Ppfia2 (PTPRF interacting protein alpha 2) - Rat Genome Database

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Gene: Ppfia2 (PTPRF interacting protein alpha 2) Rattus norvegicus
Analyze
Symbol: Ppfia2
Name: PTPRF interacting protein alpha 2
RGD ID: 1305021
Description: A structural constituent of presynapse. Involved in regulation of synaptic vesicle exocytosis. Localizes to glutamatergic synapse. Orthologous to human PPFIA2 (PTPRF interacting protein alpha 2); INTERACTS WITH (+)-schisandrin B; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: liprin-alpha-2; LOC362876
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Ppfia2Tn(sb-T2/Bart3)2.339Mcwi  
Genetic Models: F344-Ppfia2Tn(sb-T2/Bart3)2.339Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2741,765,716 - 42,240,104 (+)NCBI
Rnor_6.0 Ensembl748,867,664 - 49,042,455 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0748,548,932 - 49,045,852 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0748,563,521 - 48,568,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0748,658,858 - 49,058,116 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4745,140,154 - 45,616,620 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1745,160,426 - 45,636,728 (+)NCBI
Celera738,644,350 - 39,116,317 (+)NCBICelera
Cytogenetic Map7q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:16186258   PMID:19056867   PMID:21618221   PMID:23791195   PMID:29439199   PMID:30021165  


Genomics

Comparative Map Data
Ppfia2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2741,765,716 - 42,240,104 (+)NCBI
Rnor_6.0 Ensembl748,867,664 - 49,042,455 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0748,548,932 - 49,045,852 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0748,563,521 - 48,568,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0748,658,858 - 49,058,116 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4745,140,154 - 45,616,620 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1745,160,426 - 45,636,728 (+)NCBI
Celera738,644,350 - 39,116,317 (+)NCBICelera
Cytogenetic Map7q21NCBI
PPFIA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1281,257,975 - 81,759,553 (-)EnsemblGRCh38hg38GRCh38
GRCh381281,257,975 - 81,759,749 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371281,651,754 - 82,153,129 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361280,177,487 - 80,677,240 (-)NCBINCBI36hg18NCBI36
Build 341280,155,823 - 80,655,577NCBI
Celera1281,321,211 - 81,820,889 (-)NCBI
Cytogenetic Map12q21.31NCBI
HuRef1278,708,811 - 79,209,133 (-)NCBIHuRef
CHM1_11281,618,230 - 82,119,470 (-)NCBICHM1_1
Ppfia2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910106,305,129 - 106,769,329 (+)NCBIGRCm39mm39
GRCm39 Ensembl10106,306,200 - 106,771,813 (+)Ensembl
GRCm3810106,469,500 - 106,933,468 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10106,470,339 - 106,935,952 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710105,907,395 - 106,369,574 (+)NCBIGRCm37mm9NCBIm37
MGSCv3610105,874,449 - 106,336,628 (+)NCBImm8
Celera10108,413,090 - 108,874,050 (+)NCBICelera
Cytogenetic Map10D1NCBI
Ppfia2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540519,839,092 - 20,286,578 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540519,837,749 - 20,291,666 (-)NCBIChiLan1.0ChiLan1.0
PPFIA2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11281,879,812 - 82,381,524 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1281,879,812 - 82,376,917 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01278,768,756 - 79,271,630 (-)NCBIMhudiblu_PPA_v0panPan3
PPFIA2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11523,481,370 - 23,950,412 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1523,482,549 - 23,951,141 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1523,904,766 - 24,373,671 (-)NCBI
ROS_Cfam_1.01523,842,759 - 24,321,109 (-)NCBI
UMICH_Zoey_3.11523,428,189 - 23,897,907 (-)NCBI
UNSW_CanFamBas_1.01523,479,044 - 23,947,917 (-)NCBI
UU_Cfam_GSD_1.01523,719,822 - 24,188,937 (-)NCBI
Ppfia2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494536,381,131 - 36,821,732 (+)NCBI
SpeTri2.0NW_0049366982,090,768 - 2,531,366 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPFIA2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl599,819,405 - 100,279,028 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1599,818,591 - 100,279,029 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.25105,054,270 - 105,195,571 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PPFIA2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11176,740,204 - 77,237,990 (-)NCBI
ChlSab1.1 Ensembl1176,736,719 - 77,079,140 (-)Ensembl
Vero_WHO_p1.0NW_023666037168,176,151 - 168,685,075 (+)NCBI
Ppfia2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624837627,484 - 1,116,597 (-)NCBI

Position Markers
BE106419  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2742,224,388 - 42,224,548 (+)MAPPER
Rnor_6.0749,028,472 - 49,028,631NCBIRnor6.0
Rnor_5.0749,043,041 - 49,043,200UniSTSRnor5.0
RGSC_v3.4745,600,625 - 45,600,784UniSTSRGSC3.4
Celera739,101,136 - 39,101,295UniSTS
RH 3.4 Map7352.9UniSTS
Cytogenetic Map7q21UniSTS
BE120388  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2741,943,097 - 41,943,314 (+)MAPPER
Rnor_6.0748,726,382 - 48,726,598NCBIRnor6.0
Rnor_5.0748,740,852 - 48,741,068UniSTSRnor5.0
RGSC_v3.4745,318,191 - 45,318,407UniSTSRGSC3.4
Celera738,821,377 - 38,821,593UniSTS
RH 3.4 Map7348.41UniSTS
Cytogenetic Map7q21UniSTS
RH138710  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2742,143,149 - 42,143,307 (+)MAPPER
Rnor_6.0748,947,233 - 48,947,390NCBIRnor6.0
Rnor_5.0748,961,802 - 48,961,959UniSTSRnor5.0
RGSC_v3.4745,519,385 - 45,519,542UniSTSRGSC3.4
Celera739,019,912 - 39,020,069UniSTS
RH 3.4 Map7352.9UniSTS
Cytogenetic Map7q21UniSTS
AU048710  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2741,861,027 - 41,861,238 (+)MAPPER
Rnor_6.0748,643,650 - 48,643,860NCBIRnor6.0
Rnor_5.0748,657,799 - 48,658,009UniSTSRnor5.0
RGSC_v3.4745,234,729 - 45,234,939UniSTSRGSC3.4
Celera738,739,409 - 38,739,619UniSTS
Cytogenetic Map7q21UniSTS
AU049226  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2741,908,533 - 41,908,705 (+)MAPPER
Rnor_6.0748,691,818 - 48,691,989NCBIRnor6.0
Rnor_5.0748,706,288 - 48,706,459UniSTSRnor5.0
RGSC_v3.4745,283,627 - 45,283,798UniSTSRGSC3.4
Celera738,786,804 - 38,786,975UniSTS
Cytogenetic Map7q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71395217958952179Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)71444568559445685Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)72216841267168412Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)72473146569731465Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)72536563357064364Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)72536563357064364Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)72536563360317612Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72820465373204653Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)73138152976381529Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)73203505377035053Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)73257294277572942Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)73304444971352127Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)73586772961047824Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)73586772980867729Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)73586772993155402Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73854770683547706Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)74087268285872682Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)74087268285872682Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74530157390301573Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74789509963372754Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat


Genetic Models
This gene Ppfia2 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:111
Count of miRNA genes:75
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000005862
Prediction methods: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 64
Low 49 41 8 41 8 9 8 18 37 7 8
Below cutoff 3 27 8 11 1 2 17 4 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001108745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765333 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765336 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079456 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079461 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079462 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079463 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079465 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079466 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000005862   ⟹   ENSRNOP00000005862
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl748,867,664 - 49,042,455 (+)Ensembl
RefSeq Acc Id: NM_001108745   ⟹   NP_001102215
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,575 - 42,239,599 (+)NCBI
Rnor_6.0748,549,456 - 49,045,360 (+)NCBI
Rnor_5.0748,563,521 - 48,568,045 (+)NCBI
Rnor_5.0748,658,858 - 49,058,116 (+)NCBI
RGSC_v3.4745,140,154 - 45,616,620 (+)RGD
Celera738,644,350 - 39,116,317 (+)RGD
Sequence:
RefSeq Acc Id: XM_008765328   ⟹   XP_008763550
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765329   ⟹   XP_008763551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765330   ⟹   XP_008763552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765331   ⟹   XP_008763553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765333   ⟹   XP_008763555
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765334   ⟹   XP_008763556
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765335   ⟹   XP_008763557
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765336   ⟹   XP_008763558
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594919   ⟹   XP_017450408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0748,549,194 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594920   ⟹   XP_017450409
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0748,548,932 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594921   ⟹   XP_017450410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,770,850 - 42,240,104 (+)NCBI
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594922   ⟹   XP_017450411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0748,549,462 - 49,045,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039079441   ⟹   XP_038935369
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,765,716 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079442   ⟹   XP_038935370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079444   ⟹   XP_038935372
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079445   ⟹   XP_038935373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079446   ⟹   XP_038935374
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079447   ⟹   XP_038935375
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079448   ⟹   XP_038935376
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079449   ⟹   XP_038935377
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079450   ⟹   XP_038935378
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079451   ⟹   XP_038935379
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079452   ⟹   XP_038935380
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,240,093 (+)NCBI
RefSeq Acc Id: XM_039079454   ⟹   XP_038935382
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,770,850 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079455   ⟹   XP_038935383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,770,850 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079456   ⟹   XP_038935384
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,770,850 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079457   ⟹   XP_038935385
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,770,850 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079458   ⟹   XP_038935386
