Pex1 (peroxisomal biogenesis factor 1) - Rat Genome Database
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Gene: Pex1 (peroxisomal biogenesis factor 1) Rattus norvegicus
Analyze
Symbol: Pex1
Name: peroxisomal biogenesis factor 1
RGD ID: 1559939
Description: Predicted to have ATP binding activity; ATPase activity; and protein C-terminus binding activity. Predicted to be involved in microtubule-based peroxisome localization and protein import into peroxisome matrix. Localizes to peroxisomal membrane. Human ortholog(s) of this gene implicated in Heimler syndrome 1; infantile Refsum disease; and peroxisome biogenesis disorder 1A. Orthologous to human PEX1 (peroxisomal biogenesis factor 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; methapyrilene; pirinixic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC500006; peroxisome biogenesis factor 1; RGD1559939; similar to peroxisome biogenesis factor 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2430,519,950 - 30,558,953 (-)NCBI
Rnor_6.0 Ensembl427,659,381 - 27,698,037 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0427,659,376 - 27,698,037 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0427,562,602 - 27,601,351 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4427,235,147 - 27,275,076 (-)NCBIRGSC3.4rn4RGSC3.4
Celera425,944,627 - 25,983,247 (-)NCBICelera
Cytogenetic Map4q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO)
cytosol  (IBA,ISO)
peroxisomal membrane  (IBA,IDA,ISO)
peroxisome  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:9398847   PMID:9588209   PMID:11439091   PMID:16449325   PMID:16854980   PMID:18570454   PMID:21525035   PMID:21980954   PMID:27826738  


Genomics

Comparative Map Data
Pex1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2430,519,950 - 30,558,953 (-)NCBI
Rnor_6.0 Ensembl427,659,381 - 27,698,037 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0427,659,376 - 27,698,037 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0427,562,602 - 27,601,351 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4427,235,147 - 27,275,076 (-)NCBIRGSC3.4rn4RGSC3.4
Celera425,944,627 - 25,983,247 (-)NCBICelera
Cytogenetic Map4q13NCBI
PEX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl792,487,020 - 92,528,520 (-)EnsemblGRCh38hg38GRCh38
GRCh38792,487,023 - 92,528,520 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37792,116,337 - 92,157,845 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37792,116,339 - 92,157,834 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36791,954,273 - 91,995,781 (-)NCBINCBI36hg18NCBI36
Build 34791,760,990 - 91,802,460NCBI
Celera786,820,874 - 86,862,377 (-)NCBI
Cytogenetic Map7q21.2NCBI
HuRef786,725,109 - 86,766,599 (-)NCBIHuRef
CHM1_1792,046,373 - 92,087,866 (-)NCBICHM1_1
CRA_TCAGchr7v2791,445,547 - 91,487,069 (-)NCBI
Pex1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3953,646,066 - 3,687,230 (+)NCBIGRCm39mm39
GRCm3853,596,066 - 3,637,230 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl53,596,066 - 3,637,232 (+)EnsemblGRCm38mm10GRCm38
MGSCv3753,596,066 - 3,637,101 (+)NCBIGRCm37mm9NCBIm37
MGSCv3653,602,072 - 3,643,107 (+)NCBImm8
Celera53,532,126 - 3,572,649 (+)NCBICelera
Cytogenetic Map5A1NCBI
Pex1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554329,418,678 - 9,461,419 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554329,418,480 - 9,461,507 (-)NCBIChiLan1.0ChiLan1.0
PEX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1798,081,018 - 98,122,335 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl798,081,021 - 98,122,335 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0784,484,965 - 84,526,309 (-)NCBIMhudiblu_PPA_v0panPan3
PEX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1418,073,758 - 18,143,152 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11418,073,759 - 18,144,489 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pex1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049368031,291,867 - 1,340,123 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PEX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl972,385,263 - 72,444,616 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1972,385,755 - 72,444,718 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2979,114,205 - 79,173,283 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PEX1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12156,493,424 - 56,535,565 (+)NCBI
ChlSab1.1 Ensembl2156,493,435 - 56,535,154 (+)Ensembl
Pex1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624809668,248 - 713,036 (+)NCBI

