Pcm1 (pericentriolar material 1) - Rat Genome Database
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Gene: Pcm1 (pericentriolar material 1) Rattus norvegicus
Analyze
Symbol: Pcm1
Name: pericentriolar material 1
RGD ID: 620901
Description: Involved in protein localization to centrosome. Predicted to localize to several cellular components, including ciliary transition zone; microtubule organizing center; and nuclear membrane. Orthologous to human PCM1 (pericentriolar material 1); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: VALIDATED
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
Rnor_6.01654,040,721 - 54,137,675 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1654,040,721 - 54,137,660 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01653,754,432 - 53,851,417 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41654,321,572 - 54,419,178 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11654,321,927 - 54,330,026 (-)NCBI
Celera1648,903,540 - 49,000,197 (-)NCBICelera
Cytogenetic Map16q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Additional References at PubMed
PMID:10579718   PMID:12571289   PMID:15616553   PMID:17574030   PMID:19946888   PMID:20152126   PMID:20719959   PMID:21399614   PMID:21725312   PMID:21985783   PMID:22031837   PMID:22333836  
PMID:22797915   PMID:23533177   PMID:23789104   PMID:24415959   PMID:24421332   PMID:24469809   PMID:24550735   PMID:24648492   PMID:24816561   PMID:25697395   PMID:27979967  


Genomics

Comparative Map Data
Pcm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01654,040,721 - 54,137,675 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1654,040,721 - 54,137,660 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01653,754,432 - 53,851,417 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41654,321,572 - 54,419,178 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11654,321,927 - 54,330,026 (-)NCBI
Celera1648,903,540 - 49,000,197 (-)NCBICelera
Cytogenetic Map16q12.1NCBI
PCM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl817,922,840 - 18,027,975 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl817,922,840 - 18,029,944 (+)EnsemblGRCh38hg38GRCh38
GRCh38817,922,784 - 18,029,948 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37817,780,364 - 17,887,457 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36817,824,646 - 17,931,737 (+)NCBINCBI36hg18NCBI36
Build 34817,824,778 - 17,929,764NCBI
Celera816,746,248 - 16,853,370 (+)NCBI
Cytogenetic Map8p22NCBI
HuRef816,324,235 - 16,431,242 (+)NCBIHuRef
CHM1_1817,981,819 - 18,088,914 (+)NCBICHM1_1
Pcm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39841,692,521 - 41,787,125 (+)NCBIGRCm39mm39
GRCm38841,239,484 - 41,334,088 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl841,239,752 - 41,332,344 (+)EnsemblGRCm38mm10GRCm38
MGSCv37842,325,113 - 42,419,441 (+)NCBIGRCm37mm9NCBIm37
MGSCv36842,738,590 - 42,831,161 (+)NCBImm8
Celera843,861,512 - 43,957,470 (+)NCBICelera
Cytogenetic Map8A4NCBI
cM Map823.89NCBI
Pcm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555521,675,477 - 1,768,900 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555521,675,477 - 1,768,902 (-)NCBIChiLan1.0ChiLan1.0
PCM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1814,093,976 - 14,199,691 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl814,093,988 - 14,199,691 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0817,140,458 - 17,246,165 (+)NCBIMhudiblu_PPA_v0panPan3
PCM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1641,214,417 - 41,291,376 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11641,212,733 - 41,291,654 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pcm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365547,906 - 86,187 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl175,597,039 - 5,690,265 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1175,596,926 - 5,705,752 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2176,261,081 - 6,295,165 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PCM1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl816,017,972 - 16,125,145 (+)Ensembl
ChlSab1.1816,018,414 - 16,124,846 (+)NCBI
Pcm1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476921,153,243 - 21,262,327 (-)NCBI

Position Markers
RH133624  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01654,068,671 - 54,068,856NCBIRnor6.0
Rnor_5.01653,782,465 - 53,782,650UniSTSRnor5.0
RGSC_v3.41654,349,556 - 54,349,741UniSTSRGSC3.4
Celera1648,931,710 - 48,931,895UniSTS
Cytogenetic Map16q12.1UniSTS
RH 3.4 Map16523.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)162075555680316424Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162484654169846541Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162751998072519980Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162834031573340315Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)163530711063909364Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163900002184000021Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:36
Interacting mature miRNAs:40
Transcripts:ENSRNOT00000014202
Prediction methods: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.