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,770,850 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079459   ⟹   XP_038935387
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,770,850 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079460   ⟹   XP_038935388
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,940,169 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079461   ⟹   XP_038935389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079462   ⟹   XP_038935390
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079463   ⟹   XP_038935391
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079464   ⟹   XP_038935392
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079465   ⟹   XP_038935393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079466   ⟹   XP_038935394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079467   ⟹   XP_038935395
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079468   ⟹   XP_038935396
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079469   ⟹   XP_038935397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079470   ⟹   XP_038935398
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079471   ⟹   XP_038935399
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079472   ⟹   XP_038935400
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079473   ⟹   XP_038935401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079474   ⟹   XP_038935402
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079475   ⟹   XP_038935403
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079476   ⟹   XP_038935404
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079477   ⟹   XP_038935405
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079478   ⟹   XP_038935406
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079479   ⟹   XP_038935407
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079480   ⟹   XP_038935408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079481   ⟹   XP_038935409
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079482   ⟹   XP_038935410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,238,688 (+)NCBI
RefSeq Acc Id: XM_039079483   ⟹   XP_038935411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,790 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079484   ⟹   XP_038935412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,941,910 - 42,240,104 (+)NCBI
RefSeq Acc Id: XM_039079485   ⟹   XP_038935413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2741,766,690 - 42,175,180 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102215 (Get FASTA)   NCBI Sequence Viewer  
  XP_008763556 (Get FASTA)   NCBI Sequence Viewer  
  XP_008763557 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450410 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935369 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935370 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935372 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935373 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935374 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935375 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935376 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935377 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935378 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935379 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935380 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935382 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935383 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935384 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935385 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935386 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935387 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935388 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935389 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935390 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935391 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935392 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935393 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935394 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935395 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935396 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935397 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935398 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935399 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935400 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935401 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935402 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935403 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935404 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935405 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935406 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935407 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935408 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935409 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935410 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935411 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935412 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935413 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM16778 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102215   ⟸   NM_001108745
- Sequence:
RefSeq Acc Id: XP_008763556   ⟸   XM_008765334
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_008763557   ⟸   XM_008765335
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_008763558   ⟸   XM_008765336
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008763555   ⟸   XM_008765333
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_008763552   ⟸   XM_008765330
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008763551   ⟸   XM_008765329
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008763553   ⟸   XM_008765331
