Pdzd8 (PDZ domain containing 8) - Rat Genome Database

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Gene: Pdzd8 (PDZ domain containing 8) Rattus norvegicus
Analyze
Symbol: Pdzd8
Name: PDZ domain containing 8
RGD ID: 1308622
Description: Predicted to enable lipid binding activity and metal ion binding activity. Predicted to be involved in several processes, including mitochondrial calcium ion homeostasis; mitochondrion-endoplasmic reticulum membrane tethering; and regulation of cell morphogenesis. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in mitochondria-associated endoplasmic reticulum membrane. Orthologous to human PDZD8 (PDZ domain containing 8); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC308000; PDZ domain-containing protein 8; Pdzk8
RGD Orthologs
Human
Mouse
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
mRatBN7.21258,449,218 - 258,506,828 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1258,449,218 - 258,506,828 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1266,654,746 - 266,712,507 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01273,360,771 - 273,418,533 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01266,001,930 - 266,059,796 (-)NCBIRnor_WKY
Rnor_6.01280,458,041 - 280,515,650 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1280,458,041 - 280,515,650 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01287,818,525 - 287,876,134 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41265,825,444 - 265,883,170 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11266,039,911 - 266,094,082 (-)NCBI
Celera1254,103,043 - 254,160,651 (-)NCBICelera
Cytogenetic Map1q55NCBI
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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19946888   PMID:21834987   PMID:29097544  


Genomics

Comparative Map Data
Pdzd8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21258,449,218 - 258,506,828 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1258,449,218 - 258,506,828 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1266,654,746 - 266,712,507 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01273,360,771 - 273,418,533 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01266,001,930 - 266,059,796 (-)NCBIRnor_WKY
Rnor_6.01280,458,041 - 280,515,650 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1280,458,041 - 280,515,650 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01287,818,525 - 287,876,134 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41265,825,444 - 265,883,170 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11266,039,911 - 266,094,082 (-)NCBI
Celera1254,103,043 - 254,160,651 (-)NCBICelera
Cytogenetic Map1q55NCBI
PDZD8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3810117,277,274 - 117,375,440 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl10117,277,274 - 117,375,440 (-)EnsemblGRCh38hg38GRCh38
GRCh3710119,036,785 - 119,134,951 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3610119,032,596 - 119,124,927 (-)NCBINCBI36Build 36hg18NCBI36
Build 3410119,032,595 - 119,124,927NCBI
Celera10112,772,703 - 112,865,000 (-)NCBICelera
Cytogenetic Map10q25.3-q26.11NCBI
HuRef10112,670,274 - 112,763,195 (-)NCBIHuRef
CHM1_110119,326,798 - 119,419,104 (-)NCBICHM1_1
T2T-CHM13v2.010118,171,771 - 118,269,881 (-)NCBIT2T-CHM13v2.0
Pdzd8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391959,284,516 - 59,334,212 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1959,285,610 - 59,334,212 (-)EnsemblGRCm39 Ensembl
GRCm381959,296,084 - 59,345,780 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1959,297,178 - 59,345,780 (-)EnsemblGRCm38mm10GRCm38
MGSCv371959,370,574 - 59,420,270 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361959,351,678 - 59,399,030 (-)NCBIMGSCv36mm8
Celera1961,496,563 - 61,545,435 (-)NCBICelera
Cytogenetic Map19D3NCBI
Pdzd8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543121,980,447 - 22,060,826 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543121,980,447 - 22,060,826 (-)NCBIChiLan1.0ChiLan1.0
PDZD8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan110129,158,120 - 129,251,103 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v010113,862,457 - 113,958,281 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.110117,288,123 - 117,385,317 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10117,293,877 - 117,385,317 (-)Ensemblpanpan1.1panPan2
PDZD8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12827,768,182 - 27,853,958 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2827,772,651 - 27,853,769 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2827,902,798 - 27,997,253 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02828,289,062 - 28,383,545 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2828,302,187 - 28,383,513 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12827,861,675 - 27,945,273 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02827,863,751 - 27,958,752 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02828,058,685 - 28,153,690 (-)NCBIUU_Cfam_GSD_1.0
Pdzd8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721318,370,785 - 18,451,565 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364867,114,383 - 7,190,572 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364867,109,733 - 7,190,518 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDZD8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14127,395,823 - 127,502,400 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114127,395,842 - 127,502,421 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214138,800,410 - 138,903,648 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDZD8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.19110,081,713 - 110,184,348 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl9110,082,680 - 110,184,260 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604871,336,767 - 71,441,109 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdzd8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473729,242,196 - 29,353,336 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473729,242,198 - 29,353,336 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pdzd8
149 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:331
Count of miRNA genes:219
Interacting mature miRNAs:250
Transcripts:ENSRNOT00000068082
Prediction methods:Miranda
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
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
1581544Rf52Renal function QTL 520.05urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1233948574260522016Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1238699859259647894Rat

Markers in Region
AI058870  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21258,450,567 - 258,450,752 (+)MAPPERmRatBN7.2
Rnor_6.01280,459,391 - 280,459,575NCBIRnor6.0
Rnor_5.01287,819,875 - 287,820,059UniSTSRnor5.0
RGSC_v3.41265,826,794 - 265,826,978UniSTSRGSC3.4
Celera1254,104,393 - 254,104,577UniSTS
RH 3.4 Map11702.3UniSTS
Cytogenetic Map1q55UniSTS
D19Mgc7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21258,452,910 - 258,453,500 (+)MAPPERmRatBN7.2
Rnor_6.01280,461,734 - 280,462,323NCBIRnor6.0
Rnor_5.01287,822,218 - 287,822,807UniSTSRnor5.0
RGSC_v3.41265,829,137 - 265,829,726UniSTSRGSC3.4
Celera1254,106,736 - 254,107,325UniSTS
Cytogenetic Map1q55UniSTS


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 28 42 26 18 26 3 3 74 34 41 11 3
Low 15 15 15 1 15 5 8 1 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068082   ⟹   ENSRNOP00000063181
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1258,449,218 - 258,506,828 (-)Ensembl
Rnor_6.0 Ensembl1280,458,041 - 280,515,650 (-)Ensembl
RefSeq Acc Id: NM_001107446   ⟹   NP_001100916
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21258,449,218 - 258,506,828 (-)NCBI
Rnor_6.01280,458,041 - 280,515,650 (-)NCBI
Rnor_5.01287,818,525 - 287,876,134 (-)NCBI
RGSC_v3.41265,825,444 - 265,883,170 (-)RGD
Celera1254,103,043 - 254,160,651 (-)RGD
Sequence:
RefSeq Acc Id: XM_039110347   ⟹   XP_038966275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21258,465,520 - 258,506,808 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100916 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966275 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94558 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100916   ⟸   NM_001107446
- UniProtKB: D3ZXY2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063181   ⟸   ENSRNOT00000068082
RefSeq Acc Id: XP_038966275   ⟸   XM_039110347
- Peptide Label: isoform X1
Protein Domains
PDZ   Phorbol-ester/DAG-type   SMP-LTD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZXY2-F1-model_v2 AlphaFold D3ZXY2 1-1152 view protein structure

Transcriptome

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

Promoters
RGD ID:13691014
Promoter ID:EPDNEW_R1539
Type:initiation region
Name:Pdzd8_1
Description:PDZ domain containing 8
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_6.01280,515,639 - 280,515,699EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308622 AgrOrtholog
BioCyc Gene G2FUF-55253 BioCyc
Ensembl Genes ENSRNOG00000009460 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063181 ENTREZGENE
  ENSRNOP00000063181.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068082 ENTREZGENE
  ENSRNOT00000068082.2 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
  3.30.60.20 UniProtKB/TrEMBL
InterPro C1-like_sf UniProtKB/TrEMBL
  PDZ/DHR/GLGF UniProtKB/TrEMBL
  PDZ_6 UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  PDZD8 UniProtKB/TrEMBL
  Prot_Kinase_C-like_PE/DAG-bd UniProtKB/TrEMBL
  SMP_LBD UniProtKB/TrEMBL
KEGG Report rno:308000 UniProtKB/TrEMBL
NCBI Gene 308000 ENTREZGENE
PANTHER PDZ DOMAIN-CONTAINING PROTEIN 8 UniProtKB/TrEMBL
  PTHR21519 UniProtKB/TrEMBL
Pfam C1_1 UniProtKB/TrEMBL
  PDZ_6 UniProtKB/TrEMBL
PhenoGen Pdzd8 PhenoGen
PROSITE PDZ UniProtKB/TrEMBL
  SMP UniProtKB/TrEMBL
  ZF_DAG_PE_2 UniProtKB/TrEMBL
SMART PDZ UniProtKB/TrEMBL
  SM00109 UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
  SSF57889 UniProtKB/TrEMBL
UniProt D3ZXY2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Pdzd8  PDZ domain containing 8  Pdzk8_predicted  PDZ domain containing 8 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Pdzk8_predicted  PDZ domain containing 8 (predicted)      Symbol and Name status set to approved 70820 APPROVED