Pnpla4 (patatin like phospholipase domain containing 4) - Rat Genome Database

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Gene: Pnpla4 (patatin like phospholipase domain containing 4) Rattus norvegicus
Analyze
Symbol: Pnpla4
Name: patatin like phospholipase domain containing 4
RGD ID: 1562200
Description: Predicted to enable acylglycerol O-acyltransferase activity and carboxylic ester hydrolase activity. Predicted to be involved in lipid homeostasis and triglyceride catabolic process. Predicted to be located in mitochondrion. Predicted to be active in cytoplasm; lipid droplet; and membrane. Orthologous to human PNPLA4 (patatin like phospholipase domain containing 4); PARTICIPATES IN retinol metabolic pathway; vitamin A deficiency pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; endosulfan; paracetamol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC363471; patatin-like phospholipase domain-containing protein 4; RGD1562200; similar to GS2 gene
RGD Orthologs
Human
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X46,200,351 - 46,205,517 (-)NCBIGRCr8
mRatBN7.2X42,313,554 - 42,318,451 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX42,305,373 - 42,318,552 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX43,644,794 - 43,648,288 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X47,112,142 - 47,115,636 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X44,776,888 - 44,780,382 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X45,519,406 - 45,522,988 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX45,519,228 - 45,522,665 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X45,741,175 - 45,745,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X64,018,764 - 64,023,189 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX42,961,904 - 42,965,486 (-)NCBICelera
Cytogenetic MapXq21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
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:15364929   PMID:16741517   PMID:17603008   PMID:26741492  


Genomics

Comparative Map Data
Pnpla4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X46,200,351 - 46,205,517 (-)NCBIGRCr8
mRatBN7.2X42,313,554 - 42,318,451 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX42,305,373 - 42,318,552 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX43,644,794 - 43,648,288 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X47,112,142 - 47,115,636 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X44,776,888 - 44,780,382 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X45,519,406 - 45,522,988 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX45,519,228 - 45,522,665 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X45,741,175 - 45,745,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X64,018,764 - 64,023,189 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX42,961,904 - 42,965,486 (-)NCBICelera
Cytogenetic MapXq21NCBI
PNPLA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X7,898,247 - 7,927,724 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX7,898,247 - 7,927,739 (-)EnsemblGRCh38hg38GRCh38
GRCh37X7,866,288 - 7,895,765 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X7,826,804 - 7,855,443 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X7,676,539 - 7,705,179NCBI
CeleraX12,042,080 - 12,071,056 (-)NCBICelera
Cytogenetic MapXp22.31NCBI
HuRefX5,673,993 - 5,702,740 (-)NCBIHuRef
CHM1_1X7,847,349 - 7,876,320 (-)NCBICHM1_1
T2T-CHM13v2.0X7,451,884 - 7,481,358 (-)NCBIT2T-CHM13v2.0
Pnpla4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554995,892,761 - 5,924,736 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554995,875,706 - 5,925,809 (-)NCBIChiLan1.0ChiLan1.0
PNPLA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X9,417,953 - 9,472,996 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X9,421,621 - 9,478,793 (-)NCBINHGRI_mPanPan1
PanPan1.1X7,756,047 - 7,786,124 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX7,756,047 - 7,786,634 (-)Ensemblpanpan1.1panPan2
PNPLA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X4,775,702 - 4,925,027 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX4,874,240 - 4,924,976 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX4,772,912 - 4,880,400 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X4,756,066 - 4,863,806 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX4,812,961 - 4,864,931 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X4,754,281 - 4,861,779 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X4,785,776 - 4,893,459 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X4,784,271 - 4,891,905 (-)NCBIUU_Cfam_GSD_1.0
Pnpla4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049533,230,352 - 3,284,962 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366441,093,388 - 1,112,557 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366441,091,794 - 1,113,621 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PNPLA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X4,540,846 - 4,623,831 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1Y3,287,635 - 3,369,286 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X4,745,808 - 4,825,065 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PNPLA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X6,247,971 - 6,396,168 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX6,363,541 - 6,394,704 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660567,931,592 - 8,003,191 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pnpla4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248345,496,617 - 5,528,555 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248345,497,109 - 5,529,912 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pnpla4
15 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:40
Count of miRNA genes:39
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000030771
Prediction methods:Miranda, Pita, Rnahybrid
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
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat

Markers in Region
BI273967  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X42,314,467 - 42,315,274 (+)MAPPERmRatBN7.2
Rnor_6.0X45,519,421 - 45,520,227NCBIRnor6.0
Rnor_5.0X45,741,190 - 45,741,996UniSTSRnor5.0
RGSC_v3.4X64,019,683 - 64,020,489UniSTSRGSC3.4
CeleraX42,961,919 - 42,962,725UniSTS
RH 3.4 MapX598.1UniSTS
Cytogenetic MapXq22UniSTS