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_008763550   ⟸   XM_008765328
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450409   ⟸   XM_017594920
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450408   ⟸   XM_017594919
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450411   ⟸   XM_017594922
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017450410   ⟸   XM_017594921
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: ENSRNOP00000005862   ⟸   ENSRNOT00000005862
RefSeq Acc Id: XP_038935369   ⟸   XM_039079441
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935378   ⟸   XM_039079450
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038935375   ⟸   XM_039079447
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038935377   ⟸   XM_039079449
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038935379   ⟸   XM_039079451
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038935372   ⟸   XM_039079444
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038935376   ⟸   XM_039079448
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038935370   ⟸   XM_039079442
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038935374   ⟸   XM_039079446
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038935373   ⟸   XM_039079445
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038935380   ⟸   XM_039079452
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038935413   ⟸   XM_039079485
- Peptide Label: isoform X46
RefSeq Acc Id: XP_038935382   ⟸   XM_039079454
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038935383   ⟸   XM_039079455
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038935384   ⟸   XM_039079456
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038935386   ⟸   XM_039079458
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038935385   ⟸   XM_039079457
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038935387   ⟸   XM_039079459
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038935388   ⟸   XM_039079460
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038935389   ⟸   XM_039079461
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038935394   ⟸   XM_039079466
- Peptide Label: isoform X27
RefSeq Acc Id: XP_038935391   ⟸   XM_039079463
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038935397   ⟸   XM_039079469
- Peptide Label: isoform X30
RefSeq Acc Id: XP_038935390   ⟸   XM_039079462
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038935392   ⟸   XM_039079464
- Peptide Label: isoform X25
RefSeq Acc Id: XP_038935398   ⟸   XM_039079470
- Peptide Label: isoform X31
RefSeq Acc Id: XP_038935395   ⟸   XM_039079467
- Peptide Label: isoform X28
RefSeq Acc Id: XP_038935401   ⟸   XM_039079473
- Peptide Label: isoform X34
RefSeq Acc Id: XP_038935393   ⟸   XM_039079465
- Peptide Label: isoform X26
RefSeq Acc Id: XP_038935400   ⟸   XM_039079472
- Peptide Label: isoform X33
RefSeq Acc Id: XP_038935396   ⟸   XM_039079468
- Peptide Label: isoform X29
RefSeq Acc Id: XP_038935404   ⟸   XM_039079476
- Peptide Label: isoform X37
RefSeq Acc Id: XP_038935411   ⟸   XM_039079483
- Peptide Label: isoform X44
RefSeq Acc Id: XP_038935399   ⟸   XM_039079471
- Peptide Label: isoform X32
RefSeq Acc Id: XP_038935402   ⟸   XM_039079474
- Peptide Label: isoform X35
RefSeq Acc Id: XP_038935403   ⟸   XM_039079475
- Peptide Label: isoform X36
RefSeq Acc Id: XP_038935406   ⟸   XM_039079478
- Peptide Label: isoform X39
RefSeq Acc Id: XP_038935409   ⟸   XM_039079481
- Peptide Label: isoform X42
RefSeq Acc Id: XP_038935405   ⟸   XM_039079477
- Peptide Label: isoform X38
RefSeq Acc Id: XP_038935408   ⟸   XM_039079480
- Peptide Label: isoform X41
RefSeq Acc Id: XP_038935407   ⟸   XM_039079479
- Peptide Label: isoform X40
RefSeq Acc Id: XP_038935410   ⟸   XM_039079482
- Peptide Label: isoform X43
RefSeq Acc Id: XP_038935412   ⟸   XM_039079484
- Peptide Label: isoform X45
Protein Domains
SAM

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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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)
ACI/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
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/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 (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
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)
F344/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
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
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)
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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
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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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: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 45542158 45542159 A T snv FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305021 AgrOrtholog
Ensembl Genes ENSRNOG00000004353 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005862 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005862 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
InterPro Liprin UniProtKB/TrEMBL
  Liprin-alpha_SAM_rpt_1 UniProtKB/TrEMBL
  Liprin-alpha_SAM_rpt_2 UniProtKB/TrEMBL
  Liprin-alpha_SAM_rpt_3 UniProtKB/TrEMBL
  PPFIA2 UniProtKB/TrEMBL
  SAM UniProtKB/TrEMBL
  SAM_type UniProtKB/TrEMBL
NCBI Gene 362876 ENTREZGENE
PANTHER PTHR12587 UniProtKB/TrEMBL
  PTHR12587:SF6 UniProtKB/TrEMBL
Pfam SAM_1 UniProtKB/TrEMBL
  SAM_2 UniProtKB/TrEMBL
PhenoGen Ppfia2 PhenoGen
PROSITE SAM_DOMAIN UniProtKB/TrEMBL
SMART SAM UniProtKB/TrEMBL
Superfamily-SCOP SAM_homology UniProtKB/TrEMBL
Transposagen Ppfia2 Transposagen
UniProt F1M8A4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ppfia2  protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2   Ppfia2_predicted  protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ppfia2_predicted  protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED