Pex6 (peroxisomal biogenesis factor 6) - Rat Genome Database

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Gene: Pex6 (peroxisomal biogenesis factor 6) Rattus norvegicus
Analyze
Symbol: Pex6
Name: peroxisomal biogenesis factor 6
RGD ID: 621637
Description: Predicted to enable several functions, including ATP binding activity; ATP hydrolysis activity; and ubiquitin-modified protein reader activity. Involved in peroxisome organization. Located in peroxisomal membrane. Used to study peroxisomal disease. Human ortholog(s) of this gene implicated in Heimler syndrome 2; peroxisomal biogenesis disorder; and peroxisome biogenesis disorder 4A. Orthologous to human PEX6 (peroxisomal biogenesis factor 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC100911599; Paf-2; Paf2; peroxin-6; peroxisomal ATPase PEX6; peroxisomal-type ATPase 1; peroxisome assembly factor 2; peroxisome assembly factor 2-like
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
GRCr8921,755,747 - 21,767,939 (-)NCBIGRCr8
mRatBN7.2914,258,145 - 14,270,335 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,258,145 - 14,270,303 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx922,840,891 - 22,853,018 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0927,905,073 - 27,917,291 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0926,204,265 - 26,216,392 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0916,568,743 - 16,580,900 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,566,688 - 16,581,078 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,475,358 - 15,487,515 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,130,561 - 10,139,807 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1910,127,882 - 10,137,129 (-)NCBI
Celera912,006,590 - 12,018,743 (-)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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. 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. 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. Peroxisome assembly factor-2, a putative ATPase cloned by functional complementation on a peroxisome-deficient mammalian cell mutant. Tsukamoto T, etal., Nat Genet 1995 Dec;11(4):395-401.
11. The peroxisome biogenesis disorder group 4 gene, PXAAA1, encodes a cytoplasmic ATPase required for stability of the PTS1 receptor. Yahraus T, etal., EMBO J 1996 Jun 17;15(12):2914-23.
Additional References at PubMed
PMID:8940266   PMID:11439091   PMID:16854980   PMID:21980954   PMID:26593283  


Genomics

Comparative Map Data
Pex6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8921,755,747 - 21,767,939 (-)NCBIGRCr8
mRatBN7.2914,258,145 - 14,270,335 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,258,145 - 14,270,303 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx922,840,891 - 22,853,018 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0927,905,073 - 27,917,291 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0926,204,265 - 26,216,392 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0916,568,743 - 16,580,900 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,566,688 - 16,581,078 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,475,358 - 15,487,515 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,130,561 - 10,139,807 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1910,127,882 - 10,137,129 (-)NCBI
Celera912,006,590 - 12,018,743 (-)NCBICelera
Cytogenetic Map9q12NCBI
PEX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38642,963,865 - 42,979,181 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl642,963,865 - 42,979,181 (-)EnsemblGRCh38hg38GRCh38
GRCh37642,931,603 - 42,946,919 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36643,039,724 - 43,054,866 (-)NCBINCBI36Build 36hg18NCBI36
Build 34643,039,724 - 43,054,866NCBI
Celera644,483,862 - 44,499,224 (-)NCBICelera
Cytogenetic Map6p21.1NCBI
HuRef642,648,904 - 42,664,268 (-)NCBIHuRef
CHM1_1642,934,088 - 42,949,459 (-)NCBICHM1_1
T2T-CHM13v2.0642,793,003 - 42,808,304 (-)NCBIT2T-CHM13v2.0
Pex6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391747,022,402 - 47,036,469 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1747,022,389 - 47,036,467 (+)EnsemblGRCm39 Ensembl
GRCm381746,711,476 - 46,725,543 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,711,463 - 46,725,541 (+)EnsemblGRCm38mm10GRCm38
MGSCv371746,848,412 - 46,862,490 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361746,174,654 - 46,188,732 (+)NCBIMGSCv36mm8
Celera1750,147,145 - 50,161,227 (+)NCBICelera
Cytogenetic Map17CNCBI
cM Map1722.9NCBI
Pex6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554378,947,002 - 8,960,371 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554378,945,842 - 8,964,870 (-)NCBIChiLan1.0ChiLan1.0
PEX6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2557,462,366 - 57,479,149 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1653,332,570 - 53,354,666 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0642,554,509 - 42,570,701 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1643,849,802 - 43,865,618 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl643,850,129 - 43,865,355 (-)Ensemblpanpan1.1panPan2
PEX6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11211,503,184 - 11,514,977 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1211,503,240 - 11,514,929 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1211,530,201 - 11,541,972 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01211,984,383 - 11,996,155 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1211,984,400 - 11,996,144 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11211,512,805 - 11,524,577 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01211,597,069 - 11,608,845 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01211,691,136 - 11,702,909 (-)NCBIUU_Cfam_GSD_1.0
Pex6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494646,996,551 - 47,011,135 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647616,949,028 - 16,964,040 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647616,948,137 - 16,963,601 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PEX6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl738,039,862 - 38,052,369 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1738,039,852 - 38,052,384 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2743,488,218 - 43,500,754 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PEX6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11729,180,427 - 29,198,747 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1729,180,460 - 29,200,398 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604443,010,475 - 43,039,028 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pex6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475416,510,795 - 16,527,859 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475416,510,980 - 16,534,695 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pex6
98 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:50
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000022582
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat


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 4 42 27 10 27 68 21 31 4
Low 3 39 15 14 9 14 8 11 6 14 10 7 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000022582   ⟹   ENSRNOP00000022582
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,258,145 - 14,270,303 (-)Ensembl
Rnor_6.0 Ensembl916,566,688 - 16,581,078 (-)Ensembl
RefSeq Acc Id: NM_057125   ⟹   NP_476466
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8921,755,751 - 21,767,908 (-)NCBI
mRatBN7.2914,258,145 - 14,270,303 (-)NCBI
Rnor_6.0916,568,743 - 16,580,900 (-)NCBI
Rnor_5.0915,475,358 - 15,487,515 (-)NCBI
RGSC_v3.4910,130,561 - 10,139,807 (-)RGD
Celera912,006,590 - 12,018,743 (-)RGD
Sequence:
RefSeq Acc Id: XM_063266580   ⟹   XP_063122650
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8921,755,747 - 21,767,939 (-)NCBI
RefSeq Acc Id: XR_005488842
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8921,756,543 - 21,767,939 (-)NCBI
mRatBN7.2914,258,937 - 14,270,335 (-)NCBI
Protein Sequences
Protein RefSeqs NP_476466 (Get FASTA)   NCBI Sequence Viewer  
  XP_063122650 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA09824 (Get FASTA)   NCBI Sequence Viewer  
  BAA24931 (Get FASTA)   NCBI Sequence Viewer  
  EDM18853 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022582
  ENSRNOP00000022582.5
GenBank Protein P54777 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_476466   ⟸   NM_057125
- UniProtKB: O55097 (UniProtKB/Swiss-Prot),   P54777 (UniProtKB/Swiss-Prot),   A6JIM9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022582   ⟸   ENSRNOT00000022582
RefSeq Acc Id: XP_063122650   ⟸   XM_063266580
- Peptide Label: isoform X1
Protein Domains
AAA+ ATPase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P54777-F1-model_v2 AlphaFold P54777 1-978 view protein structure

Transcriptome

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

Promoters
RGD ID:13696507
Promoter ID:EPDNEW_R7031
Type:initiation region
Name:Pex6_1
Description:peroxisomal biogenesis factor 6
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_6.0916,580,893 - 16,580,953EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621637 AgrOrtholog
BioCyc Gene G2FUF-28241 BioCyc
Ensembl Genes ENSRNOG00000016655 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022582 ENTREZGENE
  ENSRNOT00000022582.7 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.8.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_AAA_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_AAA_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RecA-like_PEX6_r2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:117265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 117265 ENTREZGENE
PANTHER AAA-FAMILY ATPASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PEROXISOME ASSEMBLY FACTOR 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pex6 PhenoGen
PROSITE AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016655 RatGTEx
SMART AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP P-loop containing nucleoside triphosphate hydrolases UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6JIM9 ENTREZGENE, UniProtKB/TrEMBL
  O55097 ENTREZGENE
  P54777 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O55097 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Pex6  peroxisomal biogenesis factor 6  LOC100911599  peroxisome assembly factor 2-like  Data merged from RGD:6492067 737654 PROVISIONAL
2012-07-05 LOC100911599  peroxisome assembly factor 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-02-26 Pex6  peroxisomal biogenesis factor 6      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Pex6  peroxisomal biogenesis factor 6      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease functionally complements fibroblasts from patients with a peroxisomal deficiency (complementation group C) 729462