Plekhf2 (pleckstrin homology and FYVE domain containing 2) - Rat Genome Database

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Gene: Plekhf2 (pleckstrin homology and FYVE domain containing 2) Rattus norvegicus
Analyze
Symbol: Plekhf2
Name: pleckstrin homology and FYVE domain containing 2
RGD ID: 1312029
Description: Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in endosome organization and endosome to lysosome transport. Predicted to be located in transport vesicle. Predicted to be active in early endosome. Orthologous to human PLEKHF2 (pleckstrin homology and FYVE domain containing 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC362484; pleckstrin homology domain containing, family F (with FYVE domain) member 2; pleckstrin homology domain-containing family F member 2
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
GRCr8528,888,358 - 28,905,350 (-)NCBIGRCr8
mRatBN7.2524,091,077 - 24,106,758 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl524,090,688 - 24,106,601 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx526,279,691 - 26,295,002 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0527,872,690 - 27,888,001 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0527,673,644 - 27,688,951 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0524,240,241 - 24,255,922 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl524,240,242 - 24,255,606 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0528,967,291 - 28,982,656 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4524,835,705 - 24,851,069 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1524,835,704 - 24,851,062 (-)NCBI
Celera523,310,189 - 23,325,553 (-)NCBICelera
Cytogenetic Map5q13NCBI
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 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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Plekhf2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8528,888,358 - 28,905,350 (-)NCBIGRCr8
mRatBN7.2524,091,077 - 24,106,758 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl524,090,688 - 24,106,601 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx526,279,691 - 26,295,002 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0527,872,690 - 27,888,001 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0527,673,644 - 27,688,951 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0524,240,241 - 24,255,922 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl524,240,242 - 24,255,606 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0528,967,291 - 28,982,656 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4524,835,705 - 24,851,069 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1524,835,704 - 24,851,062 (-)NCBI
Celera523,310,189 - 23,325,553 (-)NCBICelera
Cytogenetic Map5q13NCBI
PLEKHF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38895,133,785 - 95,156,685 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl895,115,642 - 95,156,698 (+)EnsemblGRCh38hg38GRCh38
GRCh37896,146,013 - 96,168,913 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36896,215,208 - 96,238,089 (+)NCBINCBI36Build 36hg18NCBI36
Build 34896,215,213 - 96,238,085NCBI
Celera892,330,955 - 92,353,916 (+)NCBICelera
Cytogenetic Map8q22.1NCBI
HuRef891,353,593 - 91,376,794 (+)NCBIHuRef
CHM1_1896,186,071 - 96,209,156 (+)NCBICHM1_1
T2T-CHM13v2.0896,259,034 - 96,281,932 (+)NCBIT2T-CHM13v2.0
Plekhf2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39410,988,662 - 11,007,619 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl410,988,662 - 11,007,927 (-)EnsemblGRCm39 Ensembl
GRCm38410,988,662 - 11,007,619 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl410,988,662 - 11,007,927 (-)EnsemblGRCm38mm10GRCm38
MGSCv37410,915,809 - 10,934,766 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36410,915,809 - 10,934,707 (-)NCBIMGSCv36mm8
Celera410,797,638 - 10,816,357 (-)NCBICelera
Cytogenetic Map4A1NCBI
cM Map44.86NCBI
Plekhf2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541711,261,712 - 11,282,038 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541711,261,712 - 11,282,038 (+)NCBIChiLan1.0ChiLan1.0
PLEKHF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27112,460,612 - 112,483,570 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1887,997,640 - 88,020,634 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0891,751,383 - 91,774,320 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1893,972,161 - 93,974,814 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl893,972,170 - 93,972,919 (+)Ensemblpanpan1.1panPan2
PLEKHF2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12939,734,189 - 39,760,841 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2939,895,208 - 39,924,759 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02939,935,036 - 39,964,879 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12939,958,982 - 39,988,654 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02939,945,322 - 39,974,777 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02940,387,539 - 40,416,995 (-)NCBIUU_Cfam_GSD_1.0
Plekhf2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530339,656,326 - 39,729,348 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365448,063,392 - 8,084,956 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365448,063,374 - 8,086,104 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLEKHF2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl441,511,342 - 41,535,012 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1441,512,109 - 41,534,932 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PLEKHF2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1890,099,946 - 90,123,573 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl890,120,929 - 90,121,678 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603950,708,609 - 50,732,255 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Plekhf2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247632,506,991 - 2,507,737 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247632,506,941 - 2,509,574 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Plekhf2
112 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:242
Count of miRNA genes:158
Interacting mature miRNAs:199
Transcripts:ENSRNOT00000037483
Prediction methods:Microtar, 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
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
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
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
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
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
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat

Markers in Region
RH129644  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2524,090,898 - 24,091,086 (+)MAPPERmRatBN7.2
Rnor_6.0524,240,063 - 24,240,250NCBIRnor6.0
Rnor_5.0528,967,113 - 28,967,300UniSTSRnor5.0
RGSC_v3.4524,835,526 - 24,835,713UniSTSRGSC3.4
Celera523,310,010 - 23,310,197UniSTS
RH 3.4 Map5133.5UniSTS
Cytogenetic Map5q13UniSTS
RH136846  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2524,091,172 - 24,091,427 (+)MAPPERmRatBN7.2
Rnor_6.0524,240,337 - 24,240,591NCBIRnor6.0
Rnor_5.0528,967,387 - 28,967,641UniSTSRnor5.0
RGSC_v3.4524,835,800 - 24,836,054UniSTSRGSC3.4
Celera523,310,284 - 23,310,538UniSTS
RH 3.4 Map5136.4UniSTS
Cytogenetic Map5q13UniSTS
RH139120  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2524,093,523 - 24,093,658 (+)MAPPERmRatBN7.2
Rnor_6.0524,242,688 - 24,242,822NCBIRnor6.0
Rnor_5.0528,969,738 - 28,969,872UniSTSRnor5.0
RGSC_v3.4524,838,151 - 24,838,285UniSTSRGSC3.4
Celera523,312,635 - 23,312,769UniSTS
RH 3.4 Map5137.2UniSTS
Cytogenetic Map5q13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000037483   ⟹   ENSRNOP00000032124
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl524,090,914 - 24,104,843 (-)Ensembl
Rnor_6.0 Ensembl524,240,242 - 24,255,606 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000094306   ⟹   ENSRNOP00000095114
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl524,090,914 - 24,105,665 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000103597   ⟹   ENSRNOP00000083768
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl524,090,688 - 24,106,601 (-)Ensembl
RefSeq Acc Id: NM_001108655   ⟹   NP_001102125
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8528,888,359 - 28,903,723 (-)NCBI
mRatBN7.2524,091,078 - 24,106,442 (-)NCBI
Rnor_6.0524,240,242 - 24,255,606 (-)NCBI
Rnor_5.0528,967,291 - 28,982,656 (-)NCBI
RGSC_v3.4524,835,705 - 24,851,069 (-)RGD
Celera523,310,189 - 23,325,553 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237872   ⟹   XP_006237934
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8528,888,358 - 28,905,350 (-)NCBI
mRatBN7.2524,091,077 - 24,106,758 (-)NCBI
Rnor_6.0524,240,241 - 24,255,922 (-)NCBI
Rnor_5.0528,967,291 - 28,982,656 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102125 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237934 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61902 (Get FASTA)   NCBI Sequence Viewer  
  EDM11669 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032124.4
  ENSRNOP00000083768.1
  ENSRNOP00000095114.1
RefSeq Acc Id: NP_001102125   ⟸   NM_001108655
- UniProtKB: B1WBV4 (UniProtKB/TrEMBL),   A0A8I6A0M3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237934   ⟸   XM_006237872
- Peptide Label: isoform X1
- UniProtKB: B1WBV4 (UniProtKB/TrEMBL),   A0A8I6A0M3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000032124   ⟸   ENSRNOT00000037483
Ensembl Acc Id: ENSRNOP00000083768   ⟸   ENSRNOT00000103597
Ensembl Acc Id: ENSRNOP00000095114   ⟸   ENSRNOT00000094306
Protein Domains
FYVE-type   PH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1WBV4-F1-model_v2 AlphaFold B1WBV4 1-249 view protein structure

Transcriptome

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

Promoters
RGD ID:13693561
Promoter ID:EPDNEW_R4085
Type:initiation region
Name:Plekhf2_1
Description:pleckstrin homology and FYVE domain containing 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_6.0524,255,606 - 24,255,666EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1312029 AgrOrtholog
BioCyc Gene G2FUF-41971 BioCyc
Ensembl Genes ENSRNOG00000026662 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037483.5 UniProtKB/TrEMBL
  ENSRNOT00000094306.1 UniProtKB/TrEMBL
  ENSRNOT00000103597.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8367141 IMAGE-MGC_LOAD
InterPro PH_domain-containing_F UniProtKB/TrEMBL
  PH_Phafin UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  PLEKHF2_FYVE UniProtKB/TrEMBL
  Znf_FYVE UniProtKB/TrEMBL
  Znf_FYVE-rel UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:362484 UniProtKB/TrEMBL
MGC_CLONE MGC:187622 IMAGE-MGC_LOAD
NCBI Gene 362484 ENTREZGENE
PANTHER PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY F MEMBER 2 UniProtKB/TrEMBL
  PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY F MEMBER 2-RELATED UniProtKB/TrEMBL
Pfam FYVE UniProtKB/TrEMBL
  PF00169 UniProtKB/TrEMBL
PhenoGen Plekhf2 PhenoGen
PROSITE PH_DOMAIN UniProtKB/TrEMBL
  ZF_FYVE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000026662 RatGTEx
SMART FYVE UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
  PH domain-like UniProtKB/TrEMBL
UniProt A0A8I6A0M3 ENTREZGENE, UniProtKB/TrEMBL
  B1WBV4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Plekhf2  pleckstrin homology and FYVE domain containing 2  Plekhf2  pleckstrin homology domain containing, family F (with FYVE domain) member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Plekhf2  pleckstrin homology domain containing, family F (with FYVE domain) member 2   Plekhf2_predicted  pleckstrin homology domain containing, family F (with FYVE domain) member 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Plekhf2_predicted  pleckstrin homology domain containing, family F (with FYVE domain) member 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED