53-inducible RING-finger protein, regulates the stability of p21WAF1. (PMID: 12853982) Ng C.-C. … Nakamura Y. (Oncogene 2003) 3 4 64
  4. Widespread macromolecular interaction perturbations in human genetic disorders. (PMID: 25910212) Sahni N. … Vidal M. (Cell 2015) 3 64
  5. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3 64

Products for LCMT2 Gene

Sources for LCMT2 Gene

Content
Loading form....