Lcmt2 (leucine carboxyl methyltransferase 2) - Rat Genome Database

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Gene: Lcmt2 (leucine carboxyl methyltransferase 2) Rattus norvegicus
Analyze
Symbol: Lcmt2
Name: leucine carboxyl methyltransferase 2
RGD ID: 1305829
Description: Predicted to enable tRNA methyltransferase activity. Predicted to be involved in tRNA methylation and wybutosine biosynthetic process. Orthologous to human LCMT2 (leucine carboxyl methyltransferase 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC296098; tRNA wybutosine-synthesizing protein 4; tRNA wybutosine-synthesizing protein 4 homolog; tRNA yW-synthesizing protein 4 homolog; tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase; tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)-methyltransferase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83128,553,707 - 128,555,831 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3128,553,052 - 128,590,969 (-)EnsemblGRCr8
mRatBN7.23108,099,960 - 108,102,084 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3108,099,961 - 108,102,084 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3111,774,717 - 111,776,841 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03120,370,300 - 120,372,424 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03118,030,695 - 118,032,819 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03113,089,646 - 113,091,770 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3113,089,647 - 113,091,770 (-)Ensemblrn6Rnor6.0
Rnor_5.03119,629,543 - 119,631,667 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43107,929,444 - 107,931,568 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3107,004,026 - 107,006,150 (-)NCBICelera
RGSC_v3.13107,825,872 - 107,827,996 (-)NCBI
Cytogenetic Map3q35NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Lcmt2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83128,553,707 - 128,555,831 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3128,553,052 - 128,590,969 (-)EnsemblGRCr8
mRatBN7.23108,099,960 - 108,102,084 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3108,099,961 - 108,102,084 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3111,774,717 - 111,776,841 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03120,370,300 - 120,372,424 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03118,030,695 - 118,032,819 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03113,089,646 - 113,091,770 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3113,089,647 - 113,091,770 (-)Ensemblrn6Rnor6.0
Rnor_5.03119,629,543 - 119,631,667 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43107,929,444 - 107,931,568 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3107,004,026 - 107,006,150 (-)NCBICelera
RGSC_v3.13107,825,872 - 107,827,996 (-)NCBI
Cytogenetic Map3q35NCBI
LCMT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381543,323,649 - 43,330,573 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1543,323,649 - 43,330,582 (-)Ensemblhg38GRCh38
GRCh371543,615,847 - 43,622,771 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361541,407,266 - 41,410,183 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341541,407,267 - 41,410,183NCBI
Celera1520,390,821 - 20,393,738 (-)NCBICelera
Cytogenetic Map15q15.3NCBI
HuRef1520,468,716 - 20,471,562 (-)NCBIHuRef
CHM1_11543,738,640 - 43,741,486 (-)NCBICHM1_1
T2T-CHM13v2.01541,130,950 - 41,137,880 (-)NCBIT2T-CHM13v2.0
Lcmt2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392120,967,773 - 120,971,179 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2120,958,788 - 120,971,134 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm382121,137,292 - 121,140,698 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2121,128,307 - 121,140,653 (-)Ensemblmm10GRCm38
MGSCv372120,963,028 - 120,966,434 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362120,819,748 - 120,832,479 (-)NCBIMGSCv36mm8
Celera2122,289,530 - 122,292,947 (-)NCBICelera
Cytogenetic Map2E5NCBI
cM Map260.37NCBI
Lcmt2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554169,890,208 - 9,892,326 (-)NCBIChiLan1.0ChiLan1.0
LCMT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21632,579,427 - 32,582,140 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11536,741,161 - 36,743,874 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01522,288,992 - 22,291,814 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11540,443,981 - 40,447,059 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1540,444,633 - 40,446,693 (-)EnsemblpanPan2panpan1.1
LCMT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13010,187,424 - 10,191,213 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3010,190,243 - 10,191,114 (-)NCBIcanFam3CanFam3.1
CanFam3.1 Ensembl3010,190,243 - 10,191,114 (-)EnsemblcanFam3CanFam3.1
ROS_Cfam_1.03010,323,377 - 10,327,195 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
Lcmt2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864088,650,881 - 88,653,742 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364716,499,623 - 6,501,680 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364716,498,300 - 6,501,811 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LCMT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11128,125,674 - 128,131,064 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21142,982,328 - 142,984,549 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LCMT2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12639,670,087 - 39,672,753 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2639,670,106 - 39,672,163 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666048101,340,900 - 101,343,745 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lcmt2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480410,436,731 - 10,438,785 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462480410,436,000 - 10,438,806 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Lcmt2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1599,283,763 - 99,286,008 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lcmt2
