Pign (phosphatidylinositol glycan anchor biosynthesis, class N) - Rat Genome Database

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Gene: Pign (phosphatidylinositol glycan anchor biosynthesis, class N) Rattus norvegicus
Analyze
Symbol: Pign
Name: phosphatidylinositol glycan anchor biosynthesis, class N
RGD ID: 1311346
Description: Predicted to enable mannose-ethanolamine phosphotransferase activity. Predicted to be involved in GPI anchor biosynthetic process. Predicted to be located in cytosol and plasma membrane. Predicted to be active in endoplasmic reticulum membrane. Human ortholog(s) of this gene implicated in multiple congenital anomalies-hypotonia-seizures syndrome 1. Orthologous to human PIGN (phosphatidylinositol glycan anchor biosynthesis class N); PARTICIPATES IN glycosylphosphatidylinositol anchor biosynthetic pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; acetamide; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: GPI ethanolamine phosphate transferase 1; LOC309051; phosphatidylinositol glycan, class N
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
mRatBN7.21321,659,092 - 21,812,932 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1321,662,455 - 21,806,790 (-)Ensembl
Rnor_6.01325,510,593 - 25,662,943 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1325,513,892 - 25,652,473 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01330,779,066 - 30,820,235 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01330,676,676 - 30,740,322 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41311,668,749 - 11,833,940 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11311,442,630 - 11,828,636 (-)NCBI
Celera1321,552,506 - 21,677,358 (-)NCBICelera
Cytogenetic Map13p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:19946888  


Genomics

Comparative Map Data
Pign
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21321,659,092 - 21,812,932 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1321,662,455 - 21,806,790 (-)Ensembl
Rnor_6.01325,510,593 - 25,662,943 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1325,513,892 - 25,652,473 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01330,779,066 - 30,820,235 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01330,676,676 - 30,740,322 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41311,668,749 - 11,833,940 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11311,442,630 - 11,828,636 (-)NCBI
Celera1321,552,506 - 21,677,358 (-)NCBICelera
Cytogenetic Map13p11NCBI
PIGN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1861,905,255 - 62,187,118 (-)EnsemblGRCh38hg38GRCh38
GRCh381862,041,164 - 62,187,118 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371859,708,397 - 59,854,289 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361857,862,437 - 58,005,269 (-)NCBINCBI36hg18NCBI36
Build 341857,862,439 - 58,005,206NCBI
Celera1856,430,705 - 56,573,517 (-)NCBI
Cytogenetic Map18q21.33NCBI
HuRef1856,421,823 - 56,565,179 (-)NCBIHuRef
CHM1_11859,707,055 - 59,849,802 (-)NCBICHM1_1
Pign
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391105,446,147 - 105,591,466 (-)NCBIGRCm39mm39
GRCm39 Ensembl1105,446,147 - 105,591,402 (-)Ensembl
GRCm381105,518,421 - 105,663,741 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1105,518,422 - 105,663,677 (-)EnsemblGRCm38mm10GRCm38
MGSCv371107,417,716 - 107,560,253 (-)NCBIGRCm37mm9NCBIm37
MGSCv361107,348,686 - 107,491,209 (-)NCBImm8
Celera1108,376,436 - 108,513,016 (-)NCBICelera
Cytogenetic Map1E2.1NCBI
Pign
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540245,983,826 - 46,114,752 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540245,979,577 - 46,114,634 (-)NCBIChiLan1.0ChiLan1.0
PIGN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11858,733,740 - 58,875,183 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1858,733,740 - 58,875,183 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01855,415,182 - 55,557,092 (-)NCBIMhudiblu_PPA_v0panPan3
PIGN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1114,684,026 - 14,791,221 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl114,685,694 - 14,805,691 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha115,651,440 - 15,758,632 (+)NCBI
ROS_Cfam_1.0114,544,736 - 14,652,948 (+)NCBI
UMICH_Zoey_3.1114,580,565 - 14,688,156 (+)NCBI
UNSW_CanFamBas_1.0114,513,807 - 14,621,155 (+)NCBI
UU_Cfam_GSD_1.0114,760,723 - 14,868,433 (+)NCBI
Pign
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494427,882,060 - 27,991,301 (+)NCBI
SpeTri2.0NW_0049364973,121,184 - 3,230,912 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PIGN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1159,317,734 - 159,417,333 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11159,317,734 - 159,417,335 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21176,781,531 - 176,879,102 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PIGN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11817,589,582 - 17,725,823 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1817,589,631 - 17,725,823 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660607,936,049 - 8,099,945 (-)NCBIVero_WHO_p1.0
Pign
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247927,713,042 - 7,916,177 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D13Got214  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21321,750,826 - 21,750,935 (+)MAPPERmRatBN7.2
Rnor_6.01325,603,293 - 25,603,403NCBIRnor6.0
Rnor_5.01330,765,846 - 30,765,956UniSTSRnor5.0
RGSC_v3.41311,776,297 - 11,776,407UniSTSRGSC3.4
Celera1321,628,425 - 21,628,535UniSTS
Cytogenetic Map13p13UniSTS
RH133180  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21321,662,061 - 21,662,264 (+)MAPPERmRatBN7.2
Rnor_6.01325,513,917 - 25,514,119NCBIRnor6.0
Rnor_5.01330,676,701 - 30,676,903UniSTSRnor5.0