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 41 48 32 19 32 8 10 74 34 41 11 8
Low 2 9 9 9 1 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07025892 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01088114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01088115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01088116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01088117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01088118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01088119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01088120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U95920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000014202   ⟹   ENSRNOP00000014202
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1654,040,721 - 54,137,485 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085435   ⟹   ENSRNOP00000071613
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1654,040,847 - 54,137,660 (-)Ensembl
RefSeq Acc Id: NM_031076   ⟹   NP_112338
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,485 (-)NCBI
Rnor_5.01653,754,432 - 53,851,417 (-)NCBI
RGSC_v3.41654,321,572 - 54,419,178 (-)RGD
Celera1648,903,540 - 49,000,197 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253183   ⟹   XP_006253245
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,674 (-)NCBI
Rnor_5.01653,754,432 - 53,851,417 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253184   ⟹   XP_006253246
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,675 (-)NCBI
Rnor_5.01653,754,432 - 53,851,417 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253185   ⟹   XP_006253247
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,675 (-)NCBI
Rnor_5.01653,754,432 - 53,851,417 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253186   ⟹   XP_006253248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,674 (-)NCBI
Rnor_5.01653,754,432 - 53,851,417 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253187   ⟹   XP_006253249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,674 (-)NCBI
Rnor_5.01653,754,432 - 53,851,417 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253188   ⟹   XP_006253250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,674 (-)NCBI
Rnor_5.01653,754,432 - 53,851,417 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771284   ⟹   XP_008769506
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,675 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771285   ⟹   XP_008769507
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,136,431 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771286   ⟹   XP_008769508
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,240 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600257   ⟹   XP_017455746
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,040,721 - 54,137,673 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112338   ⟸   NM_031076
- UniProtKB: G3V7E6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253247   ⟸   XM_006253185
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006253250   ⟸   XM_006253188
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006253249   ⟸   XM_006253187
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006253248   ⟸   XM_006253186
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006253245   ⟸   XM_006253183
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0X1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253246   ⟸   XM_006253184
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0X1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769506   ⟸   XM_008771284
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0X1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769508   ⟸   XM_008771286
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0X1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769507   ⟸   XM_008771285
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0X1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455746   ⟸   XM_017600257
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000071613   ⟸   ENSRNOT00000085435
RefSeq Acc Id: ENSRNOP00000014202   ⟸   ENSRNOT00000014202
Protein Domains
PCM1_C

Transcriptome

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

Promoters
RGD ID:13700115
Promoter ID:EPDNEW_R10639
Type:multiple initiation site
Name:Pcm1_2
Description:pericentriolar material 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10640  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,137,486 - 54,137,546EPDNEW
RGD ID:13700126
Promoter ID:EPDNEW_R10640
Type:initiation region
Name:Pcm1_1
Description:pericentriolar material 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10639  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01654,137,639 - 54,137,699EPDNEW

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)
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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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 53757056 53757057 C T snv DOB/Oda (KyushuU)
16 53771395 53771396 C T snv KFRS3B/Kyo (KyushuU), GH/OmrMcwi (MCW), SBH/Ygl (MCW), MR/N (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), SDLEF7/Barth (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), BDIX.Cg-Tal/NemOda (KyushuU)
16 53797036 53797037 T G snv DOB/Oda (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 54057684 54057685 C T snv ACI/EurMcwi (MCW), WKY/NHsd (RGD), GH/OmrMcwi (MCW), SBH/Ygl (MCW), CDS, ACI/N (MCW), F344/NRrrc (MCW), MR/N (MCW), WKY/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), SBH/Ygl (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), COP/CrCrl (MCW & UW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 54338535 54338536 C T snv ACI/N (KNAW), F344/NHsd (ICAHN), MR/N (KNAW), WKY/N (KNAW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), F344/NCrl (ICL), SBH/Ygl (ICL), WAG/Rij (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), F344/NRrrc (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620901 AgrOrtholog
Ensembl Genes ENSRNOG00000010155 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014202 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071613 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014202 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085435 ENTREZGENE, UniProtKB/TrEMBL
InterPro PCM1_C UniProtKB/TrEMBL
  Pericentriolar_Pcm1 UniProtKB/TrEMBL
KEGG Report rno:81740 UniProtKB/TrEMBL
NCBI Gene 81740 ENTREZGENE
PANTHER PTHR14164 UniProtKB/TrEMBL
Pfam PCM1_C UniProtKB/TrEMBL
PhenoGen Pcm1 PhenoGen
UniGene Rn.98622 ENTREZGENE
UniProt A0A0G2K0X1 ENTREZGENE, UniProtKB/TrEMBL
  G3V7E6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pcm1  pericentriolar material 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pcm1  pericentriolar material 1      Symbol and Name status set to provisional 70820 PROVISIONAL