29 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:78
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000068132
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)396509147141509147Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)373592512136118980Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3122654702136118980Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)349872657138829559Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)3116582412136118980Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)385062224136118980Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)385062224136118980Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)3104545086149545086Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)381425008141509147Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)370845569136091483Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)393829559138829559Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)3112250810157250810Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3101255536134750886Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)396509147141509147Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3117537367162537367Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3125116475170116475Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3110225882155225882Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)390755164141509147Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3122395989167395989Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)398651826167012663Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)3125814931139636791Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3110634702155634702Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3116188400161188400Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000068132   ⟹   ENSRNOP00000060993
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3128,553,141 - 128,558,309 (-)Ensembl
mRatBN7.2 Ensembl3108,099,961 - 108,102,084 (-)Ensembl
Rnor_6.0 Ensembl3113,089,647 - 113,091,770 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000128667   ⟹   ENSRNOP00000111141
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3128,553,052 - 128,590,969 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000132231   ⟹   ENSRNOP00000099837
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3128,553,190 - 128,590,969 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000154533   ⟹   ENSRNOP00000099232
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3128,553,509 - 128,585,508 (-)Ensembl
RefSeq Acc Id: NM_001011956   ⟹   NP_001011956
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83128,553,707 - 128,555,831 (-)NCBI
mRatBN7.23108,099,960 - 108,102,084 (-)NCBI
Rnor_6.03113,089,646 - 113,091,770 (-)NCBI
Rnor_5.03119,629,543 - 119,631,667 (-)NCBI
RGSC_v3.43107,929,444 - 107,931,568 (-)RGD
Celera3107,004,026 - 107,006,150 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001011956 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83783 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000060993.1
GenBank Protein Q5XIA3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001011956   ⟸   NM_001011956
- UniProtKB: Q5XIA3 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000060993   ⟸   ENSRNOT00000068132
Ensembl Acc Id: ENSRNOP00000099837   ⟸   ENSRNOT00000132231
Ensembl Acc Id: ENSRNOP00000099232   ⟸   ENSRNOT00000154533
Ensembl Acc Id: ENSRNOP00000111141   ⟸   ENSRNOT00000128667

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIA3-F1-model_v2 AlphaFold Q5XIA3 1-686 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13692350
Promoter ID:EPDNEW_R2875
Type:single initiation site
Name:Lcmt2_1
Description:leucine carboxyl methyltransferase 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03113,091,766 - 113,091,826EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305829 AgrOrtholog
BioCyc Gene G2FUF-48145 BioCyc
Ensembl Genes ENSRNOG00000043002 Ensembl, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000068132.3 UniProtKB/Swiss-Prot
Gene3D-CATH 2.120.10.80 UniProtKB/Swiss-Prot
  3.40.50.150 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7096502 IMAGE-MGC_LOAD
InterPro Gal_Oxase/kelch_b-propeller UniProtKB/Swiss-Prot
  Kelch-typ_b-propeller UniProtKB/Swiss-Prot
  Ppm1/Ppm2/Tcmp UniProtKB/Swiss-Prot
  SAM-dependent_MTases UniProtKB/Swiss-Prot
KEGG Report rno:296098 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94756 IMAGE-MGC_LOAD
NCBI Gene 296098 ENTREZGENE
PANTHER TRNA WYBUTOSINE-SYNTHESIZING PROTEIN 4 UniProtKB/Swiss-Prot
  TRNA WYBUTOSINE-SYNTHESIZING PROTEIN 4 UniProtKB/Swiss-Prot
Pfam Kelch_KLHDC2_KLHL20_DRC7 UniProtKB/Swiss-Prot
  LCM UniProtKB/Swiss-Prot
PhenoGen Lcmt2 PhenoGen
RatGTEx ENSRNOG00000043002 RatGTEx
Superfamily-SCOP SSF117281 UniProtKB/Swiss-Prot
  SSF50965 UniProtKB/Swiss-Prot
  SSF53335 UniProtKB/Swiss-Prot
UniProt A0ABK0KX74_RAT UniProtKB/TrEMBL
  A0ABK0LAX9_RAT UniProtKB/TrEMBL
  A0ABK0M6D0_RAT UniProtKB/TrEMBL
  Q5XIA3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Lcmt2  leucine carboxyl methyltransferase 2  Lcmt2_predicted  leucine carboxyl methyltransferase 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Lcmt2_predicted  leucine carboxyl methyltransferase 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED