Pcmtd2 (protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2) - Rat Genome Database

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Gene: Pcmtd2 (protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2) Rattus norvegicus
Analyze
Symbol: Pcmtd2
Name: protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2
RGD ID: 1305684
Description: Predicted to enable protein-L-isoaspartate (D-aspartate) O-methyltransferase activity. Predicted to be involved in protein methylation. Predicted to be active in cytoplasm. Orthologous to human PCMTD2 (protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2); INTERACTS WITH (+)-schisandrin B; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC311726; protein-L-isoaspartate O-methyltransferase domain-containing protein 2; RGD1305684; similar to RIKEN cDNA 5330414D10
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23168,960,312 - 168,979,504 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,960,305 - 168,979,497 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3173,336,814 - 173,356,403 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03182,295,915 - 182,315,504 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03178,961,232 - 178,980,422 (+)NCBIRnor_WKY
Rnor_6.03177,351,505 - 177,371,470 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,351,518 - 177,371,468 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03181,059,923 - 181,079,779 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,995,554 - 171,014,586 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,901,268 - 170,918,441 (+)NCBI
Celera3163,611,163 - 163,630,268 (-)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Pcmtd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23168,960,312 - 168,979,504 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,960,305 - 168,979,497 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3173,336,814 - 173,356,403 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03182,295,915 - 182,315,504 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03178,961,232 - 178,980,422 (+)NCBIRnor_WKY
Rnor_6.03177,351,505 - 177,371,470 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,351,518 - 177,371,468 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03181,059,923 - 181,079,779 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,995,554 - 171,014,586 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,901,268 - 170,918,441 (+)NCBI
Celera3163,611,163 - 163,630,268 (-)NCBICelera
Cytogenetic Map3q43NCBI
PCMTD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382064,255,748 - 64,276,226 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2064,255,695 - 64,304,820 (+)EnsemblGRCh38hg38GRCh38
GRCh372062,887,101 - 62,907,579 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362062,357,492 - 62,378,023 (+)NCBINCBI36Build 36hg18NCBI36
Build 342062,357,564 - 62,377,837NCBI
Celera2059,571,881 - 59,592,247 (+)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2059,616,146 - 59,632,058 (+)NCBIHuRef
CHM1_12062,788,098 - 62,808,350 (+)NCBICHM1_1
T2T-CHM13v2.02066,076,524 - 66,096,786 (+)NCBIT2T-CHM13v2.0
Pcmtd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392181,471,952 - 181,499,253 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2181,479,647 - 181,499,254 (+)EnsemblGRCm39 Ensembl
GRCm382181,830,159 - 181,857,460 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2181,837,854 - 181,857,461 (+)EnsemblGRCm38mm10GRCm38
MGSCv372181,572,608 - 181,592,155 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362181,767,309 - 181,786,856 (+)NCBIMGSCv36mm8
Celera2185,913,724 - 185,933,283 (+)NCBICelera
Cytogenetic Map2H4NCBI
Pcmtd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555289,847 - 22,332 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555287,931 - 26,228 (-)NCBIChiLan1.0ChiLan1.0
PCMTD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12062,167,519 - 62,186,183 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2062,167,519 - 62,186,183 (+)Ensemblpanpan1.1panPan2
PCMTD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12447,649,520 - 47,672,218 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2447,649,555 - 47,672,121 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2446,782,969 - 46,805,871 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02448,788,619 - 48,811,498 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2448,788,622 - 48,811,495 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12447,633,163 - 47,656,033 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02447,757,486 - 47,779,955 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02448,496,932 - 48,519,375 (+)NCBIUU_Cfam_GSD_1.0
Pcmtd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640195,921,968 - 195,942,680 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651411,378,057 - 11,396,323 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493651411,378,101 - 11,396,323 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCMTD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1763,029,289 - 63,049,703 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11763,029,273 - 63,073,055 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PCMTD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1211,397 - 31,197 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605047,405,995 - 47,425,835 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcmtd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474129,861,995 - 29,871,240 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474129,857,415 - 29,871,941 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pcmtd2
38 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:756
Count of miRNA genes:317
Interacting mature miRNAs:403
Transcripts:ENSRNOT00000023989
Prediction methods:Microtar, Miranda
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat

