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

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Pathways
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 active in cytoplasm. Orthologous to human PCMTD2 (protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83189,337,758 - 189,360,525 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3189,337,816 - 189,357,001 (+)EnsemblGRCr8
mRatBN7.23168,960,312 - 168,979,504 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,960,305 - 168,979,497 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3173,336,814 - 173,356,403 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03182,295,915 - 182,315,504 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,961,232 - 178,980,422 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03177,351,505 - 177,371,470 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,351,518 - 177,371,468 (+)Ensemblrn6Rnor6.0
Rnor_5.03181,059,923 - 181,079,779 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43170,995,554 - 171,014,586 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3163,611,163 - 163,630,268 (-)NCBICelera
RGSC_v3.13170,901,268 - 170,918,441 (+)NCBI
Cytogenetic Map3q43NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,IEA)

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
GRCr83189,337,758 - 189,360,525 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3189,337,816 - 189,357,001 (+)EnsemblGRCr8
mRatBN7.23168,960,312 - 168,979,504 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,960,305 - 168,979,497 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3173,336,814 - 173,356,403 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03182,295,915 - 182,315,504 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,961,232 - 178,980,422 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03177,351,505 - 177,371,470 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,351,518 - 177,371,468 (+)Ensemblrn6Rnor6.0
Rnor_5.03181,059,923 - 181,079,779 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43170,995,554 - 171,014,586 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3163,611,163 - 163,630,268 (-)NCBICelera
RGSC_v3.13170,901,268 - 170,918,441 (+)NCBI
Cytogenetic Map3q43NCBI
PCMTD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382064,255,748 - 64,276,226 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2064,254,921 - 64,304,820 (+)Ensemblhg38GRCh38
GRCh372062,887,101 - 62,907,579 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362062,357,492 - 62,378,023 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm382181,830,159 - 181,857,460 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2181,837,854 - 181,857,461 (+)Ensemblmm10GRCm38
MGSCv372181,572,608 - 181,592,155 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362181,767,309 - 181,786,856 (+)NCBIMGSCv36mm8
Celera2185,913,724 - 185,933,283 (+)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2103.81NCBI
Pcmtd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555289,847 - 22,332 (-)Ensembl
ChiLan1.0NW_0049555287,931 - 26,228 (-)NCBIChiLan1.0ChiLan1.0
PCMTD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22170,080,659 - 70,099,745 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12070,072,671 - 70,091,757 (+)NCBINHGRI_mPanPan1
PanPan1.12062,167,519 - 62,186,183 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2062,167,519 - 62,186,183 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2446,782,969 - 46,805,871 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02448,788,619 - 48,811,498 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 Ensembl
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 (+)EnsemblsusScr11Sscrofa11.1
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474129,857,415 - 29,871,941 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pcmtd2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1181,983 - 101,557 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3152055202189428310Rat
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)3145335553189428310Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3151075912189428310Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161492708189428310Rat
1582256Insul9Insulin level QTL 94.40.0016blood insulin amount (VT:0001560)absolute change in serum insulin level (CMO:0002038)3155759447189428310Rat
1582248Insul7Insulin level QTL 73.90.0041blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3151075912189428310Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3181611379189428310Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3166376089189428310Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3151075912189428310Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3144575244189428310Rat
1582213Insul6Insulin level QTL 63.70.0009blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3166376089189428310Rat

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
GRCr83189,356,760 - 189,356,978 (+)Marker Load Pipeline
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

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 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000023989   ⟹   ENSRNOP00000023989
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3189,337,816 - 189,357,001 (+)Ensembl
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
GRCr83189,337,815 - 189,357,005 (+)NCBI
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_039105160   ⟹   XP_038961088
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,337,758 - 189,360,525 (+)NCBI
mRatBN7.23168,964,869 - 168,979,504 (+)NCBI
RefSeq Acc Id: XM_063283906   ⟹   XP_063139976
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,337,847 - 189,360,525 (+)NCBI
RefSeq Acc Id: XM_063283907   ⟹   XP_063139977
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,337,758 - 189,360,525 (+)NCBI
RefSeq Acc Id: XM_063283909   ⟹   XP_063139979
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,337,758 - 189,353,509 (+)NCBI
RefSeq Acc Id: XM_063283910   ⟹   XP_063139980
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,337,758 - 189,353,497 (+)NCBI
RefSeq Acc Id: XR_010064642
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,337,758 - 189,360,525 (+)NCBI
RefSeq Acc Id: NP_001101280   ⟸   NM_001107810
- UniProtKB: A6KLV7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000023989   ⟸   ENSRNOT00000023989
RefSeq Acc Id: XP_038961088   ⟸   XM_039105160
- Peptide Label: isoform X2
- UniProtKB: D3ZY20 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139977   ⟸   XM_063283907
- Peptide Label: isoform X1
- UniProtKB: A6KLV7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139979   ⟸   XM_063283909
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063139980   ⟸   XM_063283910
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063139976   ⟸   XM_063283906
- Peptide Label: isoform X1
- UniProtKB: A6KLV7 (UniProtKB/TrEMBL)

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 Transcript ENSRNOT00000023989 ENTREZGENE
  ENSRNOT00000023989.8 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
  PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE DOMAIN-CONTAINING PROTEIN 2 UniProtKB/TrEMBL
Pfam PCMT UniProtKB/TrEMBL
PhenoGen Pcmtd2 PhenoGen
RatGTEx ENSRNOG00000017404 RatGTEx
Superfamily-SCOP SSF53335 UniProtKB/TrEMBL
UniProt A6KLV7 ENTREZGENE, UniProtKB/TrEMBL
  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