Position Markers
AI555451  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0427,661,322 - 27,661,767NCBIRnor6.0
Rnor_5.0427,564,548 - 27,564,993UniSTSRnor5.0
RGSC_v3.4427,237,088 - 27,237,533UniSTSRGSC3.4
Celera425,946,568 - 25,947,013UniSTS
RH 3.4 Map4168.9UniSTS
Cytogenetic Map4q13UniSTS
RH134880  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0427,659,477 - 27,659,677NCBIRnor6.0
Rnor_5.0427,562,703 - 27,562,903UniSTSRnor5.0
RGSC_v3.4427,235,243 - 27,235,443UniSTSRGSC3.4
Celera425,944,723 - 25,944,923UniSTS
RH 3.4 Map4169.29UniSTS
Cytogenetic Map4q13UniSTS
RH129188  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0427,659,101 - 27,659,296NCBIRnor6.0
Rnor_5.0427,562,327 - 27,562,522UniSTSRnor5.0
RGSC_v3.4427,234,867 - 27,235,062UniSTSRGSC3.4
Celera425,944,347 - 25,944,542UniSTS
RH 3.4 Map4169.2UniSTS
Cytogenetic Map4q13UniSTS
RH131152  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0427,686,610 - 27,686,793NCBIRnor6.0
Rnor_5.0427,589,843 - 27,590,026UniSTSRnor5.0
RGSC_v3.4427,263,545 - 27,263,728UniSTSRGSC3.4
Celera425,971,798 - 25,971,981UniSTS
Cytogenetic Map4q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4128352196Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4128352196Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4128352196Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4128352196Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4129778604Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4129778604Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4131554484Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)4142118977Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4304323179575658Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)43043231145254791Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4304401755791834Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4304401764915903Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4304780755324857Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4646769343414792Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4657293937703537Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)4734240492484039Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4805218953052189Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)4805218953052189Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)4805218953052189Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4805218953052189Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4805218953052189Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)4805218953052189Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41263897457638974Rat
7387227Uae40Urinary albumin excretion QTL 402.90.0052urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)41614994161149941Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)41822218737685319Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)41822218743414792Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)41822218761039065Rat
8552803Bw144Body weight QTL 14416body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)41961886631825560Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42399172176238799Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42399172176238799Rat
1578655Bmd11Bone mineral density QTL 1111femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)42463187469631874Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42665474981874227Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:40
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000038136
Prediction methods:Miranda, Rnahybrid
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.


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 2 20 45 29 14 29 74 35 39 11
Low 1 23 12 12 5 12 8 11 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000038136   ⟹   ENSRNOP00000032605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl427,659,381 - 27,698,037 (-)Ensembl
RefSeq Acc Id: NM_001109220   ⟹   NP_001102690
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,519,955 - 30,558,898 (-)NCBI
Rnor_6.0427,659,381 - 27,698,037 (-)NCBI
Rnor_5.0427,562,602 - 27,601,351 (-)NCBI
RGSC_v3.4427,235,147 - 27,275,076 (-)RGD
Celera425,944,627 - 25,983,247 (-)RGD
Sequence:
RefSeq Acc Id: XM_006236054   ⟹   XP_006236116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,519,950 - 30,558,906 (-)NCBI
Rnor_6.0427,659,376 - 27,697,996 (-)NCBI
Rnor_5.0427,562,602 - 27,601,351 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039108094   ⟹   XP_038964022
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,519,950 - 30,544,452 (-)NCBI
RefSeq Acc Id: XM_039108095   ⟹   XP_038964023
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,532,942 - 30,558,953 (-)NCBI
RefSeq Acc Id: XR_005503290
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,525,920 - 30,558,953 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001102690 (Get FASTA)   NCBI Sequence Viewer  
  XP_006236116 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964022 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964023 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL84367 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102690   ⟸   NM_001109220
- UniProtKB: D3ZZB2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236116   ⟸   XM_006236054
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000032605   ⟸   ENSRNOT00000038136
RefSeq Acc Id: XP_038964022   ⟸   XM_039108094
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038964023   ⟸   XM_039108095
- Peptide Label: isoform X3
Protein Domains
AAA

Transcriptome

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

Promoters
RGD ID:13692847
Promoter ID:EPDNEW_R3372
Type:initiation region
Name:Pex1_1
Description:peroxisomal biogenesis factor 1
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_6.0427,698,038 - 27,698,098EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559939 AgrOrtholog
Ensembl Genes ENSRNOG00000025991 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000032605 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038136 ENTREZGENE, UniProtKB/TrEMBL
InterPro AAA_lid_3 UniProtKB/TrEMBL
  Asp_de-COase-like_fold UniProtKB/TrEMBL
  ATPase_AAA+_core UniProtKB/TrEMBL
  ATPase_AAA_core UniProtKB/TrEMBL
  ATPase_AAA_CS UniProtKB/TrEMBL
  CDC48_domain_2-like UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  Peroxisome_synth_fac_1_a/b UniProtKB/TrEMBL
  PEX-1N UniProtKB/TrEMBL
  Pex1 UniProtKB/TrEMBL
KEGG Report rno:500006 UniProtKB/TrEMBL
NCBI Gene 500006 ENTREZGENE
PANTHER PTHR23077:SF12 UniProtKB/TrEMBL
Pfam AAA UniProtKB/TrEMBL
  AAA_lid_3 UniProtKB/TrEMBL
  PEX-1N UniProtKB/TrEMBL
  PEX-2N UniProtKB/TrEMBL
PhenoGen Pex1 PhenoGen
PROSITE AAA UniProtKB/TrEMBL
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP Asp_decarb_fold UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
  SSF54585 UniProtKB/TrEMBL
UniProt D3ZZB2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Pex1  peroxisomal biogenesis factor 1  Pex1  peroxisome biogenesis factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-24 Pex1  peroxisome biogenesis factor 1  Pex1  peroxisomal biogenesis factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-03 Pex1  peroxisomal biogenesis factor 1  Pex1  peroxisome biogenesis factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Pex1  peroxisome biogenesis factor 1  RGD1559939_predicted  similar to peroxisome biogenesis factor 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1559939_predicted  similar to peroxisome biogenesis factor 1 (predicted)  LOC500006  similar to peroxisome biogenesis factor 1  Symbol and Name status set to approved 1299863 APPROVED