RGSC_v3.41311,668,774 - 11,668,976UniSTSRGSC3.4
Celera1321,552,531 - 21,552,733UniSTS
Cytogenetic Map13p13UniSTS
BE109920  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21321,724,741 - 21,724,910 (+)MAPPERmRatBN7.2
Rnor_6.01325,576,690 - 25,576,858NCBIRnor6.0
Rnor_5.01330,739,846 - 30,740,014UniSTSRnor5.0
RGSC_v3.41311,731,988 - 11,732,156UniSTSRGSC3.4
Celera1321,615,249 - 21,615,417UniSTS
Cytogenetic Map13p13UniSTS
AU047833  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21321,665,905 - 21,666,152 (+)MAPPERmRatBN7.2
Rnor_6.01325,518,049 - 25,518,295NCBIRnor6.0
Rnor_5.01330,680,833 - 30,681,079UniSTSRnor5.0
RGSC_v3.41311,672,619 - 11,672,865UniSTSRGSC3.4
Celera1321,556,384 - 21,556,652UniSTS
Cytogenetic Map13p13UniSTS
ha2188  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21321,757,607 - 21,758,475 (+)MAPPERmRatBN7.2
Rnor_6.01325,610,041 - 25,610,908NCBIRnor6.0
Rnor_5.01330,772,594 - 30,773,461UniSTSRnor5.0
RGSC_v3.41311,783,080 - 11,783,947UniSTSRGSC3.4
Celera1321,635,208 - 21,636,075UniSTS
Cytogenetic Map13p13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317027Aia22Adjuvant induced arthritis QTL 222.29joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)13134266636Rat
738036Lnnr4Liver neoplastic nodule remodeling QTL 43.64liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)13142356786Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
631672Iddm12Insulin dependent diabetes mellitus QTL 122.20.0032blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)13599466834535351Rat
61339Bp24Blood pressure QTL 240.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13599466844807491Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)13931346554313465Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)13931346554313465Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
2303031Bp326Blood pressure QTL 326arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131176653523001904Rat
2317034Aia9Adjuvant induced arthritis QTL 94.62joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131176653532331607Rat
2317044Aia23Adjuvant induced arthritis QTL 232.3joint integrity trait (VT:0010548)ankle joint diameter (CMO:0002148)131176653532331607Rat
1300163Cardf1Cardiac cell morphology QTL 14.18aorta morphology trait (VT:0000272)artery lesion measurement (CMO:0000975)131192944945417941Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131192944946193066Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131491565559915655Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)131515872260158722Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131769443653050594Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:493
Count of miRNA genes:243
Interacting mature miRNAs:291
Transcripts:ENSRNOT00000020752
Prediction methods:Microtar, Miranda, 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 1 20 44 29 15 29 33 35 34 10
Low 2 22 13 12 4 12 8 10 41 7 1 8
Below cutoff 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001100584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090844 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090846 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090849 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090851 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090852 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ976364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000020752   ⟹   ENSRNOP00000020752
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1321,662,455 - 21,806,790 (-)Ensembl
Rnor_6.0 Ensembl1325,513,892 - 25,652,473 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107206   ⟹   ENSRNOP00000094088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1321,688,166 - 21,806,780 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112543   ⟹   ENSRNOP00000091372
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1321,662,570 - 21,806,790 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117600   ⟹   ENSRNOP00000094630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1321,662,999 - 21,806,780 (-)Ensembl
RefSeq Acc Id: NM_001100584   ⟹   NP_001094054
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,662,037 - 21,806,774 (-)NCBI
Rnor_6.01325,513,892 - 25,656,785 (-)NCBI
Rnor_5.01330,676,676 - 30,740,322 (-)NCBI
Rnor_5.01330,779,066 - 30,820,235 (-)NCBI
RGSC_v3.41311,668,749 - 11,833,940 (-)RGD
Celera1321,552,506 - 21,677,358 (-)RGD
Sequence:
RefSeq Acc Id: XM_039090837   ⟹   XP_038946765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,910 (-)NCBI
RefSeq Acc Id: XM_039090838   ⟹   XP_038946766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,911 (-)NCBI
RefSeq Acc Id: XM_039090839   ⟹   XP_038946767
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,910 (-)NCBI
RefSeq Acc Id: XM_039090840   ⟹   XP_038946768
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,910 (-)NCBI
RefSeq Acc Id: XM_039090841   ⟹   XP_038946769
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,910 (-)NCBI
RefSeq Acc Id: XM_039090842   ⟹   XP_038946770
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,911 (-)NCBI
RefSeq Acc Id: XM_039090843   ⟹   XP_038946771
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,911 (-)NCBI
RefSeq Acc Id: XM_039090844   ⟹   XP_038946772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,912 (-)NCBI
RefSeq Acc Id: XM_039090845   ⟹   XP_038946773
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,812,932 (-)NCBI
RefSeq Acc Id: XM_039090846   ⟹   XP_038946774
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,662,037 - 21,806,903 (-)NCBI
RefSeq Acc Id: XM_039090847   ⟹   XP_038946775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,662,986 - 21,806,907 (-)NCBI
RefSeq Acc Id: XM_039090849   ⟹   XP_038946777
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,905 (-)NCBI
