Pex39 (peroxisomal biogenesis factor 39) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Pex39 (peroxisomal biogenesis factor 39) Rattus norvegicus
Analyze
Symbol: Pex39 (Ensembl: C9h6orf226)
Name: peroxisomal biogenesis factor 39 (Ensembl:smilar to human chromosome 6 open reading frame 226)
RGD ID: 1596723
Description: Orthologous to human PEX39 (peroxisomal biogenesis factor 39); INTERACTS WITH 17beta-estradiol (ortholog); 2-hydroxypropanoic acid (ortholog); 4,4'-sulfonyldiphenol (ortholog).
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: C9h6orf226; hypothetical protein LOC681367; LOC681367; smilar to human chromosome 6 open reading frame 226; uncharacterized protein C6orf226 homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8921,705,608 - 21,706,742 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl921,704,735 - 21,706,395 (-)EnsemblGRCr8
mRatBN7.2914,207,988 - 14,209,134 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,208,417 - 14,208,761 (-)EnsemblmRatBN7.2
Rnor_6.0916,518,374 - 16,519,474 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,518,800 - 16,519,144 (-)Ensemblrn6Rnor6.0
Rnor_5.0915,425,668 - 15,426,777 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.499,404,124 - 9,405,926 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera911,956,092 - 11,957,192 (-)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Pex39
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8921,705,608 - 21,706,742 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl921,704,735 - 21,706,395 (-)EnsemblGRCr8
mRatBN7.2914,207,988 - 14,209,134 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,208,417 - 14,208,761 (-)EnsemblmRatBN7.2
Rnor_6.0916,518,374 - 16,519,474 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,518,800 - 16,519,144 (-)Ensemblrn6Rnor6.0
Rnor_5.0915,425,668 - 15,426,777 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.499,404,124 - 9,405,926 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera911,956,092 - 11,957,192 (-)NCBICelera
Cytogenetic Map9q12NCBI
PEX39
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38642,890,265 - 42,890,821 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl642,890,265 - 42,890,821 (-)Ensemblhg38GRCh38
GRCh37642,858,003 - 42,858,559 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36642,965,981 - 42,966,532 (-)NCBIBuild 36Build 36hg18NCBI36
Celera644,410,270 - 44,410,821 (-)NCBICelera
Cytogenetic Map6p21.1NCBI
HuRef642,575,704 - 42,576,255 (-)NCBIHuRef
CHM1_1642,860,475 - 42,861,026 (-)NCBICHM1_1
T2T-CHM13v2.0642,718,982 - 42,719,538 (-)NCBIT2T-CHM13v2.0
Pex39
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391747,083,561 - 47,084,333 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1747,083,561 - 47,084,322 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381746,772,635 - 46,773,407 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,772,635 - 46,773,396 (+)Ensemblmm10GRCm38
MGSCv371746,909,584 - 46,910,356 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361746,235,826 - 46,236,586 (+)NCBIMGSCv36mm8
Celera1750,208,188 - 50,208,960 (+)NCBICelera
Cytogenetic Map17CNCBI
cM Map1722.9NCBI
Pex39
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554378,912,183 - 8,912,733 (-)NCBIChiLan1.0ChiLan1.0
PEX39
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2557,387,575 - 57,388,638 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1653,257,587 - 53,258,350 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0642,479,705 - 42,480,780 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1643,773,945 - 43,774,754 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl643,774,163 - 43,774,474 (-)EnsemblpanPan2panpan1.1
C12H6orf226
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11211,453,482 - 11,457,649 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1211,480,449 - 11,481,197 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01211,934,822 - 11,935,566 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.11211,462,710 - 11,463,454 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01211,547,011 - 11,547,746 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01211,641,037 - 11,641,781 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pex39
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494646,940,664 - 46,941,770 (-)NCBIHiC_Itri_2
C7H6orf226
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1737,986,742 - 37,988,256 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2743,435,109 - 43,436,623 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PEX39
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366604442,926,703 - 42,927,075 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pex39
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1483,092,979 - 83,093,929 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pex39
6 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:29
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000072581
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
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9121707400Rat
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

Markers in Region
D9Rat79  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8921,707,181 - 21,707,400 (+)Marker Load Pipeline
mRatBN7.2914,209,564 - 14,209,783 (+)MAPPERmRatBN7.2
Rnor_6.0916,519,948 - 16,520,166NCBIRnor6.0
Rnor_5.0915,427,242 - 15,427,460UniSTSRnor5.0
RGSC_v3.499,405,697 - 9,405,916RGDRGSC3.4
RGSC_v3.499,405,698 - 9,405,916UniSTSRGSC3.4
Celera911,957,666 - 11,957,884UniSTS
RGSC_v3.199,403,020 - 9,403,238RGD
RH 3.4 Map956.3UniSTS
RH 3.4 Map956.3RGD
RH 2.0 Map955.7RGD
FHH x ACI Map96.3799RGD
Cytogenetic Map9q12UniSTS
BE111872  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2913,765,876 - 13,766,031 (+)MAPPERmRatBN7.2
Rnor_6.0915,786,798 - 15,786,952NCBIRnor6.0
Rnor_5.0914,706,701 - 14,706,855UniSTSRnor5.0
RGSC_v3.499,440,764 - 9,440,918UniSTSRGSC3.4
Celera911,513,245 - 11,513,399UniSTS
RH 3.4 Map945.5UniSTS
Cytogenetic Map9q12UniSTS


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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000072581   ⟹   ENSRNOP00000067620
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,208,417 - 14,208,761 (-)Ensembl
Rnor_6.0 Ensembl916,518,800 - 16,519,144 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000152707   ⟹   ENSRNOP00000103785
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl921,704,735 - 21,706,395 (-)Ensembl
RefSeq Acc Id: XM_006244592   ⟹   XP_006244654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8921,705,608 - 21,706,742 (-)NCBI
mRatBN7.2914,207,988 - 14,209,134 (-)NCBI
Rnor_6.0916,518,374 - 16,519,474 (-)NCBI
Rnor_5.0915,425,668 - 15,426,777 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001420263 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244654 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM18862 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000103785
  ENSRNOP00000103785.1
RefSeq Acc Id: XP_006244654   ⟸   XM_006244592
- Sequence:
Ensembl Acc Id: ENSRNOP00000067620   ⟸   ENSRNOT00000072581
Ensembl Acc Id: ENSRNOP00000103785   ⟸   ENSRNOT00000152707
Protein Domains
Peroxisomal membrane protein PEX14-like KPWE

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RDC2-F1-model_v2 AlphaFold M0RDC2 1-114 view protein structure

Transcriptome

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

Promoters
RGD ID:13696508
Promoter ID:EPDNEW_R7028
Type:multiple initiation site
Name:LOC681367_1
Description:hypothetical protein LOC681367
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_6.0916,519,142 - 16,519,202EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596723 AgrOrtholog
BioCyc Gene G2FUF-28245 BioCyc
Ensembl Genes ENSRNOG00000046871 Ensembl
  ENSRNOG00000079593 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000152707 ENTREZGENE
  ENSRNOT00000152707.1 UniProtKB/TrEMBL
InterPro C6orf226-like UniProtKB/TrEMBL
  KPWE_PEX14_dom UniProtKB/TrEMBL
NCBI Gene 681367 ENTREZGENE
PANTHER HYPOTHETICAL PROTEIN LOC681367 UniProtKB/TrEMBL
  PTHR40657 UniProtKB/TrEMBL
Pfam DUF5572 UniProtKB/TrEMBL
PhenoGen Pex39 PhenoGen
RatGTEx ENSRNOG00000046871 RatGTEx
  ENSRNOG00000079593 RatGTEx
UniProt A0ABK0LJR9_RAT UniProtKB/TrEMBL
  A6JIM0 ENTREZGENE, UniProtKB/TrEMBL
  M0RDC2 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-11-01 Pex39  peroxisomal biogenesis factor 39  C9h6orf226  smilar to human chromosome 6 open reading frame 226  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2023-09-19 C9h6orf226  smilar to human chromosome 6 open reading frame 226  LOC681367  hypothetical protein LOC681367  Symbol and Name Changed 1299863 APPROVED
2008-01-09 LOC681367  hypothetical protein LOC681367  LOC683351  hypothetical protein LOC683351  Data merged from RGD:1588018 1643240 APPROVED
2006-11-20 LOC681367  hypothetical protein LOC681367      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC683351  hypothetical protein LOC683351      Symbol and Name status set to provisional 70820 PROVISIONAL