Pax7 (paired box 7) - Rat Genome Database
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Gene: Pax7 (paired box 7) Rattus norvegicus
Analyze
Symbol: Pax7
Name: paired box 7
RGD ID: 1564360
Description: Predicted to have DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including animal organ development; chordate embryonic development; and positive regulation of nitrogen compound metabolic process. Predicted to localize to nuclear chromatin. Human ortholog(s) of this gene implicated in alveolar rhabdomyosarcoma. Orthologous to human PAX7 (paired box 7); INTERACTS WITH bisphenol A; Monobutylphthalate; 1,2-dimethylhydrazine (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC500574; paired box gene 7; paired box protein Pax-7; RGD1564360; similar to paired box gene 7 isoform 1
Orthologs:
Homo sapiens (human) : PAX7 (paired box 7)  HGNC  Alliance
Mus musculus (house mouse) : Pax7 (paired box 7)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Pax7 (paired box 7)
Pan paniscus (bonobo/pygmy chimpanzee) : PAX7 (paired box 7)
Canis lupus familiaris (dog) : PAX7 (paired box 7)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Pax7 (paired box 7)
Sus scrofa (pig) : PAX7 (paired box 7)
Chlorocebus sabaeus (African green monkey) : PAX7 (paired box 7)
Heterocephalus glaber (naked mole-rat) : Pax7 (paired box 7)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05158,211,001 - 158,313,510 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5158,214,616 - 158,313,426 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05161,944,011 - 162,045,053 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45158,547,765 - 158,648,053 (-)NCBIRGSC3.4rn4RGSC3.4
Celera5150,374,628 - 150,471,191 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View


Cellular Component

References

Additional References at PubMed
PMID:8631261   PMID:9230312   PMID:9608680   PMID:9858722   PMID:11030621   PMID:17301672   PMID:18508329   PMID:18590716   PMID:18808442   PMID:19101644   PMID:19192888   PMID:19531352  
PMID:21131290   PMID:22358842   PMID:22862948   PMID:23070814   PMID:27434733  


Genomics

Comparative Map Data
Pax7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05158,211,001 - 158,313,510 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5158,214,616 - 158,313,426 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05161,944,011 - 162,045,053 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45158,547,765 - 158,648,053 (-)NCBIRGSC3.4rn4RGSC3.4
Celera5150,374,628 - 150,471,191 (-)NCBICelera
Cytogenetic Map5q36NCBI
PAX7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl118,630,846 - 18,748,866 (+)EnsemblGRCh38hg38GRCh38
GRCh38118,630,846 - 18,748,866 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37118,957,500 - 19,075,360 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36118,830,087 - 18,935,219 (+)NCBINCBI36hg18NCBI36
Celera117,287,191 - 17,405,157 (+)NCBI
Cytogenetic Map1p36.13NCBI
HuRef117,203,638 - 17,321,488 (+)NCBIHuRef
CHM1_1119,066,628 - 19,184,492 (+)NCBICHM1_1
Pax7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394139,464,370 - 139,560,841 (-)NCBI
GRCm384139,737,059 - 139,833,530 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4139,737,062 - 139,833,528 (-)EnsemblGRCm38mm10GRCm38
MGSCv374139,293,996 - 139,388,883 (-)NCBIGRCm37mm9NCBIm37
MGSCv364139,010,157 - 139,105,044 (-)NCBImm8
Celera4141,530,711 - 141,629,332 (-)NCBICelera
Cytogenetic Map4D3NCBI
cM Map470.83NCBI
Pax7
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955527474,403 - 574,689 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955527474,450 - 573,869 (-)NCBIChiLan1.0ChiLan1.0
PAX7
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1118,639,641 - 18,756,952 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl118,639,641 - 18,756,952 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0117,589,513 - 17,707,442 (+)NCBI
PAX7
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl279,815,748 - 79,915,003 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1279,813,835 - 79,952,490 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pax7
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364745,045,284 - 5,131,859 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PAX7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl677,161,097 - 77,267,415 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1677,160,827 - 77,268,626 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PAX7
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl20113,823,392 - 113,928,548 (-)Ensembl
ChlSab1.120113,810,646 - 113,929,136 (-)NCBI
Pax7
(Heterocephalus glaber - naked mole-rat)
No map positions available.

Position Markers
D5Got93  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.05162,032,498 - 162,032,573NCBIRnor5.0
Rnor_5.05162,032,488 - 162,032,573NCBIRnor5.0
RGSC_v3.45158,634,503 - 158,634,661RGDRGSC3.4
RGSC_v3.45158,634,513 - 158,634,638UniSTSRGSC3.4
RGSC_v3.15158,644,552 - 158,644,677RGD
Cytogenetic Map5q36UniSTS
RH 3.4 Map51043.2UniSTS
RH 3.4 Map51043.2RGD
AU047910  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05158,290,985 - 158,291,220NCBIRnor6.0
Rnor_5.05162,022,883 - 162,023,118UniSTSRnor5.0
RGSC_v3.45158,625,161 - 158,625,396UniSTSRGSC3.4
Celera5150,449,529 - 150,449,764UniSTS
Cytogenetic Map5q36UniSTS
Pax7  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05158,310,077 - 158,310,721NCBIRnor6.0
Rnor_5.05162,041,622 - 162,042,266UniSTSRnor5.0
RGSC_v3.45158,644,704 - 158,645,348UniSTSRGSC3.4
Celera5150,467,842 - 150,468,486UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114140832159140832Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114140832159140832Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116767924161767924Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116767924161767924Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116767924161767924Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116767924161767924Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132551937173707219Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5134712342173707219Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5136354114173707219Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136640731173707219Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138154677172402610Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5142307322173707219Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5142309061173707219Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149029982173687766Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5149568588167739697Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5149832180164807402Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5150340838164298744Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5150360936167946134Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5157212422167739539Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5157319671171194163Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5157319671173707219Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:64
Count of miRNA genes:59
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000025488
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.


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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 17
Low 8 11 24 7 1 8
Below cutoff 2 6 6 2 6 25 14 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07050246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07050247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01040485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000025488   ⟹   ENSRNOP00000025488
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5158,214,616 - 158,313,426 (-)Ensembl
RefSeq Acc Id: NM_001191984   ⟹   NP_001178913
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05158,214,616 - 158,313,426 (-)NCBI
Rnor_5.05161,944,011 - 162,045,053 (-)NCBI
Celera5150,374,628 - 150,471,191 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006239263   ⟹   XP_006239325
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05158,211,001 - 158,313,510 (-)NCBI
Rnor_5.05161,944,011 - 162,045,053 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178913 (Get FASTA)   NCBI Sequence Viewer  
  XP_006239325 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL80932 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001178913   ⟸   NM_001191984
- UniProtKB: D3ZRA8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239325   ⟸   XM_006239263
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000025488   ⟸   ENSRNOT00000025488
Protein Domains
Homeobox   OAR   Paired

Transcriptome

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


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)
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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564360 AgrOrtholog
Ensembl Genes ENSRNOG00000018739 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025488 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025488 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  OAR_dom UniProtKB/TrEMBL
  Paired_box_N UniProtKB/TrEMBL
  PAIRED_DNA_bd_dom UniProtKB/TrEMBL
  Pax7 UniProtKB/TrEMBL
  PAX_fam UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:500574 UniProtKB/TrEMBL
NCBI Gene 500574 ENTREZGENE
PANTHER PTHR45636 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
  PAX UniProtKB/TrEMBL
  Pax7 UniProtKB/TrEMBL
PhenoGen Pax7 PhenoGen
PRINTS PAIREDBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  OAR UniProtKB/TrEMBL
  PAIRED_1 UniProtKB/TrEMBL
  PAIRED_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
  PAX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniGene Rn.226327 ENTREZGENE
UniProt D3ZRA8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-30 Pax7  paired box 7  Pax7  paired box gene 7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Pax7  paired box gene 7  RGD1564360_predicted  similar to paired box gene 7 isoform 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564360_predicted  similar to paired box gene 7 isoform 1 (predicted)  LOC500574  similar to paired box gene 7 isoform 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500574  similar to paired box gene 7 isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL

 



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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.