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 6 1
Low 3 43 57 41 19 41 8 11 74 35 35 10 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001401181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001401182 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001401183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_001058636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227336 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773241 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063280138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000030771   ⟹   ENSRNOP00000033754
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX42,314,455 - 42,318,552 (-)Ensembl
Rnor_6.0 EnsemblX45,519,228 - 45,522,665 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097042   ⟹   ENSRNOP00000089216
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX42,305,373 - 42,317,980 (-)Ensembl
RefSeq Acc Id: NM_001401181   ⟹   NP_001388110
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,201,538 - 46,205,029 (-)NCBI
mRatBN7.2X42,314,453 - 42,317,944 (-)NCBI
RefSeq Acc Id: NM_001401182   ⟹   NP_001388111
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,201,538 - 46,205,029 (-)NCBI
mRatBN7.2X42,314,453 - 42,317,944 (-)NCBI
RefSeq Acc Id: NM_001401183   ⟹   NP_001388112
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,201,538 - 46,205,029 (-)NCBI
mRatBN7.2X42,314,453 - 42,317,944 (-)NCBI
RefSeq Acc Id: XM_006256968   ⟹   XP_006257030
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,200,351 - 46,205,508 (-)NCBI
mRatBN7.2X42,314,453 - 42,318,442 (-)NCBI
Rnor_6.0X45,519,406 - 45,522,987 (-)NCBI
Rnor_5.0X45,741,175 - 45,745,283 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256969   ⟹   XP_006257031
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,200,351 - 46,204,592 (-)NCBI
mRatBN7.2X42,314,453 - 42,317,506 (-)NCBI
Rnor_6.0X45,519,406 - 45,522,464 (-)NCBI
Rnor_5.0X45,741,175 - 45,745,283 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773241   ⟹   XP_008771463
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,200,351 - 46,205,502 (-)NCBI
mRatBN7.2X42,314,453 - 42,318,439 (-)NCBI
Rnor_6.0X45,519,406 - 45,522,985 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039100228   ⟹   XP_038956156
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,200,351 - 46,204,966 (-)NCBI
mRatBN7.2X42,314,453 - 42,317,882 (-)NCBI
RefSeq Acc Id: XM_039100229   ⟹   XP_038956157
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,200,351 - 46,205,517 (-)NCBI
mRatBN7.2X42,314,453 - 42,318,451 (-)NCBI
RefSeq Acc Id: XM_063280138   ⟹   XP_063136208
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,200,351 - 46,205,501 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_006257030   ⟸   XM_006256968
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ABA3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257031   ⟸   XM_006256969
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008771463   ⟸   XM_008773241
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000033754   ⟸   ENSRNOT00000030771
RefSeq Acc Id: XP_038956157   ⟸   XM_039100229
- Peptide Label: isoform X2
- UniProtKB: A0A8I6ABA3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038956156   ⟸   XM_039100228
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ABA3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000089216   ⟸   ENSRNOT00000097042
RefSeq Acc Id: NP_001388111   ⟸   NM_001401182
- Peptide Label: isoform a
- UniProtKB: A0A8I6ABA3 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001388112   ⟸   NM_001401183
- Peptide Label: isoform b
RefSeq Acc Id: NP_001388110   ⟸   NM_001401181
- Peptide Label: isoform a
- UniProtKB: A0A8I6ABA3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136208   ⟸   XM_063280138
- Peptide Label: isoform X4
Protein Domains
PNPLA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A227-F1-model_v2 AlphaFold D4A227 1-252 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:1562200 AgrOrtholog
BioCyc Gene G2FUF-2401 BioCyc
Ensembl Genes ENSRNOG00000026157 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030771.7 UniProtKB/TrEMBL
  ENSRNOT00000097042 ENTREZGENE
  ENSRNOT00000097042.1 UniProtKB/TrEMBL
Gene3D-CATH Cytosolic phospholipase A2 catalytic domain UniProtKB/TrEMBL
InterPro Acyl_Trfase/lysoPlipase UniProtKB/TrEMBL
  Patatin UniProtKB/TrEMBL
  PLPL UniProtKB/TrEMBL
  PNPLA4 UniProtKB/TrEMBL
KEGG Report rno:363471 UniProtKB/TrEMBL
NCBI Gene 363471 ENTREZGENE
PANTHER PATATIN-LIKE PHOSPHOLIPASE DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
  PTHR12406 UniProtKB/TrEMBL
Pfam Patatin UniProtKB/TrEMBL
PhenoGen Pnpla4 PhenoGen
PROSITE PNPLA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000026157 RatGTEx
Superfamily-SCOP Acyl_Trfase/lysoPlipase UniProtKB/TrEMBL
UniProt A0A8I6ABA3 ENTREZGENE, UniProtKB/TrEMBL
  D4A227_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-04-20 Pnpla4  patatin like phospholipase domain containing 4  RGD1562200  similar to GS2 gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1562200  similar to GS2 gene   RGD1562200_predicted  similar to GS2 gene (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1562200_predicted  similar to GS2 gene (predicted)  LOC363471  similar to GS2 gene  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363471  similar to GS2 gene      Symbol and Name status set to provisional 70820 PROVISIONAL