Pex13 (peroxisomal biogenesis factor 13) - Rat Genome Database

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Gene: Pex13 (peroxisomal biogenesis factor 13) Rattus norvegicus
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Symbol: Pex13
Name: peroxisomal biogenesis factor 13
RGD ID: 1310682
Description: Predicted to enable protein transmembrane transporter activity. Predicted to be involved in cellular response to reactive oxygen species; protein import into peroxisome matrix, docking; and protein import into peroxisome matrix, translocation. Predicted to act upstream of or within several processes, including fatty acid alpha-oxidation; microtubule-based peroxisome localization; and nervous system development. Located in peroxisomal membrane. Human ortholog(s) of this gene implicated in Peroxisome biogenesis disorder 11B and peroxisome biogenesis disorder 11A. Orthologous to human PEX13 (peroxisomal biogenesis factor 13); PARTICIPATES IN adrenoleukodystrophy pathway; carnitine-acylcarnitine translocase deficiency; fatty acid beta degradation pathway; INTERACTS WITH bisphenol A; clofibric acid; cobalt dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC305581; peroxin-13; peroxisomal membrane protein PEX13; peroxisome biogenesis factor 13
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
GRCr814101,804,673 - 101,822,367 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl14101,804,673 - 101,822,367 (-)EnsemblGRCr8
mRatBN7.21497,602,829 - 97,621,233 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1497,603,539 - 97,621,262 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx14101,936,310 - 101,954,154 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014103,180,657 - 103,198,504 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01499,652,232 - 99,670,079 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.014108,394,299 - 108,411,994 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14108,394,303 - 108,412,823 (-)Ensemblrn6Rnor6.0
Rnor_5.014105,229,224 - 105,246,919 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414104,550,699 - 104,571,485 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1496,579,668 - 96,597,394 (-)NCBICelera
RGSC_v3.114104,573,004 - 104,590,753 (-)NCBI
Cytogenetic Map14q22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)
peroxisomal importomer complex  (IBA)
peroxisomal membrane  (IBA,IDA,IEA,ISO)
peroxisome  (IDA,IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
7. Characterization of the mammalian peroxisomal import machinery: Pex2p, Pex5p, Pex12p, and Pex14p are subunits of the same protein assembly. Reguenga C, etal., J Biol Chem. 2001 Aug 10;276(32):29935-42. Epub 2001 Jun 7.
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. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8858165   PMID:11402059   PMID:11829486   PMID:12897163   PMID:16449325   PMID:17881773   PMID:19946888   PMID:21460186   PMID:21525035   PMID:30414318  


Genomics

Comparative Map Data
Pex13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814101,804,673 - 101,822,367 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl14101,804,673 - 101,822,367 (-)EnsemblGRCr8
mRatBN7.21497,602,829 - 97,621,233 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1497,603,539 - 97,621,262 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx14101,936,310 - 101,954,154 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014103,180,657 - 103,198,504 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01499,652,232 - 99,670,079 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.014108,394,299 - 108,411,994 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14108,394,303 - 108,412,823 (-)Ensemblrn6Rnor6.0
Rnor_5.014105,229,224 - 105,246,919 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414104,550,699 - 104,571,485 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1496,579,668 - 96,597,394 (-)NCBICelera
RGSC_v3.114104,573,004 - 104,590,753 (-)NCBI
Cytogenetic Map14q22NCBI
PEX13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38261,017,720 - 61,051,990 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl261,017,225 - 61,051,990 (+)Ensemblhg38GRCh38
GRCh37261,244,855 - 61,279,125 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36261,098,374 - 61,129,896 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34261,156,520 - 61,188,042NCBI
Celera261,088,403 - 61,122,717 (+)NCBICelera
Cytogenetic Map2p15NCBI
HuRef260,985,309 - 61,019,608 (+)NCBIHuRef
CHM1_1261,175,398 - 61,209,708 (+)NCBICHM1_1
T2T-CHM13v2.0261,023,561 - 61,057,833 (+)NCBIT2T-CHM13v2.0
Pex13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391123,597,283 - 23,615,883 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1123,596,479 - 23,615,959 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381123,646,843 - 23,665,883 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1123,646,479 - 23,665,959 (-)Ensemblmm10GRCm38
MGSCv371123,546,479 - 23,565,935 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361123,546,479 - 23,565,935 (-)NCBIMGSCv36mm8
Celera1125,768,364 - 25,787,821 (-)NCBICelera
Cytogenetic Map11A3.2NCBI
cM Map1114.34NCBI
Pex13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542422,799,568 - 22,830,718 (-)Ensembl
ChiLan1.0NW_00495542422,799,568 - 22,830,718 (-)NCBIChiLan1.0ChiLan1.0
PEX13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21265,325,084 - 65,359,640 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A65,329,035 - 65,363,588 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A61,108,970 - 61,143,615 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A62,250,887 - 62,285,163 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A62,250,887 - 62,285,151 (+)EnsemblpanPan2panpan1.1
PEX13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11061,113,213 - 61,130,157 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1061,123,655 - 61,193,241 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1060,993,422 - 61,021,277 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01062,112,178 - 62,140,036 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1062,112,186 - 62,139,182 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11061,815,043 - 61,842,830 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01062,099,662 - 62,127,580 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01062,395,168 - 62,422,982 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pex13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629222,011,973 - 22,040,921 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364916,529,779 - 6,562,590 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364916,530,385 - 6,559,706 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PEX13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl380,753,908 - 80,791,056 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1380,757,470 - 80,791,107 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2384,852,155 - 84,883,629 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PEX13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11445,939,181 - 45,973,049 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1445,938,940 - 45,973,125 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604565,823,893 - 65,860,756 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pex13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624833913,337 - 940,611 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624833914,621 - 940,661 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Pex13
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11193,298,294 - 93,316,267 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pex13
110 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:149
Count of miRNA genes:116
Interacting mature miRNAs:124
Transcripts:ENSRNOT00000007853
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
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1459848686104848686Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1460854936105854936Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1474255551109089856Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1477914838104348525Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1459848686104848686Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1474255551109089856Rat

