Ptprm (protein tyrosine phosphatase, receptor type, M) - Rat Genome Database

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Gene: Ptprm (protein tyrosine phosphatase, receptor type, M) Rattus norvegicus
Analyze
Symbol: Ptprm
Name: protein tyrosine phosphatase, receptor type, M
RGD ID: 620776
Description: Predicted to enable cadherin binding activity; identical protein binding activity; and transmembrane receptor protein tyrosine phosphatase activity. Predicted to be involved in several processes, including homophilic cell adhesion via plasma membrane adhesion molecules; retina layer formation; and retinal ganglion cell axon guidance. Predicted to act upstream of or within vasodilation. Predicted to be located in several cellular components, including adherens junction; lamellipodium; and perinuclear region of cytoplasm. Orthologous to human PTPRM (protein tyrosine phosphatase receptor type M); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: protein tyrosine phosphatase receptor-type M; protein tyrosine phosphatase, receptor-type, M; receptor-type tyrosine-protein phosphatase mu
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
mRatBN7.29106,639,573 - 107,343,698 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl9106,639,573 - 107,343,698 (-)Ensembl
Rnor_6.09114,846,095 - 115,555,261 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9114,846,095 - 115,555,261 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09114,341,760 - 115,047,495 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49105,784,922 - 106,503,148 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19106,019,977 - 106,025,031 (-)NCBI
Celera9103,813,416 - 104,503,006 (-)NCBICelera
Cytogenetic Map9q37NCBI
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:8393854   PMID:9531566   PMID:10809770   PMID:14623235   PMID:15080886   PMID:15491993   PMID:15706045   PMID:15978577   PMID:16380380   PMID:17276081   PMID:17965016   PMID:18566238  


Genomics

Comparative Map Data
Ptprm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.29106,639,573 - 107,343,698 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl9106,639,573 - 107,343,698 (-)Ensembl
Rnor_6.09114,846,095 - 115,555,261 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9114,846,095 - 115,555,261 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09114,341,760 - 115,047,495 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49105,784,922 - 106,503,148 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19106,019,977 - 106,025,031 (-)NCBI
Celera9103,813,416 - 104,503,006 (-)NCBICelera
Cytogenetic Map9q37NCBI
PTPRM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl187,566,782 - 8,406,861 (+)EnsemblGRCh38hg38GRCh38
GRCh38187,567,316 - 8,406,859 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37187,567,314 - 8,406,854 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36187,557,314 - 8,396,859 (+)NCBINCBI36hg18NCBI36
Build 34187,557,816 - 8,396,852NCBI
Celera187,451,391 - 8,291,215 (+)NCBI
Cytogenetic Map18p11.23NCBI
HuRef187,531,039 - 8,371,216 (+)NCBIHuRef
CHM1_1187,567,289 - 8,407,034 (+)NCBICHM1_1
Ptprm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391766,973,843 - 67,661,486 (-)NCBIGRCm39mm39
GRCm39 Ensembl1766,973,942 - 67,661,452 (-)Ensembl
GRCm381766,666,848 - 67,354,491 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1766,666,947 - 67,354,457 (-)EnsemblGRCm38mm10GRCm38
MGSCv371767,016,188 - 67,703,799 (-)NCBIGRCm37mm9NCBIm37
MGSCv361766,572,488 - 67,259,332 (-)NCBImm8
Celera1770,960,452 - 71,652,526 (-)NCBICelera
Cytogenetic Map17E1.1NCBI
cM Map1737.88NCBI
Ptprm
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554023,244,222 - 3,756,925 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554023,243,447 - 3,756,457 (-)NCBIChiLan1.0ChiLan1.0
PTPRM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1188,205,978 - 9,030,683 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl188,206,677 - 9,030,286 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0185,879,556 - 6,706,824 (-)NCBIMhudiblu_PPA_v0panPan3
PTPRM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1774,005,682 - 74,597,498 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl773,815,186 - 74,609,116 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha773,205,288 - 73,988,613 (+)NCBI
ROS_Cfam_1.0773,864,685 - 74,648,938 (+)NCBI
UMICH_Zoey_3.1773,566,351 - 74,351,414 (+)NCBI
UNSW_CanFamBas_1.0773,596,130 - 74,369,637 (+)NCBI
UU_Cfam_GSD_1.0773,895,451 - 74,674,439 (+)NCBI
Ptprm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494470,374,418 - 71,176,141 (+)NCBI
SpeTri2.0NW_004936670890,316 - 1,692,033 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl699,216,236 - 100,092,938 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1699,350,301 - 100,092,966 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2692,516,719 - 92,550,399 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11866,564,562 - 67,398,541 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1866,773,588 - 67,398,542 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605041,491,594 - 42,326,520 (+)NCBIVero_WHO_p1.0
Ptprm
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477016,900,925 - 17,507,775 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D9Rat71  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29107,078,745 - 107,078,837 (+)MAPPERmRatBN7.2
Rnor_6.09115,291,868 - 115,291,959NCBIRnor6.0
Rnor_5.09114,784,005 - 114,784,096UniSTSRnor5.0
RGSC_v3.49106,234,733 - 106,234,825RGDRGSC3.4
RGSC_v3.49106,234,734 - 106,234,825UniSTSRGSC3.4
RGSC_v3.19106,444,213 - 106,444,305RGD
Celera9104,238,125 - 104,238,216UniSTS
RH 2.0 Map91078.6RGD
SHRSP x BN Map977.2299RGD
FHH x ACI Map985.72RGD
Cytogenetic Map9q37UniSTS
D9Rat166  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29107,094,693 - 107,094,916 (+)MAPPERmRatBN7.2
Rnor_6.09115,307,816 - 115,308,038NCBIRnor6.0
Rnor_5.09114,799,953 - 114,800,175UniSTSRnor5.0
RGSC_v3.49106,250,681 - 106,250,903RGDRGSC3.4
RGSC_v3.49106,250,682 - 106,250,904UniSTSRGSC3.4
RGSC_v3.19106,460,161 - 106,460,383RGD
Celera9104,254,044 - 104,254,266UniSTS
SHRSP x BN Map977.2299RGD
SHRSP x BN Map977.2299UniSTS
Cytogenetic Map9q37UniSTS
RH143821  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29106,849,488 - 106,850,733 (+)MAPPERmRatBN7.2
Rnor_6.09115,056,475 - 115,057,719NCBIRnor6.0
Rnor_5.09114,549,344 - 114,550,588UniSTSRnor5.0
RGSC_v3.49106,004,398 - 106,005,642UniSTSRGSC3.4
Celera9104,016,441 - 104,017,685UniSTS
RH 3.4 Map4924.41UniSTS
Cytogenetic Map9q37UniSTS
BG371570  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29106,639,761 - 106,639,857 (+)MAPPERmRatBN7.2
Rnor_6.09114,846,284 - 114,846,379NCBIRnor6.0
Rnor_5.09114,341,949 - 114,342,044UniSTSRnor5.0
RGSC_v3.49105,785,111 - 105,785,206UniSTSRGSC3.4
Celera9103,813,605 - 103,813,700UniSTS
Cytogenetic Map9q37UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:548
Count of miRNA genes:254
Interacting mature miRNAs:322
Transcripts:ENSRNOT00000056366
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


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 43 7 12 8 11 64 29 34 11 8
Low 3 50 41 7 41 10 6 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001168632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596312 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083121 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U66567 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000056366   ⟹   ENSRNOP00000053204
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9106,639,573 - 107,343,698 (-)Ensembl
Rnor_6.0 Ensembl9114,846,095 - 115,555,261 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091316   ⟹   ENSRNOP00000074746
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9106,639,573 - 107,343,698 (-)Ensembl
Rnor_6.0 Ensembl9114,846,161 - 115,382,445 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106479   ⟹   ENSRNOP00000085971
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9106,654,353 - 107,343,698 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107262   ⟹   ENSRNOP00000080359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9106,639,573 - 107,343,698 (-)Ensembl
RefSeq Acc Id: NM_001168632   ⟹   NP_001162103
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,573 - 107,343,698 (-)NCBI
Rnor_6.09114,846,095 - 115,555,261 (-)NCBI
Rnor_5.09114,341,760 - 115,047,495 (-)NCBI
RGSC_v3.49105,784,922 - 106,503,148 (-)RGD
Celera9103,813,416 - 104,503,006 (-)RGD
Sequence:
RefSeq Acc Id: XM_017596313   ⟹   XP_017451802
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,658 (-)NCBI
Rnor_6.09114,846,192 - 115,382,418 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596314   ⟹   XP_017451803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,653 (-)NCBI
Rnor_6.09114,846,192 - 115,382,418 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083117   ⟹   XP_038939045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,660 (-)NCBI
RefSeq Acc Id: XM_039083118   ⟹   XP_038939046
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,659 (-)NCBI
RefSeq Acc Id: XM_039083119   ⟹   XP_038939047
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,659 (-)NCBI
RefSeq Acc Id: XM_039083120   ⟹   XP_038939048
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,656 (-)NCBI
RefSeq Acc Id: XM_039083121   ⟹   XP_038939049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,657 (-)NCBI
RefSeq Acc Id: XM_039083122   ⟹   XP_038939050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,654 (-)NCBI
RefSeq Acc Id: XM_039083123   ⟹   XP_038939051
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,655 (-)NCBI
RefSeq Acc Id: XM_039083124   ⟹   XP_038939052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,657 (-)NCBI
RefSeq Acc Id: XM_039083125   ⟹   XP_038939053
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,651 (-)NCBI
RefSeq Acc Id: XM_039083126   ⟹   XP_038939054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,651 (-)NCBI
RefSeq Acc Id: XM_039083127   ⟹   XP_038939055
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,280,647 (-)NCBI
RefSeq Acc Id: XM_039083128   ⟹   XP_038939056
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29106,639,674 - 107,024,987 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001162103   ⟸   NM_001168632
- Peptide Label: precursor
- UniProtKB: F1LPJ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451803   ⟸   XM_017596314
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017451802   ⟸   XM_017596313
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: ENSRNOP00000053204   ⟸   ENSRNOT00000056366
RefSeq Acc Id: ENSRNOP00000074746   ⟸   ENSRNOT00000091316
RefSeq Acc Id: XP_038939045   ⟸   XM_039083117
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939047   ⟸   XM_039083119
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038939046   ⟸   XM_039083118
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939052   ⟸   XM_039083124
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038939049   ⟸   XM_039083121
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038939048   ⟸   XM_039083120
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038939051   ⟸   XM_039083123
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038939050   ⟸   XM_039083122
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038939054   ⟸   XM_039083126
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038939053   ⟸   XM_039083125
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038939055   ⟸   XM_039083127
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038939056   ⟸   XM_039083128
- Peptide Label: isoform X14
RefSeq Acc Id: ENSRNOP00000085971   ⟸   ENSRNOT00000106479
RefSeq Acc Id: ENSRNOP00000080359   ⟸   ENSRNOT00000107262
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NHsd (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
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620776 AgrOrtholog
Ensembl Genes ENSRNOG00000011700 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000053204 UniProtKB/TrEMBL
  ENSRNOP00000074746 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056366 UniProtKB/TrEMBL
  ENSRNOT00000091316 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.90.190.10 UniProtKB/TrEMBL
InterPro ConA-like_dom UniProtKB/TrEMBL
  Fibronectin_type3 UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Immunoglobulin UniProtKB/TrEMBL
  MAM_dom UniProtKB/TrEMBL
  Prot-tyrosine_phosphatase-like UniProtKB/TrEMBL
  Tyr/Dual-specificity_Pase UniProtKB/TrEMBL
  Tyr_Pase_AS UniProtKB/TrEMBL
  Tyr_Pase_cat UniProtKB/TrEMBL
  Tyr_Pase_rcpt/non-rcpt UniProtKB/TrEMBL
KEGG Report rno:29616 UniProtKB/TrEMBL
NCBI Gene 29616 ENTREZGENE
Pfam fn3 UniProtKB/TrEMBL
  MAM UniProtKB/TrEMBL
  PF00047 UniProtKB/TrEMBL
  Y_phosphatase UniProtKB/TrEMBL
PhenoGen Ptprm PhenoGen
PRINTS MAMDOMAIN UniProtKB/TrEMBL
  PRTYPHPHTASE UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/TrEMBL
  IG_LIKE UniProtKB/TrEMBL
  MAM_1 UniProtKB/TrEMBL
  MAM_2 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_1 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_2 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_PTP UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
  MAM UniProtKB/TrEMBL
  PTPc UniProtKB/TrEMBL
  PTPc_motif UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
  FN_III-like UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
  SSF52799 UniProtKB/TrEMBL
UniProt A0A0G2K8V0_RAT UniProtKB/TrEMBL
  F1LPJ1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Ptprm  protein tyrosine phosphatase, receptor type, M    protein tyrosine phosphatase, receptor-type, M  Name updated 1299863 APPROVED
2002-08-07 Ptprm  protein tyrosine phosphatase, receptor-type, M      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA is expressed in embryonic day 13.5 neural tube 633862