Pnpla6 (patatin-like phospholipase domain containing 6) - Rat Genome Database

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Gene: Pnpla6 (patatin-like phospholipase domain containing 6) Rattus norvegicus
Analyze
Symbol: Pnpla6
Name: patatin-like phospholipase domain containing 6
RGD ID: 1564611
Description: Predicted to have lysophospholipase activity. Predicted to be involved in angiogenesis and animal organ morphogenesis. Predicted to localize to cytosol; endoplasmic reticulum; and membrane. Human ortholog(s) of this gene implicated in Boucher-Neuhauser syndrome; Laurence-Moon syndrome; Oliver-McFarlane syndrome; and hereditary spastic paraplegia 39. Orthologous to human PNPLA6 (patatin like phospholipase domain containing 6); PARTICIPATES IN glycerophospholipid metabolic pathway; INTERACTS WITH bisphenol A; carbaryl; cyclosporin A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC360753; neuropathy target esterase; patatin-like phospholipase domain-containing protein 6; RGD1564611; similar to neuropathy target esterase homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2121,574,387 - 1,603,735 (+)NCBI
Rnor_6.0 Ensembl122,069,959 - 2,097,904 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0122,068,749 - 2,098,139 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0124,232,111 - 4,260,327 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,610,552 - 2,638,753 (-)NCBIRGSC3.4rn4RGSC3.4
Celera123,430,758 - 3,460,163 (+)NCBICelera
Cytogenetic Map12p12NCBI
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

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12514188   PMID:14749382   PMID:15044461   PMID:18086666   PMID:19946888   PMID:28206686  


Genomics

Comparative Map Data
Pnpla6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2121,574,387 - 1,603,735 (+)NCBI
Rnor_6.0 Ensembl122,069,959 - 2,097,904 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0122,068,749 - 2,098,139 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0124,232,111 - 4,260,327 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,610,552 - 2,638,753 (-)NCBIRGSC3.4rn4RGSC3.4
Celera123,430,758 - 3,460,163 (+)NCBICelera
Cytogenetic Map12p12NCBI
PNPLA6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl197,534,004 - 7,561,764 (+)EnsemblGRCh38hg38GRCh38
GRCh38197,534,164 - 7,561,767 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37197,599,050 - 7,626,653 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36197,505,043 - 7,532,652 (+)NCBINCBI36hg18NCBI36
Celera197,471,561 - 7,499,172 (+)NCBI
Cytogenetic Map19p13.2NCBI
HuRef197,270,194 - 7,297,789 (+)NCBIHuRef
CHM1_1197,598,956 - 7,626,567 (+)NCBICHM1_1
Pnpla6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3983,565,341 - 3,594,267 (+)NCBIGRCm39mm39
GRCm39 Ensembl83,565,384 - 3,594,267 (+)Ensembl
GRCm3883,515,235 - 3,544,267 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl83,515,384 - 3,544,267 (+)EnsemblGRCm38mm10GRCm38
MGSCv3783,515,384 - 3,544,267 (+)NCBIGRCm37mm9NCBIm37
MGSCv3683,515,384 - 3,544,267 (+)NCBImm8
Celera83,741,358 - 3,770,284 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map81.92NCBI
Pnpla6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555631,680,818 - 1,703,287 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555631,681,112 - 1,703,287 (-)NCBIChiLan1.0ChiLan1.0
PNPLA6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1197,683,241 - 7,710,444 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl197,683,789 - 7,710,241 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0196,825,299 - 6,852,900 (+)NCBIMhudiblu_PPA_v0panPan3
PNPLA6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12052,327,547 - 52,349,006 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2052,318,408 - 52,348,963 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2052,115,682 - 52,153,150 (+)NCBI
ROS_Cfam_1.02052,840,755 - 52,878,224 (+)NCBI
UMICH_Zoey_3.12052,060,536 - 52,081,963 (+)NCBI
UNSW_CanFamBas_1.02052,488,224 - 52,525,671 (+)NCBI
UU_Cfam_GSD_1.02052,719,117 - 52,756,573 (+)NCBI
Pnpla6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118213,202,585 - 213,225,879 (-)NCBI
SpeTri2.0NW_0049365884,608,856 - 4,632,198 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PNPLA6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl271,577,166 - 71,602,818 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1271,577,165 - 71,602,756 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2272,031,152 - 72,056,544 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PNPLA6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.167,030,802 - 7,056,664 (+)NCBI
ChlSab1.1 Ensembl67,032,445 - 7,056,661 (+)Ensembl
Vero_WHO_p1.0NW_023666081809,119 - 837,403 (-)NCBI
Pnpla6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624828643,552 - 664,665 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)12111765163Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12122650917Rat
10450854Stl34Serum triglyceride level QTL 343.50.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)12122853017Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12123035872Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123758197Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12125813910257059Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:140
Count of miRNA genes:60
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000001298, ENSRNOT00000072952
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 6 8 2 8 2 72 35 34 11
Low 1 37 49 39 11 39 8 11 2 7 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_008758450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758453 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758463 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758465 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758466 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769007 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089897 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000001298   ⟹   ENSRNOP00000001298
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl122,069,959 - 2,097,904 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000072952   ⟹   ENSRNOP00000065231
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl122,070,365 - 2,097,904 (+)Ensembl
RefSeq Acc Id: XM_008758450   ⟹   XP_008756672
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera123,432,174 - 3,460,163 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758453   ⟹   XP_008756675
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera123,432,174 - 3,460,163 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758457   ⟹   XP_008756679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera123,432,174 - 3,460,163 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758460   ⟹   XP_008756682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera123,430,758 - 3,460,163 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758463   ⟹   XP_008756685
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera123,430,758 - 3,460,163 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758465   ⟹   XP_008756687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera123,431,082 - 3,460,163 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758466   ⟹   XP_008756688
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera123,430,758 - 3,460,163 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769005   ⟹   XP_008767227
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,575,747 - 1,603,735 (+)NCBI
Rnor_6.0122,070,165 - 2,098,139 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769007   ⟹   XP_008767229
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,575,747 - 1,603,735 (+)NCBI
Rnor_6.0122,070,165 - 2,098,139 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769008   ⟹   XP_008767230
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,575,748 - 1,603,735 (+)NCBI
Rnor_6.0122,070,165 - 2,098,139 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769009   ⟹   XP_008767231
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,574,387 - 1,603,735 (+)NCBI
Rnor_6.0122,068,749 - 2,098,139 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769010   ⟹   XP_008767232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,574,387 - 1,603,735 (+)NCBI
Rnor_6.0122,068,749 - 2,098,139 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769012   ⟹   XP_008767234
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,574,387 - 1,603,735 (+)NCBI
Rnor_6.0122,069,073 - 2,098,139 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769013   ⟹   XP_008767235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,574,387 - 1,603,735 (+)NCBI
Rnor_6.0122,068,749 - 2,098,139 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598469   ⟹   XP_017453958
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0122,069,054 - 2,098,139 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604415   ⟹   XP_017459904
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera123,431,063 - 3,460,163 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039089893   ⟹   XP_038945821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,575,935 - 1,603,735 (+)NCBI
RefSeq Acc Id: XM_039089894   ⟹   XP_038945822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,575,747 - 1,603,735 (+)NCBI
RefSeq Acc Id: XM_039089895   ⟹   XP_038945823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,575,935 - 1,603,735 (+)NCBI
RefSeq Acc Id: XM_039089896   ⟹   XP_038945824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,574,387 - 1,603,735 (+)NCBI
RefSeq Acc Id: XM_039089897   ⟹   XP_038945825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,574,387 - 1,603,735 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_008756682   ⟸   XM_008758460
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008756685   ⟸   XM_008758463
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008756688   ⟸   XM_008758466
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008756687   ⟸   XM_008758465
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008756675   ⟸   XM_008758453
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008756679   ⟸   XM_008758457
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008756672   ⟸   XM_008758450
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008767231   ⟸   XM_008769009
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008767232   ⟸   XM_008769010
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008767235   ⟸   XM_008769013
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_008767234   ⟸   XM_008769012
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_008767229   ⟸   XM_008769007
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008767230   ⟸   XM_008769008
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008767227   ⟸   XM_008769005
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017459904   ⟸   XM_017604415
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017453958   ⟸   XM_017598469
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000065231   ⟸   ENSRNOT00000072952
RefSeq Acc Id: ENSRNOP00000001298   ⟸   ENSRNOT00000001298
RefSeq Acc Id: XP_038945825   ⟸   XM_039089897
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038945824   ⟸   XM_039089896
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038945822   ⟸   XM_039089894
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038945821   ⟸   XM_039089893
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038945823   ⟸   XM_039089895
- Peptide Label: isoform X6
Protein Domains
Cyclic nucleotide-binding   PNPLA

Transcriptome

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


Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564611 AgrOrtholog
Ensembl Genes ENSRNOG00000000977 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001298 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000065231 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001298 UniProtKB/TrEMBL
  ENSRNOT00000072952 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.10 UniProtKB/TrEMBL
InterPro Acyl_Trfase/lysoPLipase UniProtKB/TrEMBL
  cNMP-bd-like UniProtKB/TrEMBL
  cNMP-bd_dom UniProtKB/TrEMBL
  LysoPLipase_patatin_CS UniProtKB/TrEMBL
  Patatin/PLipase_A2-rel UniProtKB/TrEMBL
  RmlC-like_jellyroll UniProtKB/TrEMBL
NCBI Gene 360753 ENTREZGENE
Pfam cNMP_binding UniProtKB/TrEMBL
  Patatin UniProtKB/TrEMBL
PhenoGen Pnpla6 PhenoGen
PROSITE CNMP_BINDING_3 UniProtKB/TrEMBL
  PNPLA UniProtKB/TrEMBL
  UPF0028 UniProtKB/TrEMBL
SMART cNMP UniProtKB/TrEMBL
Superfamily-SCOP Acyl_Trfase/lysoPlipase UniProtKB/TrEMBL
  cNMP_binding UniProtKB/TrEMBL
UniProt D3ZRF6_RAT UniProtKB/TrEMBL
  M0R715_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Pnpla6  patatin-like phospholipase domain containing 6  RGD1564611_predicted  similar to neuropathy target esterase homolog (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564611_predicted  similar to neuropathy target esterase homolog (predicted)  LOC360753  similar to neuropathy target esterase homolog  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC360753  similar to neuropathy target esterase homolog      Symbol and Name status set to provisional 70820 PROVISIONAL