Markers in Region
RH129817  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21497,603,671 - 97,603,874 (+)MAPPERmRatBN7.2
Rnor_6.014108,394,432 - 108,394,634NCBIRnor6.0
Rnor_5.014105,229,357 - 105,229,559UniSTSRnor5.0
RGSC_v3.414104,553,882 - 104,554,084UniSTSRGSC3.4
Celera1496,579,801 - 96,580,003UniSTS
RH 3.4 Map14780.5UniSTS
Cytogenetic Map14q22UniSTS


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 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000081405   ⟹   ENSRNOP00000068751
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl14101,804,673 - 101,813,166 (-)Ensembl
mRatBN7.2 Ensembl1497,603,539 - 97,612,032 (-)Ensembl
Rnor_6.0 Ensembl14108,394,303 - 108,412,823 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000104301   ⟹   ENSRNOP00000097867
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl14101,804,673 - 101,822,367 (-)Ensembl
mRatBN7.2 Ensembl1497,603,553 - 97,621,262 (-)Ensembl
RefSeq Acc Id: NM_001107242   ⟹   NP_001100712
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814101,804,673 - 101,822,367 (-)NCBI
mRatBN7.21497,603,539 - 97,621,233 (-)NCBI
Rnor_6.014108,394,299 - 108,411,994 (-)NCBI
Rnor_5.014105,229,224 - 105,246,919 (-)NCBI
RGSC_v3.414104,550,699 - 104,571,485 (-)RGD
Celera1496,579,668 - 96,597,394 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039092099   ⟹   XP_038948027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814101,804,675 - 101,821,960 (-)NCBI
mRatBN7.21497,603,536 - 97,620,824 (-)NCBI
RefSeq Acc Id: XM_039092101   ⟹   XP_038948029
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814101,804,675 - 101,817,029 (-)NCBI
mRatBN7.21497,602,829 - 97,617,106 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100712 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948027 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948029 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D4A2Y9 (Get FASTA)   NCBI Sequence Viewer  
  EDL97993 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000097867
  ENSRNOP00000097867.1
RefSeq Acc Id: NP_001100712   ⟸   NM_001107242
- UniProtKB: D4A2Y9 (UniProtKB/TrEMBL),   A0A8I6AVL0 (UniProtKB/TrEMBL),   A0A996RY22 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000068751   ⟸   ENSRNOT00000081405
RefSeq Acc Id: XP_038948029   ⟸   XM_039092101
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948027   ⟸   XM_039092099
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000097867   ⟸   ENSRNOT00000104301
Protein Domains
SH3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A2Y9-F1-model_v2 AlphaFold D4A2Y9 1-403 view protein structure

Transcriptome

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

Promoters
RGD ID:13699523
Promoter ID:EPDNEW_R10047
Type:initiation region
Name:Pex13_1
Description:peroxisomal biogenesis factor 13
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_6.014108,411,983 - 108,412,043EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310682 AgrOrtholog
BioCyc Gene G2FUF-14765 BioCyc
Ensembl Genes ENSRNOG00000054896 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000104301 ENTREZGENE
  ENSRNOT00000104301.1 UniProtKB/Swiss-Prot
Gene3D-CATH SH3 Domains UniProtKB/Swiss-Prot
InterPro Peroxin-13_N UniProtKB/Swiss-Prot
  Pex13 UniProtKB/Swiss-Prot
  SH3-like_dom_sf UniProtKB/Swiss-Prot
  SH3_domain UniProtKB/Swiss-Prot
KEGG Report rno:305581 UniProtKB/Swiss-Prot
NCBI Gene 305581 ENTREZGENE
PANTHER PEROXISOMAL MEMBRANE PROTEIN PEX13 UniProtKB/Swiss-Prot
  PEROXISOMAL MEMBRANE PROTEIN PEX13 UniProtKB/Swiss-Prot
Pfam Peroxin-13_N UniProtKB/Swiss-Prot
  SH3_9 UniProtKB/Swiss-Prot
PhenoGen Pex13 PhenoGen
PRINTS SH3DOMAIN UniProtKB/Swiss-Prot
PROSITE SH3 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000054896 RatGTEx
SMART SH3 UniProtKB/Swiss-Prot
Superfamily-SCOP SH3-domain UniProtKB/Swiss-Prot
UniProt A0A8I6AVL0 ENTREZGENE
  A0A996RY22 ENTREZGENE, UniProtKB/TrEMBL
  D4A2Y9 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A0A8I6AVL0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pex13  peroxisomal biogenesis factor 13   Pex13_predicted  peroxisomal biogenesis factor 13 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pex13_predicted  peroxisomal biogenesis factor 13 (predicted)      Symbol and Name status set to approved 70820 APPROVED