Pcmt1 (protein-L-isoaspartate (D-aspartate) O-methyltransferase 1) - Rat Genome Database

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Gene: Pcmt1 (protein-L-isoaspartate (D-aspartate) O-methyltransferase 1) Rattus norvegicus
Analyze
Symbol: Pcmt1
Name: protein-L-isoaspartate (D-aspartate) O-methyltransferase 1
RGD ID: 3268
Description: Exhibits protein-L-isoaspartate (D-aspartate) O-methyltransferase activity. Involved in several processes, including S-adenosylhomocysteine metabolic process; negative regulation of cardiac muscle cell apoptotic process; and response to ethanol. Localizes to several cellular components, including basolateral plasma membrane; brush border membrane; and perikaryon. Biomarker of high grade glioma. Orthologous to human PCMT1 (protein-L-isoaspartate (D-aspartate) O-methyltransferase); PARTICIPATES IN homocysteine metabolic pathway; methionine cycle/metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: L-isoaspartyl protein carboxyl methyltransferase; MGC95039; PCM; PIMT; protein L-isoaspartyl/D-aspartyl methyltransferase; protein-beta-aspartate methyltransferase; Protein-L-isoaspartate (D-aspartate) O-methyltransferase; protein-L-isoaspartate(D-aspartate) O-methyltransferase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.212,111,756 - 2,160,354 (-)NCBI
Rnor_6.0 Ensembl11,736,276 - 1,767,618 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.011,734,863 - 1,767,759 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013,432,543 - 3,464,945 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.412,287,981 - 2,304,638 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.112,287,981 - 2,304,638 (-)NCBI
Celera1659,884 - 692,976 (-)NCBICelera
Cytogenetic Map1p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12023972   PMID:12477932   PMID:12943661   PMID:15489334   PMID:16959769   PMID:23376485   PMID:23533145   PMID:24358311   PMID:24769233   PMID:25468996   PMID:26973341  


Genomics

Comparative Map Data
Pcmt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.212,111,756 - 2,160,354 (-)NCBI
Rnor_6.0 Ensembl11,736,276 - 1,767,618 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.011,734,863 - 1,767,759 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013,432,543 - 3,464,945 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.412,287,981 - 2,304,638 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.112,287,981 - 2,304,638 (-)NCBI
Celera1659,884 - 692,976 (-)NCBICelera
Cytogenetic Map1p13NCBI
PCMT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6149,749,443 - 149,811,420 (+)EnsemblGRCh38hg38GRCh38
GRCh386149,749,695 - 149,811,421 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376150,070,831 - 150,132,557 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366150,112,658 - 150,174,249 (+)NCBINCBI36hg18NCBI36
Build 346150,163,078 - 150,224,670NCBI
Celera6150,806,092 - 150,867,242 (+)NCBI
Cytogenetic Map6q25.1NCBI
HuRef6147,636,598 - 147,698,401 (+)NCBIHuRef
CHM1_16150,335,452 - 150,397,161 (+)NCBICHM1_1
Pcmt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39107,503,609 - 7,557,101 (-)NCBIGRCm39mm39
GRCm39 Ensembl107,505,137 - 7,556,900 (-)Ensembl
GRCm38107,627,845 - 7,681,337 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl107,629,373 - 7,681,136 (-)EnsemblGRCm38mm10GRCm38
MGSCv37107,350,034 - 7,383,382 (-)NCBIGRCm37mm9NCBIm37
MGSCv36107,320,426 - 7,353,440 (-)NCBImm8
Celera107,508,777 - 7,541,151 (-)NCBICelera
Cytogenetic Map10A1NCBI
cM Map102.26NCBI
Pcmt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543911,480,101 - 11,531,839 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543911,480,094 - 11,531,842 (-)NCBIChiLan1.0ChiLan1.0
PCMT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16152,271,206 - 152,329,221 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v06147,564,783 - 147,623,402 (+)NCBIMhudiblu_PPA_v0panPan3
PCMT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1140,494,441 - 40,539,453 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl140,494,461 - 40,538,937 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha141,333,804 - 41,378,660 (+)NCBI
ROS_Cfam_1.0140,676,439 - 40,721,295 (+)NCBI
UMICH_Zoey_3.1140,552,247 - 40,597,034 (+)NCBI
UNSW_CanFamBas_1.0140,418,203 - 40,463,029 (+)NCBI
UU_Cfam_GSD_1.0140,758,673 - 40,803,514 (+)NCBI
Pcmt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946135,425,633 - 135,470,265 (+)NCBI
SpeTri2.0NW_0049364892,677,740 - 2,720,387 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCMT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl116,198,223 - 16,249,531 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1116,202,859 - 16,249,879 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2118,440,912 - 18,462,186 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PCMT1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11321,808,583 - 21,867,309 (-)NCBI
ChlSab1.1 Ensembl1321,807,710 - 21,866,768 (-)Ensembl
Pcmt1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247858,267,328 - 8,326,550 (-)NCBI

