Pdzrn3 (PDZ domain containing RING finger 3) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pdzrn3 (PDZ domain containing RING finger 3) Mus musculus
Analyze
Symbol: Pdzrn3
Name: PDZ domain containing RING finger 3
RGD ID: 1313170
MGI Page MGI
Description: Is expressed in forebrain; genitourinary system; and tail paraxial mesenchyme. Orthologous to human PDZRN3 (PDZ domain containing ring finger 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 1110020C07Rik; AI429718; AL023082; E3 ubiquitin-protein ligase PDZRN3; LN; LNX3; PDZ domain containing RING finger 3A; PDZ domain-containing RING finger protein 3; RING-type E3 ubiquitin transferase PDZRN3; SEMACAP3; semaphorin cytoplasmic domain-associated protein 3; semaphorin cytoplasmic domain-associated protein 3A; Semc; Semcap3
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396101,126,568 - 101,354,858 (-)NCBIGRCm39mm39
GRCm39 Ensembl6101,126,570 - 101,354,858 (-)Ensembl
GRCm386101,149,607 - 101,377,897 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6101,149,609 - 101,377,897 (-)EnsemblGRCm38mm10GRCm38
MGSCv376101,099,601 - 101,327,891 (-)NCBIGRCm37mm9NCBIm37
MGSCv366101,115,712 - 101,343,995 (-)NCBImm8
Celera6103,016,258 - 103,244,142 (-)NCBICelera
Cytogenetic Map6D3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:7671812   PMID:10349636   PMID:11042159   PMID:11076861   PMID:12477932   PMID:15188402   PMID:15368895   PMID:15489334   PMID:15511637   PMID:15618518   PMID:15782199   PMID:16141072  
PMID:16141073   PMID:16602821   PMID:17118964   PMID:17576800   PMID:18287559   PMID:20668165   PMID:21267068   PMID:21862448   PMID:21873635   PMID:23576576   PMID:24931612   PMID:25198863  
PMID:26671461   PMID:28143902   PMID:29779941   PMID:30066954   PMID:30529950   PMID:30635555   PMID:31980707   PMID:32325033   PMID:33238113  


Genomics

Comparative Map Data
Pdzrn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396101,126,568 - 101,354,858 (-)NCBIGRCm39mm39
GRCm39 Ensembl6101,126,570 - 101,354,858 (-)Ensembl
GRCm386101,149,607 - 101,377,897 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6101,149,609 - 101,377,897 (-)EnsemblGRCm38mm10GRCm38
MGSCv376101,099,601 - 101,327,891 (-)NCBIGRCm37mm9NCBIm37
MGSCv366101,115,712 - 101,343,995 (-)NCBImm8
Celera6103,016,258 - 103,244,142 (-)NCBICelera
Cytogenetic Map6D3NCBI
PDZRN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl373,382,431 - 73,624,941 (-)EnsemblGRCh38hg38GRCh38
GRCh38373,382,430 - 73,624,997 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37373,431,582 - 73,674,092 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36373,514,342 - 73,756,762 (-)NCBINCBI36hg18NCBI36
Celera373,365,735 - 73,608,750 (-)NCBI
Cytogenetic Map3p13NCBI
HuRef373,434,331 - 73,676,506 (-)NCBIHuRef
CHM1_1373,384,942 - 73,627,407 (-)NCBICHM1_1
Pdzrn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24133,770,736 - 133,996,959 (-)NCBI
Rnor_6.0 Ensembl4133,717,139 - 133,951,264 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04133,717,139 - 133,951,282 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04198,194,465 - 198,429,457 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44136,044,210 - 136,254,969 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14136,260,810 - 136,311,636 (-)NCBI
Celera4122,607,053 - 122,831,741 (-)NCBICelera
Cytogenetic Map4q34NCBI
Pdzrn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542114,648,524 - 14,877,822 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542114,648,436 - 14,878,759 (+)NCBIChiLan1.0ChiLan1.0
PDZRN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1375,245,623 - 75,488,415 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl375,246,558 - 75,488,499 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0373,322,613 - 73,565,929 (-)NCBIMhudiblu_PPA_v0panPan3
PDZRN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2018,622,069 - 18,859,550 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12018,621,960 - 18,859,620 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pdzrn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366034,218,675 - 4,423,450 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDZRN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1354,659,589 - 54,904,900 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11354,659,657 - 54,904,742 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21360,422,724 - 60,650,319 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDZRN3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12234,325,208 - 34,567,748 (-)NCBI
