Prox1 (prospero homeobox 1) - Rat Genome Database
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Gene: Prox1 (prospero homeobox 1) Rattus norvegicus
Analyze
Symbol: Prox1
Name: prospero homeobox 1
RGD ID: 1306890
Description: Predicted to have several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; nuclear receptor binding activity; and protein domain specific binding activity. Involved in brain development; liver development; and response to nutrient levels. Localizes to nucleus. Biomarker of status epilepticus. Orthologous to human PROX1 (prospero homeobox 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 2-acetamidofluorene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: prospero homeobox protein 1; prospero-related homeobox 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
mRatBN7.213101,669,184 - 101,719,804 (-)NCBI
Rnor_6.0 Ensembl13108,382,399 - 108,443,294 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013108,382,536 - 108,444,107 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013113,004,568 - 113,064,606 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413106,421,541 - 106,471,350 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113106,611,772 - 106,660,015 (-)NCBI
Celera13101,149,597 - 101,200,064 (-)NCBICelera
Cytogenetic Map13q27NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Biological Process
acinar cell differentiation  (ISO)
aorta smooth muscle tissue morphogenesis  (ISO)
atrial cardiac muscle tissue morphogenesis  (ISO)
brain development  (IEP,ISO)
branching involved in pancreas morphogenesis  (ISO)
cell fate determination  (ISO)
cerebellar granule cell differentiation  (ISO)
circadian rhythm  (ISO)
dentate gyrus development  (ISO)
embryonic retina morphogenesis in camera-type eye  (ISO)
endocardium formation  (ISO)
endothelial cell differentiation  (ISO)
hepatocyte cell migration  (ISO)
hepatocyte differentiation  (ISO)
hepatocyte proliferation  (ISO)
inner ear development  (ISO)
kidney development  (ISO)
lens development in camera-type eye  (ISO)
lens fiber cell morphogenesis  (ISO)
lens morphogenesis in camera-type eye  (ISO)
liver development  (IEP,ISO)
lung development  (ISO)
lymph vessel development  (ISO)
lymphangiogenesis  (ISO)
lymphatic endothelial cell differentiation  (ISO)
lymphatic endothelial cell fate commitment  (IEA,ISO)
negative regulation of bile acid biosynthetic process  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of DNA-binding transcription factor activity  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
negative regulation of viral genome replication  (ISO)
neuronal stem cell population maintenance  (ISO)
optic placode formation involved in camera-type eye formation  (ISO)
pancreas development  (ISO)
positive regulation of cell cycle  (ISO)
positive regulation of cell cycle checkpoint  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cyclin-dependent protein serine/threonine kinase activity  (ISO)
positive regulation of endothelial cell migration  (ISO)
positive regulation of endothelial cell proliferation  (ISO)
positive regulation of forebrain neuron differentiation  (ISO)
positive regulation of heart growth  (ISO)
positive regulation of neural precursor cell proliferation  (ISO)
positive regulation of sarcomere organization  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
regulation of circadian rhythm  (ISO)
regulation of gene expression  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
response to nutrient levels  (IEP)
skeletal muscle thin filament assembly  (ISO)
venous blood vessel morphogenesis  (ISO)
ventricular cardiac muscle tissue morphogenesis  (ISO)
ventricular cardiac myofibril assembly  (ISO)
ventricular septum morphogenesis  (ISO)

Cellular Component
cytoplasm  (ISO)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA,ISO)

References

Additional References at PubMed
PMID:8812486   PMID:10080188   PMID:10888866   PMID:11789987   PMID:11850194   PMID:11927535   PMID:12198161   PMID:12412020   PMID:12692551   PMID:15143342   PMID:15205472   PMID:15232737  
PMID:16170315   PMID:16291864   PMID:16488887   PMID:17062673   PMID:17828556   PMID:18815287   PMID:19023449   PMID:19056883   PMID:19091769   PMID:19210544   PMID:19264593   PMID:19901262  
PMID:20186345   PMID:20808958   PMID:21040746   PMID:21300049   PMID:22178591   PMID:23723244   PMID:27731315  


Genomics

Comparative Map Data
Prox1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.213101,669,184 - 101,719,804 (-)NCBI
Rnor_6.0 Ensembl13108,382,399 - 108,443,294 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013108,382,536 - 108,444,107 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013113,004,568 - 113,064,606 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413106,421,541 - 106,471,350 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113106,611,772 - 106,660,015 (-)NCBI
Celera13101,149,597 - 101,200,064 (-)NCBICelera
Cytogenetic Map13q27NCBI
PROX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1213,983,181 - 214,041,510 (+)EnsemblGRCh38hg38GRCh38
GRCh381213,983,239 - 214,041,510 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371214,161,316 - 214,214,853 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361212,228,483 - 212,276,389 (+)NCBINCBI36hg18NCBI36
Build 341210,550,254 - 210,598,155NCBI
Celera1187,384,890 - 187,432,754 (+)NCBI
Cytogenetic Map1q32.3NCBI
HuRef1184,835,849 - 184,890,058 (+)NCBIHuRef
CHM1_11215,433,762 - 215,487,303 (+)NCBICHM1_1
Prox1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391189,850,232 - 189,903,024 (-)NCBIGRCm39mm39
GRCm39 Ensembl1189,850,232 - 189,902,911 (-)Ensembl
GRCm381190,118,035 - 190,170,827 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1190,118,035 - 190,170,714 (-)EnsemblGRCm38mm10GRCm38
MGSCv371191,945,654 - 191,994,559 (-)NCBIGRCm37mm9NCBIm37
MGSCv361191,822,563 - 191,871,468 (-)NCBImm8
Celera1197,032,975 - 197,082,606 (-)NCBICelera
Cytogenetic Map1H6NCBI
cM Map195.85NCBI
Prox1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554063,719,972 - 3,770,555 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554063,715,140 - 3,770,019 (-)NCBIChiLan1.0ChiLan1.0
PROX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11194,412,980 - 194,466,170 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1194,412,980 - 194,460,763 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01189,556,124 - 189,609,297 (+)NCBIMhudiblu_PPA_v0panPan3
PROX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl711,996,703 - 12,044,036 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1711,996,282 - 12,047,693 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Prox1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366284,185,712 - 4,240,680 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PROX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9129,532,164 - 129,580,979 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19129,527,704 - 129,583,693 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29142,424,393 - 142,480,770 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PROX1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12515,533,546 - 15,592,834 (-)NCBI
ChlSab1.1 Ensembl2515,538,964 - 15,587,059 (-)Ensembl
Prox1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477119,188,543 - 19,238,621 (+)NCBI