Markers in Region
D3Mco36  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,974,481 - 168,974,694 (+)MAPPERmRatBN7.2
Rnor_6.03177,366,448 - 177,366,660NCBIRnor6.0
Rnor_5.03181,074,759 - 181,074,971UniSTSRnor5.0
RGSC_v3.43171,009,566 - 171,009,778UniSTSRGSC3.4
Celera3163,615,971 - 163,616,183UniSTS
Cytogenetic Map3q43UniSTS
RH139806  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,979,257 - 168,979,475 (+)MAPPERmRatBN7.2
Rnor_6.03177,371,224 - 177,371,441NCBIRnor6.0
Rnor_5.03181,079,535 - 181,079,752UniSTSRnor5.0
RGSC_v3.43171,014,342 - 171,014,559UniSTSRGSC3.4
Celera3163,611,190 - 163,611,407UniSTS
RH 3.4 Map31556.2UniSTS
Cytogenetic Map3q43UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 10 74 35 39 11 8
Low 1 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023989   ⟹   ENSRNOP00000023989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,960,305 - 168,979,497 (+)Ensembl
Rnor_6.0 Ensembl3177,351,518 - 177,371,468 (+)Ensembl
RefSeq Acc Id: NM_001107810   ⟹   NP_001101280
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,960,312 - 168,979,502 (+)NCBI
Rnor_6.03177,351,518 - 177,371,468 (+)NCBI
Rnor_5.03181,059,923 - 181,079,779 (+)NCBI
RGSC_v3.43170,995,554 - 171,014,586 (+)RGD
Celera3163,611,163 - 163,630,268 (-)RGD
Sequence:
RefSeq Acc Id: XM_039105159   ⟹   XP_038961087
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,964,869 - 168,979,504 (+)NCBI
RefSeq Acc Id: XM_039105160   ⟹   XP_038961088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,964,869 - 168,979,504 (+)NCBI
RefSeq Acc Id: XR_005501904
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,964,869 - 168,977,085 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101280   ⟸   NM_001107810
- UniProtKB: D3ZY20 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023989   ⟸   ENSRNOT00000023989
RefSeq Acc Id: XP_038961088   ⟸   XM_039105160
- Peptide Label: isoform X2
- UniProtKB: D3ZY20 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961087   ⟸   XM_039105159
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZY20-F1-model_v2 AlphaFold D3ZY20 1-359 view protein structure

Transcriptome

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

Promoters
RGD ID:13692767
Promoter ID:EPDNEW_R3290
Type:initiation region
Name:Pcmtd2_1
Description:protein-L-isoaspartate (D-aspartate) O-methyltransferase domaincontaining 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_6.03177,351,519 - 177,351,579EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305684 AgrOrtholog
BioCyc Gene G2FUF-46258 BioCyc
Ensembl Genes ENSRNOG00000017404 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000023989 ENTREZGENE
  ENSRNOP00000023989.7 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023989 ENTREZGENE
  ENSRNOT00000023989.7 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.150 UniProtKB/TrEMBL
InterPro PCMT UniProtKB/TrEMBL
  SAM-dependent_MTases-like UniProtKB/TrEMBL
KEGG Report rno:311726 UniProtKB/TrEMBL
NCBI Gene 311726 ENTREZGENE
PANTHER PCMT UniProtKB/TrEMBL
PhenoGen Pcmtd2 PhenoGen
Superfamily-SCOP SSF53335 UniProtKB/TrEMBL
UniProt B5DF20_RAT UniProtKB/TrEMBL
  D3ZY20 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pcmtd2  protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2   Pcmtd2_predicted  protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Pcmtd2_predicted  protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2 (predicted)  RGD1305684_predicted  similar to RIKEN cDNA 5330414D10 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1305684_predicted  similar to RIKEN cDNA 5330414D10 (predicted)  LOC311726_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC311726_predicted  similar to RIKEN cDNA 5330414D10 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL