Pdzd4 (PDZ domain containing 4) - Rat Genome Database

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Gene: Pdzd4 (PDZ domain containing 4) Rattus norvegicus
Analyze
Symbol: Pdzd4
Name: PDZ domain containing 4
RGD ID: 1561214
Description: Orthologous to human PDZD4 (PDZ domain containing 4); INTERACTS WITH 17beta-estradiol; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC293856; PDZ domain-containing protein 4; RGD1561214; similar to PDZ domain containing 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X156,681,717 - 156,712,031 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX156,681,717 - 156,713,028 (-)EnsemblGRCr8
mRatBN7.2X151,530,390 - 151,560,779 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,530,390 - 151,560,826 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX153,671,555 - 153,701,275 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,234,785 - 157,264,506 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,906,609 - 154,936,330 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,963,343 - 156,993,591 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,963,870 - 156,993,591 (+)Ensemblrn6Rnor6.0
Rnor_5.01152,711,639 - 152,741,657 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X159,716,489 - 159,746,210 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1136,329,561 - 136,359,280 (+)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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

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

Genomics

Comparative Map Data
Pdzd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X156,681,717 - 156,712,031 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX156,681,717 - 156,713,028 (-)EnsemblGRCr8
mRatBN7.2X151,530,390 - 151,560,779 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,530,390 - 151,560,826 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX153,671,555 - 153,701,275 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,234,785 - 157,264,506 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,906,609 - 154,936,330 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,963,343 - 156,993,591 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,963,870 - 156,993,591 (+)Ensemblrn6Rnor6.0
Rnor_5.01152,711,639 - 152,741,657 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X159,716,489 - 159,746,210 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1136,329,561 - 136,359,280 (+)NCBICelera
Cytogenetic MapXq37NCBI
PDZD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X153,802,166 - 153,830,544 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX153,802,166 - 153,830,930 (-)Ensemblhg38GRCh38
GRCh37X153,067,621 - 153,095,999 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X152,720,817 - 152,749,197 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X152,588,469 - 152,616,850NCBI
CeleraX153,301,304 - 153,329,683 (-)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX141,724,655 - 141,753,458 (-)NCBIHuRef
CHM1_1X152,942,032 - 152,970,411 (-)NCBICHM1_1
T2T-CHM13v2.0X152,075,829 - 152,104,208 (-)NCBIT2T-CHM13v2.0
Pdzd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,836,963 - 72,868,649 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX72,836,965 - 72,868,575 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X73,793,357 - 73,825,043 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,793,359 - 73,824,969 (-)Ensemblmm10GRCm38
MGSCv37X71,038,696 - 71,070,308 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X70,046,077 - 70,077,689 (-)NCBIMGSCv36mm8
CeleraX65,045,630 - 65,077,262 (-)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.41NCBI
Pdzd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580512,925 - 535,917 (-)Ensembl
ChiLan1.0NW_004955580512,963 - 535,911 (-)NCBIChiLan1.0ChiLan1.0
PDZD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X153,842,925 - 153,871,329 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X153,846,530 - 153,875,015 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X143,352,944 - 143,381,428 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X153,240,182 - 153,267,880 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX153,240,182 - 153,267,874 (-)EnsemblpanPan2panpan1.1
PDZD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X121,616,122 - 121,647,326 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX121,616,114 - 121,647,697 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX106,945,175 - 106,976,007 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X124,757,487 - 124,788,337 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX124,757,479 - 124,788,851 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X120,526,759 - 120,557,616 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X123,041,753 - 123,072,883 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X122,803,951 - 122,834,817 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pdzd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X118,943,641 - 118,970,161 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936809679,938 - 707,938 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936809681,412 - 707,932 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDZD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,544,944 - 124,567,369 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X124,543,845 - 124,567,477 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X142,108,442 - 142,132,247 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDZD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,229,495 - 128,255,341 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX128,229,300 - 128,255,312 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606566,096,825 - 66,122,903 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdzd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624946477,156 - 496,750 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624946477,125 - 496,871 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Pdzd4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X128,757,588 - 128,788,088 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:314
Count of miRNA genes:198
Interacting mature miRNAs:239
Transcripts:ENSRNOT00000056376
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118973754157758123Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 65 161 89 88 57 92 57 6 345 189 11 140 75 92 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000077109   ⟹   ENSRNOP00000072313
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX156,681,717 - 156,712,031 (-)Ensembl
mRatBN7.2 EnsemblX151,530,390 - 151,560,826 (-)Ensembl
Rnor_6.0 EnsemblX156,963,870 - 156,993,591 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000100363   ⟹   ENSRNOP00000082756
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX156,681,717 - 156,711,415 (-)Ensembl
mRatBN7.2 EnsemblX151,530,390 - 151,560,826 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108114   ⟹   ENSRNOP00000088024
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX156,681,717 - 156,713,028 (-)Ensembl
mRatBN7.2 EnsemblX151,530,390 - 151,560,826 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000115095   ⟹   ENSRNOP00000093710
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,530,390 - 151,560,826 (-)Ensembl
RefSeq Acc Id: NM_001135836   ⟹   NP_001129308
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,681,717 - 156,711,436 (-)NCBI
mRatBN7.2X151,530,390 - 151,560,112 (-)NCBI
Rnor_6.0X156,963,870 - 156,993,591 (+)NCBI
Rnor_5.01152,711,639 - 152,741,657 (+)NCBI
RGSC_v3.4X159,716,489 - 159,746,210 (-)RGD
Celera1136,329,561 - 136,359,280 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001414724   ⟹   NP_001401653
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,681,717 - 156,712,031 (-)NCBI
mRatBN7.2X151,530,390 - 151,560,707 (-)NCBI
RefSeq Acc Id: XM_006229564   ⟹   XP_006229626
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,681,721 - 156,711,509 (-)NCBI
mRatBN7.2X151,530,392 - 151,560,779 (-)NCBI
Rnor_6.0X156,963,343 - 156,993,589 (+)NCBI
Rnor_5.01152,711,639 - 152,741,657 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229565   ⟹   XP_006229627
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,681,721 - 156,711,511 (-)NCBI
mRatBN7.2X151,530,392 - 151,560,773 (-)NCBI
Rnor_6.0X156,963,343 - 156,993,589 (+)NCBI
Rnor_5.01152,711,639 - 152,741,657 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099532   ⟹   XP_038955460
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,681,721 - 156,711,511 (-)NCBI
mRatBN7.2X151,530,392 - 151,560,775 (-)NCBI
RefSeq Acc Id: XM_039099533   ⟹   XP_038955461
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,681,721 - 156,711,509 (-)NCBI
mRatBN7.2X151,530,392 - 151,560,774 (-)NCBI
RefSeq Acc Id: NP_001129308   ⟸   NM_001135836
- Peptide Label: isoform 2
- UniProtKB: A6KRU8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229626   ⟸   XM_006229564
- Peptide Label: isoform X1
- UniProtKB: A6KRU8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229627   ⟸   XM_006229565
- Peptide Label: isoform X2
- UniProtKB: A0A8I6AHV5 (UniProtKB/TrEMBL),   A0A8I5ZXV3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000072313   ⟸   ENSRNOT00000077109
RefSeq Acc Id: XP_038955460   ⟸   XM_039099532
- Peptide Label: isoform X3
- UniProtKB: A0A8I6AJE7 (UniProtKB/TrEMBL),   A0A8I5ZXV3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955461   ⟸   XM_039099533
- Peptide Label: isoform X4
Ensembl Acc Id: ENSRNOP00000093710   ⟸   ENSRNOT00000115095
Ensembl Acc Id: ENSRNOP00000088024   ⟸   ENSRNOT00000108114
Ensembl Acc Id: ENSRNOP00000082756   ⟸   ENSRNOT00000100363
RefSeq Acc Id: NP_001401653   ⟸   NM_001414724
- Peptide Label: isoform 1
- UniProtKB: D3ZLI9 (UniProtKB/TrEMBL),   A6KRU8 (UniProtKB/TrEMBL)
Protein Domains
PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZLI9-F1-model_v2 AlphaFold D3ZLI9 1-766 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:1561214 AgrOrtholog
BioCyc Gene G2FUF-659 BioCyc
Ensembl Genes ENSRNOG00000056174 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077109 ENTREZGENE
  ENSRNOT00000077109.3 UniProtKB/TrEMBL
  ENSRNOT00000100363.2 UniProtKB/TrEMBL
  ENSRNOT00000108114 ENTREZGENE
  ENSRNOT00000108114.2 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
InterPro E3_ubiquitin-PDZ_ligase UniProtKB/TrEMBL
  PDZ/DHR/GLGF UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
NCBI Gene 293856 ENTREZGENE
PANTHER PDZ DOMAIN CONTAINING RING FINGER PROTEIN 3, 4 UniProtKB/TrEMBL
  PDZ DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
PhenoGen Pdzd4 PhenoGen
PROSITE PDZ UniProtKB/TrEMBL
RatGTEx ENSRNOG00000056174 RatGTEx
SMART PDZ UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
UniProt A0A8I5ZXV3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AHV5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AJE7 ENTREZGENE
  A6KRU8 ENTREZGENE, UniProtKB/TrEMBL
  D3ZLI9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pdzd4  PDZ domain containing 4   Pdzd4_predicted  PDZ domain containing 4 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Pdzd4_predicted  PDZ domain containing 4 (predicted)  RGD1561214_predicted  similar to PDZ domain containing 4 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1561214_predicted  similar to PDZ domain containing 4 (predicted)  LOC293856  similar to PDZ domain containing 4  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC293856  similar to PDZ domain containing 4      Symbol and Name status set to provisional 70820 PROVISIONAL