Position Markers
D13Rat162  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013108,394,664 - 108,394,906NCBIRnor6.0
Rnor_5.013113,016,428 - 113,016,670UniSTSRnor5.0
RGSC_v3.413106,459,162 - 106,459,405RGDRGSC3.4
RGSC_v3.413106,459,163 - 106,459,405UniSTSRGSC3.4
RGSC_v3.113106,648,266 - 106,648,509RGD
Celera13101,187,887 - 101,188,129UniSTS
FHH x ACI Map1360.0699UniSTS
FHH x ACI Map1360.0699RGD
Cytogenetic Map13q27UniSTS
BG373964  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013108,403,822 - 108,403,929NCBIRnor6.0
Rnor_5.013113,025,586 - 113,025,693UniSTSRnor5.0
RGSC_v3.413106,450,011 - 106,450,118UniSTSRGSC3.4
Celera13101,178,801 - 101,178,908UniSTS
RH 3.4 Map13697.1UniSTS
Cytogenetic Map13q27UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:287
Count of miRNA genes:173
Interacting mature miRNAs:221
Transcripts:ENSRNOT00000004905
Prediction methods:Microtar, Miranda, 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.


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 33 42 35 35 40
Low 3 10 11 6 15 6 8 9 34 35 41 11 8
Below cutoff 4 4 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004905   ⟹   ENSRNOP00000004905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl13108,382,399 - 108,443,294 (+)Ensembl
RefSeq Acc Id: NM_001107201   ⟹   NP_001100671
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.213101,669,184 - 101,719,804 (-)NCBI
Rnor_6.013108,382,662 - 108,440,346 (+)NCBI
Rnor_5.013113,004,568 - 113,064,606 (+)NCBI
RGSC_v3.413106,421,541 - 106,471,350 (-)RGD
Celera13101,149,597 - 101,200,064 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250454   ⟹   XP_006250516
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013108,382,536 - 108,444,107 (+)NCBI
Rnor_5.013113,004,568 - 113,064,606 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250455   ⟹   XP_006250517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013108,383,081 - 108,444,107 (+)NCBI
Rnor_5.013113,004,568 - 113,064,606 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250456   ⟹   XP_006250518
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013108,383,317 - 108,444,107 (+)NCBI
Rnor_5.013113,004,568 - 113,064,606 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250458   ⟹   XP_006250520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013108,382,536 - 108,440,273 (+)NCBI
Rnor_5.013113,004,568 - 113,064,606 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598838   ⟹   XP_017454327
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013108,385,038 - 108,444,107 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100671 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94973 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100671   ⟸   NM_001107201
- Sequence:
RefSeq Acc Id: XP_006250516   ⟸   XM_006250454
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006250520   ⟸   XM_006250458
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006250517   ⟸   XM_006250455
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006250518   ⟸   XM_006250456
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017454327   ⟸   XM_017598838
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000004905   ⟸   ENSRNOT00000004905
Protein Domains
Prospero

Transcriptome

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

Promoters
RGD ID:13699105
Promoter ID:EPDNEW_R9630
Type:multiple initiation site
Name:Prox1_1
Description:prospero homeobox 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_6.013108,382,661 - 108,382,721EPDNEW

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)
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
LL/MavRrrc (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
LN/MavRrrc (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
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)
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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
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 108392875 108392876 G A snv WN/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306890 AgrOrtholog
Ensembl Genes ENSRNOG00000003694 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004905 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004905 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.500 UniProtKB/TrEMBL
InterPro Homeo_prospero_dom UniProtKB/TrEMBL
  Homeo_prospero_dom_sf UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Prospero_homeodomain UniProtKB/TrEMBL
  Prox1 UniProtKB/TrEMBL
NCBI Gene 305066 ENTREZGENE
PANTHER PTHR12198 UniProtKB/TrEMBL
  PTHR12198:SF6 UniProtKB/TrEMBL
Pfam HPD UniProtKB/TrEMBL
PhenoGen Prox1 PhenoGen
PROSITE HOMEO_PROSPERO UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt D3ZU00_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-24 Prox1  prospero homeobox 1  Prox1  prospero-related homeobox 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Prox1  prospero-related homeobox 1   Prox1_predicted  prospero-related homeobox 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Prox1_predicted  prospero-related homeobox 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED