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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 tRNA processing and Gene Expression. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for LCMT2 Gene

Promoters and enhancers for LCMT2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J043328 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.4 436 3 PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ADAL LCMT2 LRRC57 CDAN1 ZSCAN29 WDR76 UBR1 TP53BP1 MFAP1 RPS3AP47
GH15J044286 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 40.5 -958.2 -958171 3.7 HDGF PKNOX1 SMAD1 NEUROD1 SIN3A FEZF1 DMAP1 IRF4 YY1 ZNF207 GC15M044288 CASC4 CTDSPL2 LCMT2 ENSG00000259563 ZSCAN29 WDR76 SPG11 TUBGCP4 ENSG00000249839
GH15J043823 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 31.7 -495.4 -495406 5.7 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 GLIS1 NBN WDR76 MFAP1 CTDSPL2 SPG11 ZSCAN29 ENSG00000259563 LCMT2 ENSG00000249839 ELL3 ADAL
GH15J043508 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.9 -179.5 -179509 3.5 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B E2F8 TP53BP1 MAP1A GC15M043498 ZSCAN29 CTDSPL2 ADAL CDAN1 LRRC57 LCMT2 UBR1
GH15J042493 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.1 +835.3 835317 3.7 HDGF PKNOX1 ARNT ARID4B SIN3A YBX1 DMAP1 ZNF2 YY1 SLC30A9 SNAP23 LRRC57 CDAN1 GANC ZSCAN29 HAUS2 MGA LCMT2 LOC105370795 VPS39
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCMT2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LCMT2 gene promoter:
  • TBP
  • NF-AT4
  • NF-AT3
  • NF-AT2
  • NF-AT1
  • NF-AT
  • HTF
  • Evi-1
  • POU3F2
  • CHOP-10

Genomic Locations for LCMT2 Gene

Genomic Locations for LCMT2 Gene
chr15:43,323,649-43,330,622
(GRCh38/hg38)
Size:
6,974 bases
Orientation:
Minus strand
chr15:43,619,974-43,622,820
(GRCh37/hg19)
Size:
2,847 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=401401, isoforms=356, and isoforms=24
  • 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

Gene Families for LCMT2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

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 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.
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).

Enzyme Numbers (IUBMB) for LCMT2 Gene

Phenotypes From GWAS Catalog 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
genes like me logo Genes that share phenotypes with LCMT2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCMT2

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

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:0006481 C-terminal protein methylation IBA --
GO:0008033 tRNA processing IEA --
GO:0030488 tRNA methylation IBA --
GO:0031591 wybutosine biosynthetic process IBA --
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

(1) 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

(1) Additional Compounds for LCMT2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with LCMT2: view

Transcripts for LCMT2 Gene

mRNA/cDNA for LCMT2 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(94) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LCMT2 Gene

Leucine carboxyl methyltransferase 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCMT2

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, 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

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 33
  • 86.91 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LCMT2 34 33
  • 85.74 (n)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LCMT2 34
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lcmt2 16 34 33
  • 80.86 (n)
rat
(Rattus norvegicus)
Mammalia Lcmt2 33
  • 80.03 (n)
chicken
(Gallus gallus)
Aves LCMT2 34 33
  • 57.53 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LCMT2 34
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lcmt2 33
  • 53.98 (n)
zebrafish
(Danio rerio)
Actinopterygii lcmt2 34 33
  • 52.57 (n)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL194W 33
  • 43.48 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PPM2 36 34 33
  • 41.63 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05392 33
  • 43.21 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC19C7.08c 33
  • 37.74 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10693 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for LCMT2: view image

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 Variation AA Info Type
rs1001536599 -- 43,329,894(-) G/A coding_sequence_variant, missense_variant
rs1001757263 -- 43,332,342(-) T/A upstream_transcript_variant
rs1001798952 -- 43,327,787(-) A/G 3_prime_UTR_variant
rs1002134103 -- 43,329,239(-) G/C coding_sequence_variant, synonymous_variant
rs1002655249 -- 43,331,720(-) G/C upstream_transcript_variant

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)

Additional Variant Information for LCMT2 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LCMT2 Gene

Additional Disease Information for 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 research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. p53RFP, a p53-inducible RING-finger protein, regulates the stability of p21WAF1. (PMID: 12853982) Ng CC … Nakamura Y (Oncogene 2003) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Widespread macromolecular interaction perturbations in human genetic disorders. (PMID: 25910212) Sahni N … Vidal M (Cell 2015) 3 58

Products for LCMT2 Gene

Sources for LCMT2 Gene

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