RefSeq Acc Id: XM_039090850   ⟹   XP_038946778
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,806,905 (-)NCBI
RefSeq Acc Id: XM_039090851   ⟹   XP_038946779
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,794,599 (-)NCBI
RefSeq Acc Id: XM_039090852   ⟹   XP_038946780
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,659,092 - 21,753,242 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001094054   ⟸   NM_001100584
- Sequence:
RefSeq Acc Id: ENSRNOP00000020752   ⟸   ENSRNOT00000020752
RefSeq Acc Id: XP_038946773   ⟸   XM_039090845
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946772   ⟸   XM_039090844
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946770   ⟸   XM_039090842
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946766   ⟸   XM_039090838
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946771   ⟸   XM_039090843
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946768   ⟸   XM_039090840
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946765   ⟸   XM_039090837
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946769   ⟸   XM_039090841
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946767   ⟸   XM_039090839
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946777   ⟸   XM_039090849
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038946778   ⟸   XM_039090850
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038946779   ⟸   XM_039090851
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038946780   ⟸   XM_039090852
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038946774   ⟸   XM_039090846
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946775   ⟸   XM_039090847
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000094088   ⟸   ENSRNOT00000107206
RefSeq Acc Id: ENSRNOP00000091372   ⟸   ENSRNOT00000112543
RefSeq Acc Id: ENSRNOP00000094630   ⟸   ENSRNOT00000117600
Protein Domains
PigN

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)
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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
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)
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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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
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)
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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 (2020)
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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/SsN (2020)
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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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
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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: 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)
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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
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)
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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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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: 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)
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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
F344/Stm (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: 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)
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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)
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)
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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: 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)
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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/RijCrl (2020)
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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: 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)
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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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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: 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)
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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 (2020)
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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: 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:1311346 AgrOrtholog
Ensembl Genes ENSRNOG00000014866 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020752 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020752 UniProtKB/TrEMBL
Gene3D-CATH 3.40.720.10 UniProtKB/TrEMBL
InterPro Alkaline_phosphatase_core UniProtKB/TrEMBL
  GPI_EtnP_transferase_1 UniProtKB/TrEMBL
  GPI_EtnP_transferase_1_C UniProtKB/TrEMBL
  Phosphodiest/P_Trfase UniProtKB/TrEMBL
  PIGN_N UniProtKB/TrEMBL
NCBI Gene 309051 ENTREZGENE
PANTHER PigN UniProtKB/TrEMBL
Pfam Phosphodiest UniProtKB/TrEMBL
  PigN UniProtKB/TrEMBL
PhenoGen Pign PhenoGen
Superfamily-SCOP Alkaline_phosphatase_core UniProtKB/TrEMBL
UniProt E9PTA5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-09 Pign  phosphatidylinositol glycan anchor biosynthesis, class N  Pign  phosphatidylinositol glycan, class N  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pign  phosphatidylinositol glycan, class N   Pign_predicted  phosphatidylinositol glycan, class N (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pign_predicted  phosphatidylinositol glycan, class N (predicted)      Symbol and Name status set to approved 70820 APPROVED