ChlSab1.1 Ensembl2234,326,144 - 34,567,633 (-)Ensembl
Pdzrn3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247737,901,560 - 8,144,455 (-)NCBI

Position Markers
RH128427  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm386101,149,673 - 101,149,858UniSTSGRCm38
MGSCv376101,099,667 - 101,099,852UniSTSGRCm37
Celera6103,016,324 - 103,016,509UniSTS
Cytogenetic Map6D3UniSTS
AI429718  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm386101,149,826 - 101,149,943UniSTSGRCm38
MGSCv376101,099,820 - 101,099,937UniSTSGRCm37
Celera6103,016,477 - 103,016,594UniSTS
Cytogenetic Map6D3UniSTS
Whitehead/MRC_RH61012.9UniSTS
RH125416  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm386101,150,023 - 101,150,142UniSTSGRCm38
MGSCv376101,100,017 - 101,100,136UniSTSGRCm37
Celera6103,016,674 - 103,016,793UniSTS
Cytogenetic Map6D3UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25440480Moaq2_mmodifier of alien QTL 2 (mouse)61117500000Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139100000Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645314059128835032Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46935985136423692Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648720000125360000Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648720000148450000Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648726556125356785Mouse
1357683Igf1sl1_mIGF-1 serum levels 1 (mouse)Not determined652161713116155267Mouse
1301876Bits2_mbitterness sensitivity 2 (mouse)Not determined670425898104426034Mouse
1301813Skl3_mskeletal size (tail length) 3 (mouse)Not determined670425898104426034Mouse
1301034Egrm2_mearly growth rate (mouse)Not determined670425898104426034Mouse
1300869Stheal5_msoft tissue heal 5 (mouse)Not determined671575060105575178Mouse
1300954Fcsa1_mfemoral cross-sectional area 1 (mouse)Not determined671981024105981170Mouse
1301521Pas1c_mpulmonary adenoma susceptibility 1c (mouse)Not determined671981024105981170Mouse
13506930Recrq9_mrecombination rate in male meiosis QTL 9 (mouse)673500000134700000Mouse
1301320Ots1_movarian teratoma susceptibility 1 (mouse)Not determined675447583104503555Mouse
10043901Pfat5_mpredicted fat percentage 5 (mouse)Not determined675607306109607450Mouse
10412208Cypr4_mcytokine production 4 (mouse)Not determined675716503109716697Mouse
1357875Pfat2_mpredicted fat percentage 2 (mouse)Not determined676463949110464093Mouse
4141376Dbm1_mdiabetes modifier 1 (mouse)Not determined678629504121115387Mouse
14696731Pairq1_mP. aeruginosa infection resistance QTL 1 (mouse)681500000102200000Mouse
10043864T2dm4sa_mtype 2 diabetes mellitus 4 in SMXA RI mice (mouse)Not determined683713869147052561Mouse
11251720Ewc4_methanol withdrawal and consumption 4 (mouse)684122513118122513Mouse
1301687Mnic2_mmacronutrient intake (mouse)Not determined686806805113544602Mouse
1301744Hdlq11_mHDL QTL 11 (mouse)Not determined687503360121503555Mouse
1301262Gasa3_mgastritis type A susceptibility locus 3 (mouse)Not determined689005405123005603Mouse
1301244Ichs_mimmediate cutaneous hypersensitivity QTL (mouse)Not determined690795610124795846Mouse
4141578Obrq1_mobesity resistance QTL 1 (mouse)Not determined92607306112004738Mouse
11353842Bmiq4_mbody mass index QTL 4 (mouse)692607306146429238Mouse
1301292Cfbw2_mcystic fibrosis body weight 2 (mouse)Not determined695004651129004738Mouse
1300704Cia3_mcollagen induced arthritis QTL 3 (mouse)Not determined696347325130347522Mouse
11040599Lmr4b_mleishmaniasis resistance 4b (mouse)696347325130347522Mouse
4141940W6q5_mweight 6 weeks QTL 5 (mouse)Not determined96655951146633626Mouse
4142416Egq11_mearly growth QTL 11 (mouse)Not determined96655951146633626Mouse
1357555Tesq2_mtestis weight QTL 2 (mouse)Not determined696655951146633626Mouse
10043923Bhr7_mbronchial hyperresponsiveness 7 (mouse)Not determined698242853132242977Mouse
1301518Bbaa5_mB.burgdorferi-associated arthritis 5 (mouse)Not determined698506837145935444Mouse
1301923Lith6_mlithogenic gene 6 (mouse)Not determined698717516132717715Mouse
1301915Chab3_mcholesterol absorption 3 (mouse)Not determined698931748132940036Mouse
