Pip4p2 (phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2) - Rat Genome Database

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Gene: Pip4p2 (phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2) Rattus norvegicus
Analyze
Symbol: Pip4p2
Name: phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2
RGD ID: 1306225
Description: Predicted to enable phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity. Predicted to be involved in negative regulation of phagocytosis and phosphatidylinositol dephosphorylation. Predicted to be active in bounding membrane of organelle and plasma membrane. Orthologous to human PIP4P2 (phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC362490; MGC114565; ptdIns-4,5-P2 4-Ptase II; RGD1306225; similar to RIKEN cDNA 2610319K07; Tmem55a; transmembrane protein 55A; type 2 phosphatidylinositol 4,5-bisphosphate 4-phosphatase; type 2 PtdIns-4,5-P2 4-Ptase; type II phosphatidylinositol 4,5-bisphosphate 4-phosphatase
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
GRCr8533,057,046 - 33,104,448 (+)NCBIGRCr8
mRatBN7.2528,259,821 - 28,307,225 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl528,259,760 - 28,307,225 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx530,414,507 - 30,461,769 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0532,007,188 - 32,054,448 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0531,967,347 - 32,014,607 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0528,395,517 - 28,442,924 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl528,395,296 - 28,442,924 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0533,079,533 - 33,126,623 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4529,329,329 - 29,376,733 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1529,329,328 - 29,376,729 (+)NCBI
Celera527,511,708 - 27,556,541 (+)NCBICelera
Cytogenetic Map5q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
late endosome membrane  (IBA,IEA,ISO,ISS)
lysosomal membrane  (IBA,IEA,ISO)
phagocytic vesicle membrane  (IBA,IEA,ISO,ISS)
plasma membrane  (IBA,ISO,ISS)

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:16365287   PMID:29378918  


Genomics

Comparative Map Data
Pip4p2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8533,057,046 - 33,104,448 (+)NCBIGRCr8
mRatBN7.2528,259,821 - 28,307,225 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl528,259,760 - 28,307,225 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx530,414,507 - 30,461,769 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0532,007,188 - 32,054,448 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0531,967,347 - 32,014,607 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0528,395,517 - 28,442,924 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl528,395,296 - 28,442,924 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0533,079,533 - 33,126,623 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4529,329,329 - 29,376,733 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1529,329,328 - 29,376,729 (+)NCBI
Celera527,511,708 - 27,556,541 (+)NCBICelera
Cytogenetic Map5q13NCBI
PIP4P2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38890,993,802 - 91,040,859 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl890,993,802 - 91,040,872 (-)EnsemblGRCh38hg38GRCh38
GRCh37892,006,030 - 92,053,087 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36892,075,675 - 92,122,227 (-)NCBINCBI36Build 36hg18NCBI36
Celera888,201,253 - 88,248,229 (-)NCBICelera
Cytogenetic Map8q21.3NCBI
HuRef887,216,426 - 87,263,709 (-)NCBIHuRef
CHM1_1892,047,148 - 92,093,868 (-)NCBICHM1_1
T2T-CHM13v2.0892,118,724 - 92,165,782 (-)NCBIT2T-CHM13v2.0
Pip4p2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39414,864,219 - 14,915,501 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl414,864,076 - 14,915,176 (+)EnsemblGRCm39 Ensembl
GRCm38414,864,219 - 14,915,260 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl414,864,076 - 14,915,176 (+)EnsemblGRCm38mm10GRCm38
MGSCv37414,791,366 - 14,842,407 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36414,791,366 - 14,842,407 (+)NCBIMGSCv36mm8
Celera414,666,242 - 14,716,763 (+)NCBICelera
Cytogenetic Map4A1NCBI
cM Map46.41NCBI
Pip4p2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554177,771,218 - 7,825,799 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554177,769,365 - 7,825,892 (-)NCBIChiLan1.0ChiLan1.0
PIP4P2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27108,365,016 - 108,411,716 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1883,904,246 - 83,950,250 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0887,657,202 - 87,704,355 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1889,610,315 - 89,640,736 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl889,611,726 - 89,639,419 (-)Ensemblpanpan1.1panPan2
PIP4P2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12936,376,211 - 36,410,680 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2936,377,413 - 36,419,132 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2936,528,349 - 36,584,476 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02936,577,248 - 36,633,018 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12936,597,823 - 36,653,297 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02936,579,206 - 36,635,139 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02937,017,626 - 37,073,778 (-)NCBIUU_Cfam_GSD_1.0
Pip4p2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530343,122,960 - 43,172,916 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365444,618,660 - 4,670,140 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365444,621,222 - 4,669,808 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PIP4P2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl445,826,326 - 45,892,417 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1445,825,415 - 45,891,192 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2449,447,375 - 49,512,725 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PIP4P2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1886,059,522 - 86,111,027 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl886,059,397 - 86,107,014 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603954,723,306 - 54,803,988 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pip4p2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624744924,211 - 978,625 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pip4p2
410 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:198
Count of miRNA genes:130
Interacting mature miRNAs:169
Transcripts:ENSRNOT00000009375
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)52483871044045280Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat

Markers in Region
AV001360  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2528,306,937 - 28,307,056 (+)MAPPERmRatBN7.2
Rnor_6.0528,442,637 - 28,442,755NCBIRnor6.0
Rnor_5.0533,126,336 - 33,126,454UniSTSRnor5.0
RGSC_v3.4529,376,446 - 29,376,564UniSTSRGSC3.4
Celera527,556,254 - 27,556,372UniSTS
Cytogenetic Map5q13UniSTS
RH127862  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2528,306,829 - 28,307,031 (+)MAPPERmRatBN7.2
Rnor_6.0528,442,529 - 28,442,730NCBIRnor6.0
Rnor_5.0533,126,228 - 33,126,429UniSTSRnor5.0
RGSC_v3.4529,376,338 - 29,376,539UniSTSRGSC3.4
Celera527,556,146 - 27,556,347UniSTS
Cytogenetic Map5q13UniSTS
RH128877  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2528,305,717 - 28,305,903 (+)MAPPERmRatBN7.2
Rnor_6.0528,441,417 - 28,441,602NCBIRnor6.0
Rnor_5.0533,125,116 - 33,125,301UniSTSRnor5.0
RGSC_v3.4529,375,226 - 29,375,411UniSTSRGSC3.4
Celera527,555,034 - 27,555,219UniSTS
Cytogenetic Map5q13UniSTS
UniSTS:234872  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2528,306,975 - 28,307,198 (+)MAPPERmRatBN7.2
Rnor_6.0528,442,675 - 28,442,897NCBIRnor6.0
Rnor_5.0533,126,374 - 33,126,596UniSTSRnor5.0
RGSC_v3.4529,376,484 - 29,376,706UniSTSRGSC3.4
Celera527,556,292 - 27,556,514UniSTS
Cytogenetic Map5q13UniSTS


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 3 43 47 37 13 37 8 11 74 35 34 11 8
Low 10 4 6 4 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009375   ⟹   ENSRNOP00000009375
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl528,259,760 - 28,307,225 (+)Ensembl
Rnor_6.0 Ensembl528,395,296 - 28,442,924 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095769   ⟹   ENSRNOP00000091783
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl528,259,868 - 28,307,225 (+)Ensembl
RefSeq Acc Id: NM_001024900   ⟹   NP_001020071
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8533,057,046 - 33,104,448 (+)NCBI
mRatBN7.2528,259,821 - 28,307,225 (+)NCBI
Rnor_6.0528,395,517 - 28,442,924 (+)NCBI
Rnor_5.0533,079,533 - 33,126,623 (+)NCBI
RGSC_v3.4529,329,329 - 29,376,733 (+)RGD
Celera527,511,708 - 27,556,541 (+)RGD
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001020071   ⟸   NM_001024900
- UniProtKB: Q4V888 (UniProtKB/Swiss-Prot),   A6II98 (UniProtKB/TrEMBL),   A0A8I6AGE6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009375   ⟸   ENSRNOT00000009375
RefSeq Acc Id: ENSRNOP00000091783   ⟸   ENSRNOT00000095769

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4V888-F1-model_v2 AlphaFold Q4V888 1-257 view protein structure

Transcriptome

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

Promoters
RGD ID:13693577
Promoter ID:EPDNEW_R4101
Type:initiation region
Name:Pip4p2_1
Description:phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0528,395,502 - 28,395,562EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306225 AgrOrtholog
BioCyc Gene G2FUF-41884 BioCyc
Ensembl Genes ENSRNOG00000006697 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055000327 UniProtKB/Swiss-Prot
  ENSRNOG00060017480 UniProtKB/Swiss-Prot
  ENSRNOG00065015743 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009375 ENTREZGENE
  ENSRNOT00000009375.8 UniProtKB/Swiss-Prot
  ENSRNOT00000095769.1 UniProtKB/TrEMBL
  ENSRNOT00055000571 UniProtKB/Swiss-Prot
  ENSRNOT00060029878 UniProtKB/Swiss-Prot
  ENSRNOT00065026143 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7461463 IMAGE-MGC_LOAD
InterPro PtdIns-P2-Ptase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:362490 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:114565 IMAGE-MGC_LOAD
NCBI Gene 362490 ENTREZGENE
PANTHER PTHR21014 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYPE 2 PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 4-PHOSPHATASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Tmemb_55A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pip4p2 PhenoGen
RatGTEx ENSRNOG00000006697 RatGTEx
  ENSRNOG00055000327 RatGTEx
  ENSRNOG00060017480 RatGTEx
  ENSRNOG00065015743 RatGTEx
UniProt A0A8I6AGE6 ENTREZGENE, UniProtKB/TrEMBL
  A6II98 ENTREZGENE, UniProtKB/TrEMBL
  PP4P2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-07-31 Pip4p2  phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2  Tmem55a  transmembrane protein 55A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Tmem55a  transmembrane protein 55A  RGD1306225  similar to RIKEN cDNA 2610319K07  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1306225  similar to RIKEN cDNA 2610319K07  RGD1306225_predicted  similar to RIKEN cDNA 2610319K07 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1306225_predicted  similar to RIKEN cDNA 2610319K07 (predicted)  LOC362490_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362490_predicted  similar to RIKEN cDNA 2610319K07 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL