Pex3 (peroxisomal biogenesis factor 3) - Rat Genome Database

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Gene: Pex3 (peroxisomal biogenesis factor 3) Rattus norvegicus
Analyze
Symbol: Pex3
Name: peroxisomal biogenesis factor 3
RGD ID: 621636
Description: Predicted to enable lipid binding activity and protein-macromolecule adaptor activity. Involved in peroxisome membrane biogenesis. Located in cytosol and peroxisomal membrane. Human ortholog(s) of this gene implicated in peroxisomal biogenesis disorder and peroxisome biogenesis disorder 10A. Orthologous to human PEX3 (peroxisomal biogenesis factor 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: peroxin-3; peroxisomal assembly protein PEX3
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
GRCr819,732,641 - 9,774,479 (-)NCBIGRCr8
mRatBN7.217,912,508 - 7,954,474 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl17,912,506 - 7,954,518 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx17,608,756 - 7,650,735 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0113,607,881 - 13,649,860 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.017,890,775 - 7,933,010 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.017,685,209 - 7,726,238 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl17,685,338 - 7,726,401 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.019,313,347 - 9,354,522 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.418,316,117 - 8,357,955 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.118,316,120 - 8,357,955 (-)NCBI
Celera16,397,513 - 6,439,330 (-)NCBICelera
Cytogenetic Map1p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IDA,TAS)
endoplasmic reticulum  (IEA,ISO)
nucleoplasm  (IEA,ISO)
peroxisomal membrane  (IBA,IDA,IEA,ISO,TAS)
peroxisome  (IDA,ISO)
protein-containing complex  (ISO)
protein-lipid complex  (IEA,ISO)

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. The peroxin pex3p initiates membrane assembly in peroxisome biogenesis. Ghaedi K, etal., Mol Biol Cell 2000 Jun;11(6):2085-102.
3. Proteomic analysis of rat liver peroxisome: presence of peroxisome-specific isozyme of Lon protease. Kikuchi M, etal., J Biol Chem. 2004 Jan 2;279(1):421-8. Epub 2003 Oct 15.
4. The peroxisomal membrane protein import receptor Pex3p is directly transported to peroxisomes by a novel Pex19p- and Pex16p-dependent pathway. Matsuzaki T and Fujiki Y, J Cell Biol. 2008 Dec 29;183(7):1275-86. doi: 10.1083/jcb.200806062.
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:9657383   PMID:9922452   PMID:10430017   PMID:10527525   PMID:10958759   PMID:12924628   PMID:15007061   PMID:15489334   PMID:18174172   PMID:19479899   PMID:19686593   PMID:19715730  
PMID:19946888   PMID:21525035   PMID:21768384  


Genomics

Comparative Map Data
Pex3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819,732,641 - 9,774,479 (-)NCBIGRCr8
mRatBN7.217,912,508 - 7,954,474 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl17,912,506 - 7,954,518 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx17,608,756 - 7,650,735 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0113,607,881 - 13,649,860 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.017,890,775 - 7,933,010 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.017,685,209 - 7,726,238 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl17,685,338 - 7,726,401 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.019,313,347 - 9,354,522 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.418,316,117 - 8,357,955 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.118,316,120 - 8,357,955 (-)NCBI
Celera16,397,513 - 6,439,330 (-)NCBICelera
Cytogenetic Map1p13NCBI
PEX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386143,450,805 - 143,490,616 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6143,450,805 - 143,490,616 (+)EnsemblGRCh38hg38GRCh38
GRCh376143,771,942 - 143,811,753 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366143,813,810 - 143,852,838 (+)NCBINCBI36Build 36hg18NCBI36
Build 346143,813,809 - 143,852,834NCBI
Celera6144,512,345 - 144,552,176 (+)NCBICelera
Cytogenetic Map6q24.2NCBI
HuRef6141,335,806 - 141,375,875 (+)NCBIHuRef
CHM1_16144,034,452 - 144,074,661 (+)NCBICHM1_1
T2T-CHM13v2.06144,643,215 - 144,683,024 (+)NCBIT2T-CHM13v2.0
Pex3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391013,399,586 - 13,428,886 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1013,399,586 - 13,428,886 (-)EnsemblGRCm39 Ensembl
GRCm381013,523,842 - 13,553,142 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1013,523,842 - 13,553,142 (-)EnsemblGRCm38mm10GRCm38
MGSCv371013,243,648 - 13,272,948 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361013,214,314 - 13,243,291 (-)NCBIMGSCv36mm8
Celera1013,424,011 - 13,452,957 (-)NCBICelera
Cytogenetic Map10A2NCBI
cM Map104.89NCBI
Pex3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543616,917,008 - 16,956,242 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543616,918,259 - 16,956,242 (-)NCBIChiLan1.0ChiLan1.0
PEX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25163,433,164 - 163,472,702 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16161,327,988 - 161,367,495 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06141,226,738 - 141,266,233 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16145,947,954 - 145,987,194 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6145,947,954 - 145,987,188 (+)Ensemblpanpan1.1panPan2
PEX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1134,994,092 - 35,030,453 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl134,994,197 - 35,023,975 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha135,892,376 - 35,928,520 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0135,169,295 - 35,212,126 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl135,169,269 - 35,209,374 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1135,037,632 - 35,073,783 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0134,920,560 - 34,956,715 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0135,232,840 - 35,268,988 (+)NCBIUU_Cfam_GSD_1.0
Pex3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946129,940,927 - 129,977,768 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366252,656,452 - 2,694,744 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366252,657,511 - 2,694,668 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PEX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl121,766,000 - 21,802,182 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1121,750,194 - 21,801,625 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2124,137,242 - 24,188,753 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PEX3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11329,753,203 - 29,792,300 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1329,751,233 - 29,792,247 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660401,888,016 - 1,926,938 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pex3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475310,786,599 - 10,826,255 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475310,787,513 - 10,826,099 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pex3
247 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:74
Interacting mature miRNAs:89
Transcripts:ENSRNOT00000021524
Prediction methods:Miranda, 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
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat
1300170Rf6Renal function QTL 63.14renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)1416280711481482Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1592587724697545Rat

Markers in Region
RH142832  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map1103.72UniSTS
Cytogenetic Map1p13UniSTS
RH141589  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.217,912,731 - 7,912,947 (+)MAPPERmRatBN7.2
Rnor_6.017,685,433 - 7,685,648NCBIRnor6.0
Rnor_5.019,313,571 - 9,313,786UniSTSRnor5.0
RGSC_v3.418,316,341 - 8,316,556UniSTSRGSC3.4
Celera16,397,737 - 6,397,952UniSTS
RH 3.4 Map1102.5UniSTS
Cytogenetic Map1p13UniSTS


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 36 54 38 19 38 74 35 41 11
Low 7 3 3 3 8 11 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000021524   ⟹   ENSRNOP00000021524
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl17,912,506 - 7,954,518 (-)Ensembl
Rnor_6.0 Ensembl17,685,338 - 7,726,401 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114484   ⟹   ENSRNOP00000096147
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl17,914,087 - 7,954,518 (-)Ensembl
RefSeq Acc Id: NM_031350   ⟹   NP_112640
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819,732,641 - 9,774,479 (-)NCBI
mRatBN7.217,912,508 - 7,954,348 (-)NCBI
Rnor_6.017,685,209 - 7,726,238 (-)NCBI
Rnor_5.019,313,347 - 9,354,522 (-)NCBI
RGSC_v3.418,316,117 - 8,357,955 (-)RGD
Celera16,397,513 - 6,439,330 (-)RGD
Sequence:
RefSeq Acc Id: XM_039092487   ⟹   XP_038948415
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819,733,251 - 9,774,463 (-)NCBI
mRatBN7.217,913,299 - 7,954,474 (-)NCBI
RefSeq Acc Id: XM_039092495   ⟹   XP_038948423
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819,733,251 - 9,774,463 (-)NCBI
mRatBN7.217,913,275 - 7,954,474 (-)NCBI
RefSeq Acc Id: NP_112640   ⟸   NM_031350
- UniProtKB: Q9JJK4 (UniProtKB/Swiss-Prot),   A6JP61 (UniProtKB/TrEMBL),   A0A8I6AUP3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021524   ⟸   ENSRNOT00000021524
RefSeq Acc Id: XP_038948423   ⟸   XM_039092495
- Peptide Label: isoform X2
- UniProtKB: A0A8L2QAW4 (UniProtKB/TrEMBL),   A0A8I6AUP3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038948415   ⟸   XM_039092487
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AUP3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000096147   ⟸   ENSRNOT00000114484

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JJK4-F1-model_v2 AlphaFold Q9JJK4 1-372 view protein structure

Transcriptome

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

Promoters
RGD ID:13689496
Promoter ID:EPDNEW_R21
Type:multiple initiation site
Name:Pex3_1
Description:peroxisomal biogenesis factor 3
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_6.017,726,385 - 7,726,445EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621636 AgrOrtholog
BioCyc Gene G2FUF-62360 BioCyc
Ensembl Genes ENSRNOG00000015660 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00055002055 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000021524.5 UniProtKB/TrEMBL
  ENSRNOT00000114484.1 UniProtKB/TrEMBL
  ENSRNOT00055003285 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5597999 IMAGE-MGC_LOAD
InterPro Peroxin-3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83519 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:72404 IMAGE-MGC_LOAD
NCBI Gene 83519 ENTREZGENE
PANTHER PEROXISOMAL BIOGENESIS FACTOR 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR28080 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Peroxin-3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pex3 PhenoGen
RatGTEx ENSRNOG00000015660 RatGTEx
  ENSRNOG00055002055 RatGTEx
UniProt A0A8I6AUP3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2QAW4 ENTREZGENE, UniProtKB/TrEMBL
  A6JP61 ENTREZGENE, UniProtKB/TrEMBL
  PEX3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pex3  peroxisomal biogenesis factor 3      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pex3  peroxisomal biogenesis factor 3      Symbol and Name status set to provisional 70820 PROVISIONAL