Position Markers
RH130061  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.212,111,812 - 2,112,007 (+)MAPPER
Rnor_6.011,734,913 - 1,735,107NCBIRnor6.0
Rnor_5.013,432,593 - 3,432,787UniSTSRnor5.0
RGSC_v3.412,288,031 - 2,288,225UniSTSRGSC3.4
Celera1659,934 - 660,128UniSTS
RH 3.4 Map51057.3UniSTS
Cytogenetic Map1p13UniSTS
RH130661  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.212,112,576 - 2,112,788 (+)MAPPER
Rnor_6.011,735,677 - 1,735,888NCBIRnor6.0
Rnor_5.013,433,357 - 3,433,568UniSTSRnor5.0
RGSC_v3.412,288,795 - 2,289,006UniSTSRGSC3.4
Celera1660,698 - 660,909UniSTS
RH 3.4 Map112.3UniSTS
Cytogenetic Map1p13UniSTS
RH140246  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.011,736,221 - 1,736,421NCBIRnor6.0
Rnor_5.013,433,901 - 3,434,101UniSTSRnor5.0
RGSC_v3.412,289,339 - 2,289,532UniSTSRGSC3.4
Celera1661,242 - 661,435UniSTS
RH 3.4 Map119.3UniSTS
Cytogenetic Map1p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124368159Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128468970Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1134993530Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1134993530Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1134993530Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1164407321Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)125439343579402Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)125439343579402Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)125439343579402Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:145
Count of miRNA genes:120
Interacting mature miRNAs:126
Transcripts:ENSRNOT00000019623
Prediction methods:Microtar, Miranda, Rnahybrid
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.


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 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_013073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC088417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D11475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000019623   ⟹   ENSRNOP00000019623
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl11,736,276 - 1,767,618 (-)Ensembl
RefSeq Acc Id: NM_013073   ⟹   NP_037205
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,763 - 2,144,094 (-)NCBI
Rnor_6.011,734,863 - 1,767,759 (-)NCBI
Rnor_5.013,432,543 - 3,464,945 (-)NCBI
RGSC_v3.412,287,981 - 2,304,638 (-)RGD
Celera1659,884 - 692,976 (-)RGD
Sequence:
RefSeq Acc Id: XM_039102029   ⟹   XP_038957957
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,763 - 2,144,368 (-)NCBI
RefSeq Acc Id: XM_039102032   ⟹   XP_038957960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,763 - 2,144,368 (-)NCBI
RefSeq Acc Id: XM_039102033   ⟹   XP_038957961
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,763 - 2,144,368 (-)NCBI
RefSeq Acc Id: XM_039102034   ⟹   XP_038957962
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,763 - 2,144,368 (-)NCBI
RefSeq Acc Id: XM_039102037   ⟹   XP_038957965
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,763 - 2,144,368 (-)NCBI
RefSeq Acc Id: XM_039102040   ⟹   XP_038957968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,763 - 2,144,368 (-)NCBI
RefSeq Acc Id: XM_039102043   ⟹   XP_038957971
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,763 - 2,144,368 (-)NCBI
RefSeq Acc Id: XM_039102046   ⟹   XP_038957974
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,756 - 2,133,297 (-)NCBI
RefSeq Acc Id: XM_039102049   ⟹   XP_038957977
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,756 - 2,143,676 (-)NCBI
RefSeq Acc Id: XM_039102053   ⟹   XP_038957981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,756 - 2,160,062 (-)NCBI
RefSeq Acc Id: XM_039102058   ⟹   XP_038957986
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212,111,763 - 2,160,354 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_037205   ⟸   NM_013073
- UniProtKB: P22062 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019623   ⟸   ENSRNOT00000019623
RefSeq Acc Id: XP_038957981   ⟸   XM_039102053
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038957977   ⟸   XM_039102049
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038957974   ⟸   XM_039102046
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038957986   ⟸   XM_039102058
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038957965   ⟸   XM_039102037
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038957968   ⟸   XM_039102040
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038957971   ⟸   XM_039102043
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038957962   ⟸   XM_039102034
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038957961   ⟸   XM_039102033
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038957957   ⟸   XM_039102029
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957960   ⟸   XM_039102032
- Peptide Label: isoform X2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3268 AgrOrtholog
Ensembl Genes ENSRNOG00000014330 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019623 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019623 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123213 IMAGE-MGC_LOAD
InterPro PCMT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM-dependent_MTases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25604 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95039 IMAGE-MGC_LOAD
NCBI Gene 25604 ENTREZGENE
PANTHER PTHR11579 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pcmt1 PhenoGen
PROSITE PCMT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53335 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs pimt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140TAB9_RAT UniProtKB/TrEMBL
  P22062 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5M7V6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Pcmt1  Protein-L-isoaspartate (D-aspartate) O-methyltransferase      Symbol and Name status set to approved 70586 APPROVED