Pdzph1 (PDZ and pleckstrin homology domains 1) - Rat Genome Database

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Gene: Pdzph1 (PDZ and pleckstrin homology domains 1) Rattus norvegicus
Analyze
Symbol: Pdzph1
Name: PDZ and pleckstrin homology domains 1
RGD ID: 1560925
Description: INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC501196; RGD1560925; similar to 2610034M16Rik protein
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89106,038,530 - 106,176,711 (-)NCBIGRCr8
mRatBN7.2998,591,222 - 98,729,409 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl998,591,228 - 98,690,913 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9107,006,879 - 107,147,978 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09112,134,645 - 112,275,749 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09110,478,261 - 110,619,350 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.09105,530,933 - 105,660,227 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9105,531,195 - 105,655,471 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09105,131,605 - 105,269,691 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4997,387,503 - 97,522,016 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera996,033,506 - 96,163,017 (-)NCBICelera
Cytogenetic Map9q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Pdzph1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89106,038,530 - 106,176,711 (-)NCBIGRCr8
mRatBN7.2998,591,222 - 98,729,409 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl998,591,228 - 98,690,913 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9107,006,879 - 107,147,978 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09112,134,645 - 112,275,749 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09110,478,261 - 110,619,350 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.09105,530,933 - 105,660,227 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9105,531,195 - 105,655,471 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09105,131,605 - 105,269,691 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4997,387,503 - 97,522,016 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera996,033,506 - 96,163,017 (-)NCBICelera
Cytogenetic Map9q36NCBI
PDZPH1P
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385103,430,533 - 103,526,618 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5103,430,533 - 103,526,618 (-)EnsemblGRCh38hg38GRCh38
GRCh375102,766,234 - 102,862,319 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q21.2NCBI
CHM1_15102,199,413 - 102,295,495 (-)NCBICHM1_1
T2T-CHM13v2.05103,938,714 - 104,034,792 (-)NCBIT2T-CHM13v2.0
Pdzph1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391759,185,803 - 59,298,344 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1759,185,803 - 59,298,370 (-)EnsemblGRCm39 Ensembl
GRCm381758,878,808 - 58,991,375 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1758,878,808 - 58,991,375 (-)EnsemblGRCm38mm10GRCm38
MGSCv371759,018,231 - 59,130,798 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361758,564,143 - 58,676,706 (-)NCBIMGSCv36mm8
Celera1763,218,091 - 63,330,714 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1730.57NCBI

Variants

.
Variants in Pdzph1
879 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:118
Count of miRNA genes:69
Interacting mature miRNAs:73
Transcripts:ENSRNOT00000014921, ENSRNOT00000056434
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
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)992491589100929786Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat


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 2 6 3 3 29 8 1
Below cutoff 2 6 40 31 14 31 2 2 45 15 19 7 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014921   ⟹   ENSRNOP00000014922
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9105,531,198 - 105,655,471 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000056434   ⟹   ENSRNOP00000053273
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl998,591,228 - 98,690,913 (-)Ensembl
Rnor_6.0 Ensembl9105,531,195 - 105,545,854 (-)Ensembl
RefSeq Acc Id: NM_001402237   ⟹   NP_001389166
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89106,038,530 - 106,176,711 (-)NCBI
mRatBN7.2998,591,222 - 98,729,409 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001389166 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH97996 (Get FASTA)   NCBI Sequence Viewer  
  EDL91847 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000053273.4
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000014922   ⟸   ENSRNOT00000014921
RefSeq Acc Id: ENSRNOP00000053273   ⟸   ENSRNOT00000056434
RefSeq Acc Id: NP_001389166   ⟸   NM_001402237
- UniProtKB: A6JR89 (UniProtKB/TrEMBL)
Protein Domains
PDZ   PH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M611-F1-model_v2 AlphaFold F1M611 1-1230 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:1560925 AgrOrtholog
BioCyc Gene G2FUF-26575 BioCyc
Ensembl Genes ENSRNOG00000011042 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056434.4 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
  2.30.42.10 UniProtKB/TrEMBL
InterPro PDZ UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
NCBI Gene 501196 ENTREZGENE
PANTHER AGAP008221-PA UniProtKB/TrEMBL
  SEA DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
  PF00169 UniProtKB/TrEMBL
PhenoGen Pdzph1 PhenoGen
PROSITE PDZ UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011042 RatGTEx
SMART PDZ UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP PDZ domain-like UniProtKB/TrEMBL
  PH domain-like UniProtKB/TrEMBL
UniProt A6JR89 ENTREZGENE, UniProtKB/TrEMBL
  F7EX58_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-03-18 Pdzph1  PDZ and pleckstrin homology domains 1  RGD1560925  similar to 2610034M16Rik protein  Name and Symbol changed 629549 APPROVED
2008-04-30 RGD1560925  similar to 2610034M16Rik protein   RGD1560925_predicted  similar to 2610034M16Rik protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560925_predicted  similar to 2610034M16Rik protein (predicted)  LOC501196  similar to 2610034M16Rik protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501196  similar to 2610034M16Rik protein      Symbol and Name status set to provisional 70820 PROVISIONAL