Pex13 (peroxisomal biogenesis factor 13) - Rat Genome Database

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Gene: Pex13 (peroxisomal biogenesis factor 13) Rattus norvegicus
Analyze
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 peroxisomal biogenesis disorder 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814101,804,673 - 101,822,367 (-)NCBIGRCr8
mRatBN7.21497,602,829 - 97,621,233 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1497,603,539 - 97,621,262 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14101,936,310 - 101,954,154 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014103,180,657 - 103,198,504 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01499,652,232 - 99,670,079 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.014108,394,299 - 108,411,994 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14108,394,303 - 108,412,823 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014105,229,224 - 105,246,919 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414104,550,699 - 104,571,485 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114104,573,004 - 104,590,753 (-)NCBI
Celera1496,579,668 - 96,597,394 (-)NCBICelera
Cytogenetic Map14q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
peroxisomal importomer complex  (IBA,IEA)
peroxisomal membrane  (IBA,IDA,IEA,ISO)
peroxisome  (IDA,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 (-)NCBIGRCr8
mRatBN7.21497,602,829 - 97,621,233 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1497,603,539 - 97,621,262 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14101,936,310 - 101,954,154 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014103,180,657 - 103,198,504 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01499,652,232 - 99,670,079 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.014108,394,299 - 108,411,994 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14108,394,303 - 108,412,823 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014105,229,224 - 105,246,919 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414104,550,699 - 104,571,485 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114104,573,004 - 104,590,753 (-)NCBI
Celera1496,579,668 - 96,597,394 (-)NCBICelera
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 (+)EnsemblGRCh38hg38GRCh38
GRCh37261,244,855 - 61,279,125 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36261,098,374 - 61,129,896 (+)NCBINCBI36Build 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 Ensembl
GRCm381123,646,843 - 23,665,883 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1123,646,479 - 23,665,959 (-)EnsemblGRCm38mm10GRCm38
MGSCv371123,546,479 - 23,565,935 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1060,993,422 - 61,021,277 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01062,112,178 - 62,140,036 (+)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624833914,621 - 940,661 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pex13
87 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat

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
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 30 57 41 19 41 8 10 74 35 41 11 8
Low 13 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000081405   ⟹   ENSRNOP00000068751
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1497,603,539 - 97,612,032 (-)Ensembl
Rnor_6.0 Ensembl14108,394,303 - 108,412,823 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104301   ⟹   ENSRNOP00000097867
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
Reference Protein Sequences
RefSeq Acc Id: NP_001100712   ⟸   NM_001107242
- UniProtKB: D4A2Y9 (UniProtKB/TrEMBL),   A0A8I6AVL0 (UniProtKB/TrEMBL),   A0A996RY22 (UniProtKB/TrEMBL)
- Sequence:
RefSeq 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
RefSeq 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, UniProtKB/TrEMBL
  ENSRNOG00055004104 UniProtKB/Swiss-Prot
  ENSRNOG00060007388 UniProtKB/Swiss-Prot
  ENSRNOG00065006008 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000081405.2 UniProtKB/TrEMBL
  ENSRNOT00000104301 ENTREZGENE
  ENSRNOT00000104301.1 UniProtKB/Swiss-Prot
  ENSRNOT00055006556 UniProtKB/Swiss-Prot
  ENSRNOT00060012147 UniProtKB/Swiss-Prot
  ENSRNOT00065009077 UniProtKB/Swiss-Prot
Gene3D-CATH SH3 Domains UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Peroxin-13_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pex13 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
  PEROXISOMAL MEMBRANE PROTEIN PEX13 UniProtKB/TrEMBL
  PEROXISOMAL MEMBRANE PROTEIN PEX13 UniProtKB/TrEMBL
Pfam Peroxin-13_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pex13 PhenoGen
PRINTS SH3DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000054896 RatGTEx
  ENSRNOG00055004104 RatGTEx
  ENSRNOG00060007388 RatGTEx
  ENSRNOG00065006008 RatGTEx
SMART SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SH3-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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