1302131Bmd8_mbone mineral density 8 (mouse)Not determined699155128133155267Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:456
Count of miRNA genes:327
Interacting mature miRNAs:388
Transcripts:ENSMUST00000075994, ENSMUST00000124884, ENSMUST00000144505, ENSMUST00000151175
Prediction methods: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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000075994   ⟹   ENSMUSP00000075376
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl6101,149,609 - 101,377,897 (-)Ensembl
RefSeq Acc Id: ENSMUST00000124884
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl6101,156,973 - 101,355,010 (-)Ensembl
RefSeq Acc Id: ENSMUST00000144505
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl6101,169,856 - 101,199,200 (-)Ensembl
RefSeq Acc Id: ENSMUST00000151175
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl6101,179,878 - 101,377,342 (-)Ensembl
RefSeq Acc Id: ENSMUST00000239140   ⟹   ENSMUSP00000158931
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl6101,151,341 - 101,199,186 (-)Ensembl
RefSeq Acc Id: NM_018884   ⟹   NP_061372
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm396101,126,568 - 101,354,858 (-)NCBI
GRCm386101,149,607 - 101,377,897 (-)ENTREZGENE
MGSCv376101,099,601 - 101,327,891 (-)RGD
Celera6103,016,258 - 103,244,142 (-)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006506405   ⟹   XP_006506468
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm396101,126,575 - 101,176,183 (-)NCBI
GRCm386101,149,614 - 101,199,224 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_061372   ⟸   NM_018884
- UniProtKB: Q69ZS0 (UniProtKB/Swiss-Prot),   Q3UPS8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006506468   ⟸   XM_006506405
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSMUSP00000158931   ⟸   ENSMUST00000239140
RefSeq Acc Id: ENSMUSP00000075376   ⟸   ENSMUST00000075994
Protein Domains
PDZ

Promoters
RGD ID:6839733
Promoter ID:MM_KWN:47061
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain
Transcripts:OTTMUST00000066669
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv366101,148,836 - 101,149,336 (-)MPROMDB
RGD ID:6890554
Promoter ID:EPDNEW_M8728
Type:single initiation site
Name:Pdzrn3_1
Description:Mus musculus PDZ domain containing RING finger 3 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm386101,199,198 - 101,199,258EPDNEW
RGD ID:6839739
Promoter ID:MM_KWN:47063
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:MEF_B6
Transcripts:OTTMUST00000066671
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv366101,304,501 - 101,305,001 (-)MPROMDB
RGD ID:6840013
Promoter ID:MM_KWN:47064
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   Brain,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6
Transcripts:ENSMUST00000101117,   NM_018884,   NM_018884_PDZRN3,   UC009DCF.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv366101,327,246 - 101,328,052 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1933157 AgrOrtholog
Ensembl Genes ENSMUSG00000035357 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000075376 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000158931 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000075994 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000239140 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/Swiss-Prot
InterPro PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRAF-like UniProtKB/Swiss-Prot
  Znf_RING UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
  Znf_RING_CS UniProtKB/Swiss-Prot
  Znf_TRAF UniProtKB/Swiss-Prot
KEGG Report mmu:55983 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1933157 ENTREZGENE
NCBI Gene 55983 ENTREZGENE
Pfam PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pdzrn3 PhenoGen
PROSITE PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/Swiss-Prot
  ZF_RING_2 UniProtKB/Swiss-Prot
  ZF_TRAF UniProtKB/Swiss-Prot
SMART PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RING UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49599 UniProtKB/Swiss-Prot
  SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A5F8MPS6_MOUSE UniProtKB/TrEMBL
  PZRN3_MOUSE UniProtKB/Swiss-Prot
  Q3UPS8 ENTREZGENE, UniProtKB/TrEMBL
  Q3UXA7_MOUSE UniProtKB/TrEMBL
  Q69ZS0 ENTREZGENE
UniProt Secondary Q91Z03 UniProtKB/Swiss-Prot
  Q9QY54 UniProtKB/Swiss-Prot
  Q9QY55 UniProtKB/Swiss-Prot