Pex6 (peroxisomal biogenesis factor 6) - Rat Genome Database

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Gene: Pex6 (peroxisomal biogenesis factor 6) Rattus norvegicus
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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; Peroxisome biogenesis disorder 4B; 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8921,755,747 - 21,767,939 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl921,755,751 - 21,767,908 (-)EnsemblGRCr8
mRatBN7.2914,258,145 - 14,270,335 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,258,145 - 14,270,303 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx922,840,891 - 22,853,018 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0927,905,073 - 27,917,291 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0926,204,265 - 26,216,392 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0916,568,743 - 16,580,900 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,566,688 - 16,581,078 (-)Ensemblrn6Rnor6.0
Rnor_5.0915,475,358 - 15,487,515 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4910,130,561 - 10,139,807 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera912,006,590 - 12,018,743 (-)NCBICelera
RGSC_v3.1910,127,882 - 10,137,129 (-)NCBI
Cytogenetic Map9q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)
cytosol  (IBA,IEA,ISO)
peroxisomal membrane  (IBA,IDA,IEA,ISO)
peroxisome  (IEA,ISO)
photoreceptor cell cilium  (IEA,ISO,ISS)
photoreceptor outer segment  (IEA)

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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl921,755,751 - 21,767,908 (-)EnsemblGRCr8
mRatBN7.2914,258,145 - 14,270,335 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,258,145 - 14,270,303 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx922,840,891 - 22,853,018 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0927,905,073 - 27,917,291 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0926,204,265 - 26,216,392 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0916,568,743 - 16,580,900 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,566,688 - 16,581,078 (-)Ensemblrn6Rnor6.0
Rnor_5.0915,475,358 - 15,487,515 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4910,130,561 - 10,139,807 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera912,006,590 - 12,018,743 (-)NCBICelera
RGSC_v3.1910,127,882 - 10,137,129 (-)NCBI
Cytogenetic Map9q12NCBI
PEX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38642,963,865 - 42,979,181 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl642,959,717 - 42,979,243 (-)Ensemblhg38GRCh38
GRCh37642,931,603 - 42,946,919 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36643,039,724 - 43,054,866 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381746,711,476 - 46,725,543 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,711,463 - 46,725,541 (+)Ensemblmm10GRCm38
MGSCv371746,848,412 - 46,862,490 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1211,530,201 - 11,541,972 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01211,984,383 - 11,996,155 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 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 (-)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475416,510,980 - 16,534,695 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pex6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1483,141,804 - 83,153,684 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pex6
169 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9534647950346479Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9875049253750492Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)9131250552Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9621499551214995Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9875049253750492Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9534647950416711Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9671488829567695Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)92103143049025574Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9621499551214995Rat


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 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000022582   ⟹   ENSRNOP00000022582
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl921,755,751 - 21,767,908 (-)Ensembl
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:
Ensembl 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
  3.40.50.300 UniProtKB/Swiss-Prot
InterPro AAA+_ATPase UniProtKB/Swiss-Prot
  AAA_ATPase_domain UniProtKB/Swiss-Prot
  ATPase_AAA_core UniProtKB/Swiss-Prot
  ATPase_AAA_CS UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
  RecA-like_PEX6_r2 UniProtKB/Swiss-Prot
KEGG Report rno:117265 UniProtKB/Swiss-Prot
NCBI Gene 117265 ENTREZGENE
PANTHER AAA-FAMILY ATPASE UniProtKB/Swiss-Prot
  PEROXISOME ASSEMBLY FACTOR 2 UniProtKB/Swiss-Prot
Pfam AAA UniProtKB/Swiss-Prot
  DPBB_PEX6 UniProtKB/Swiss-Prot
  PEX6_vert_N UniProtKB/Swiss-Prot
PhenoGen Pex6 PhenoGen
PROSITE AAA UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000016655 RatGTEx
SMART AAA UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 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