Pnpla1 (patatin-like phospholipase domain containing 1) - Rat Genome Database

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Gene: Pnpla1 (patatin-like phospholipase domain containing 1) Rattus norvegicus
Analyze
Symbol: Pnpla1
Name: patatin-like phospholipase domain containing 1
RGD ID: 1306685
Description: Predicted to enable omega-hydroxyceramide transacylase activity and triglyceride lipase activity. Predicted to be a structural constituent of skin epidermis. Predicted to be involved in several processes, including establishment of skin barrier; omega-hydroxyceramide biosynthetic process; and triglyceride catabolic process. Predicted to be active in cytoplasm; lipid droplet; and membrane. Human ortholog(s) of this gene implicated in autosomal recessive congenital ichthyosis 10. Orthologous to human PNPLA1 (patatin like phospholipase domain containing 1); INTERACTS WITH 6-propyl-2-thiouracil; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC361812; omega-hydroxyceramide transacylase; patatin-like phospholipase domain-containing protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8206,919,689 - 6,953,850 (+)NCBIGRCr8
mRatBN7.2206,917,993 - 6,952,157 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl206,917,931 - 6,952,375 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx207,629,833 - 7,663,579 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0206,991,691 - 7,025,435 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0207,473,220 - 7,506,575 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0206,101,061 - 6,143,762 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl206,102,277 - 6,143,707 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0208,355,252 - 8,393,878 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4207,139,384 - 7,173,440 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1207,139,610 - 7,172,044 (+)NCBI
Celera208,471,789 - 8,505,049 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,ISO)
lipid droplet  (IBA)
membrane  (IBA)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:22246504  


Genomics

Comparative Map Data
Pnpla1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8206,919,689 - 6,953,850 (+)NCBIGRCr8
mRatBN7.2206,917,993 - 6,952,157 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl206,917,931 - 6,952,375 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx207,629,833 - 7,663,579 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0206,991,691 - 7,025,435 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0207,473,220 - 7,506,575 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0206,101,061 - 6,143,762 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl206,102,277 - 6,143,707 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0208,355,252 - 8,393,878 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4207,139,384 - 7,173,440 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1207,139,610 - 7,172,044 (+)NCBI
Celera208,471,789 - 8,505,049 (+)NCBICelera
Cytogenetic Map20p12NCBI
PNPLA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38636,243,168 - 36,313,955 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl636,243,203 - 36,313,955 (+)EnsemblGRCh38hg38GRCh38
GRCh37636,210,945 - 36,281,732 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36636,318,923 - 36,384,350 (+)NCBINCBI36Build 36hg18NCBI36
Build 34636,318,922 - 36,384,350NCBI
Celera637,765,485 - 37,830,961 (+)NCBICelera
Cytogenetic Map6p21.31NCBI
HuRef635,930,494 - 35,995,688 (+)NCBIHuRef
CHM1_1636,212,708 - 36,278,194 (+)NCBICHM1_1
T2T-CHM13v2.0636,059,864 - 36,134,277 (+)NCBIT2T-CHM13v2.0
Pnpla1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391729,077,262 - 29,109,282 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1729,077,385 - 29,109,283 (+)EnsemblGRCm39 Ensembl
GRCm381728,858,286 - 28,890,308 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1728,858,411 - 28,890,309 (+)EnsemblGRCm38mm10GRCm38
MGSCv371728,995,356 - 29,027,253 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361728,586,000 - 28,617,897 (+)NCBIMGSCv36mm8
Celera1729,412,978 - 29,445,667 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1715.03NCBI
Pnpla1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554374,008,545 - 4,048,033 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554374,008,814 - 4,047,895 (+)NCBIChiLan1.0ChiLan1.0
PNPLA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2550,734,769 - 50,778,413 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1646,604,554 - 46,648,196 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0635,828,778 - 35,872,129 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1637,002,466 - 37,067,190 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl637,002,466 - 37,067,190 (+)Ensemblpanpan1.1panPan2
PNPLA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1125,377,430 - 5,423,556 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl125,377,430 - 5,423,556 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha125,397,344 - 5,443,474 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0125,725,170 - 5,771,521 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl125,725,365 - 5,771,521 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1125,381,148 - 5,427,257 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0125,458,997 - 5,505,125 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0125,559,044 - 5,605,194 (+)NCBIUU_Cfam_GSD_1.0
Pnpla1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494640,859,983 - 40,899,613 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647623,061,854 - 23,099,720 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647623,066,840 - 23,100,126 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PNPLA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl731,988,197 - 32,025,245 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1731,987,596 - 32,025,673 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2736,888,056 - 36,925,909 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PNPLA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11735,808,652 - 35,854,069 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1735,814,590 - 35,851,985 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604436,225,386 - 36,266,877 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pnpla1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475421,375,463 - 21,410,961 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475421,370,872 - 21,410,804 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pnpla1
364 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:47
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000033064
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat

Markers in Region
RH140032  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2206,951,640 - 6,951,855 (+)MAPPERmRatBN7.2
Rnor_6.0206,143,246 - 6,143,460NCBIRnor6.0
Rnor_6.0206,135,142 - 6,135,356NCBIRnor6.0
Rnor_5.0208,387,327 - 8,387,541UniSTSRnor5.0
Rnor_5.0208,393,362 - 8,393,576UniSTSRnor5.0
RGSC_v3.4207,173,431 - 7,173,645UniSTSRGSC3.4
Celera208,505,040 - 8,505,254UniSTS
Cytogenetic Map20p12UniSTS
RH140432  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2206,951,843 - 6,952,011 (+)MAPPERmRatBN7.2
Rnor_6.0206,143,449 - 6,143,616NCBIRnor6.0
Rnor_6.0206,135,345 - 6,135,512NCBIRnor6.0
Rnor_5.0208,393,565 - 8,393,732UniSTSRnor5.0
Rnor_5.0208,387,530 - 8,387,697UniSTSRnor5.0
RGSC_v3.4207,173,634 - 7,173,801UniSTSRGSC3.4
Celera208,505,243 - 8,505,410UniSTS
RH 3.4 Map2077.1UniSTS
Cytogenetic Map20p12UniSTS


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
Low 1 2 4 46 25 5
Below cutoff 2 23 51 39 15 39 3 5 28 22 14 6 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000033064   ⟹   ENSRNOP00000035242
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl206,917,931 - 6,952,375 (+)Ensembl
Rnor_6.0 Ensembl206,102,277 - 6,143,707 (+)Ensembl
RefSeq Acc Id: NM_001191841   ⟹   NP_001178770
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8206,919,689 - 6,953,850 (+)NCBI
mRatBN7.2206,917,993 - 6,952,157 (+)NCBI
Rnor_6.0206,102,371 - 6,143,255 (+)NCBI
Rnor_5.0208,355,252 - 8,393,878 (+)NCBI
Celera208,471,789 - 8,505,049 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178770 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000035242
  ENSRNOP00000035242.4
Reference Protein Sequences
RefSeq Acc Id: NP_001178770   ⟸   NM_001191841
- UniProtKB: D4A3G9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000035242   ⟸   ENSRNOT00000033064
Protein Domains
PNPLA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A3G9-F1-model_v2 AlphaFold D4A3G9 1-589 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306685 AgrOrtholog
BioCyc Gene G2FUF-4404 BioCyc
Ensembl Genes ENSRNOG00000028622 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033064 ENTREZGENE
  ENSRNOT00000033064.8 UniProtKB/TrEMBL
Gene3D-CATH Cytosolic phospholipase A2 catalytic domain UniProtKB/TrEMBL
InterPro Acyl_Trfase/lysoPlipase UniProtKB/TrEMBL
  Patatin UniProtKB/TrEMBL
  PLPL UniProtKB/TrEMBL
KEGG Report rno:361812 UniProtKB/TrEMBL
NCBI Gene 361812 ENTREZGENE
PANTHER OMEGA-HYDROXYCERAMIDE TRANSACYLASE UniProtKB/TrEMBL
  PTHR12406 UniProtKB/TrEMBL
Pfam Patatin UniProtKB/TrEMBL
PhenoGen Pnpla1 PhenoGen
PROSITE PNPLA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028622 RatGTEx
Superfamily-SCOP Acyl_Trfase/lysoPlipase UniProtKB/TrEMBL
UniProt D4A3G9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pnpla1  patatin-like phospholipase domain containing 1   Pnpla1_predicted  patatin-like phospholipase domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pnpla1_predicted  patatin-like phospholipase domain containing 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED