Sox5 (SRY-box transcription factor 5) - Rat Genome Database

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Gene: Sox5 (SRY-box transcription factor 5) Rattus norvegicus
Analyze
Symbol: Sox5
Name: SRY-box transcription factor 5
RGD ID: 620471
Description: Enables cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including asymmetric neuroblast division; cartilage development; and positive regulation of cell differentiation. Predicted to act upstream of or within several processes, including neurogenesis; regulation of timing of neuron differentiation; and regulation of transcription, DNA-templated. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human SOX5 (SRY-box transcription factor 5); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Sox5l1; SRY (sex determining region Y)-box 5; SRY box 5; SRY-box containing gene 5; SRY-box containing gene 5-like 1; transcription factor SOX-5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24176,781,375 - 177,736,833 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4176,785,892 - 177,736,852 (-)Ensembl
Rnor_6.04178,062,267 - 179,031,991 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4178,066,165 - 178,441,547 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04242,266,295 - 243,221,217 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44181,558,995 - 181,931,117 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14181,825,983 - 182,011,429 (-)NCBI
Celera4165,313,274 - 165,629,808 (-)NCBICelera
Cytogenetic Map4q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:9755172   PMID:15634692   PMID:17084361   PMID:18215621   PMID:20668334   PMID:20940257   PMID:21073445   PMID:21401405   PMID:22344693   PMID:23946438   PMID:24854956   PMID:26345464  
PMID:26525805  


Genomics

Comparative Map Data
Sox5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24176,781,375 - 177,736,833 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4176,785,892 - 177,736,852 (-)Ensembl
Rnor_6.04178,062,267 - 179,031,991 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4178,066,165 - 178,441,547 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04242,266,295 - 243,221,217 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44181,558,995 - 181,931,117 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14181,825,983 - 182,011,429 (-)NCBI
Celera4165,313,274 - 165,629,808 (-)NCBICelera
Cytogenetic Map4q44NCBI
SOX5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1223,529,504 - 24,562,544 (-)EnsemblGRCh38hg38GRCh38
GRCh381223,529,499 - 24,562,701 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371223,682,438 - 24,715,425 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361223,576,498 - 24,606,647 (-)NCBINCBI36hg18NCBI36
Celera1228,833,198 - 29,862,278 (-)NCBI
Cytogenetic Map12p12.1NCBI
HuRef1223,452,599 - 24,484,456 (-)NCBIHuRef
CHM1_11223,650,324 - 24,680,623 (-)NCBICHM1_1
Sox5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396143,774,151 - 144,728,008 (-)NCBIGRCm39mm39
GRCm39 Ensembl6143,774,151 - 144,727,703 (-)Ensembl
GRCm386143,828,425 - 144,782,287 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6143,828,425 - 144,781,977 (-)EnsemblGRCm38mm10GRCm38
MGSCv376143,781,349 - 144,158,078 (-)NCBIGRCm37mm9NCBIm37
MGSCv366143,790,051 - 144,166,639 (-)NCBImm8
Celera6146,885,590 - 147,265,302 (-)NCBICelera
Cytogenetic Map6G3NCBI
cM Map676.14NCBI
Sox5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541318,831,931 - 19,204,217 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541318,831,931 - 19,676,371 (-)NCBIChiLan1.0ChiLan1.0
SOX5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11264,973,019 - 65,391,500 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1264,971,818 - 65,388,694 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01262,361,631 - 62,780,805 (+)NCBIMhudiblu_PPA_v0panPan3
SOX5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12722,857,661 - 23,855,709 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2723,452,985 - 23,851,380 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2722,515,990 - 23,511,350 (-)NCBI
ROS_Cfam_1.02723,058,695 - 24,061,457 (+)NCBI
UMICH_Zoey_3.12722,871,574 - 23,867,072 (+)NCBI
UNSW_CanFamBas_1.02722,890,892 - 23,887,914 (+)NCBI
UU_Cfam_GSD_1.02722,685,794 - 23,683,255 (-)NCBI
Sox5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494584,725,370 - 85,677,233 (+)NCBI
SpeTri2.0NW_0049365483,213,305 - 3,599,876 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl549,160,723 - 50,161,570 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1549,159,950 - 50,166,463 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2553,008,491 - 53,806,316 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SOX5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11123,298,622 - 24,131,712 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1123,303,325 - 23,715,492 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606910,803,456 - 11,833,677 (+)NCBIVero_WHO_p1.0
Sox5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475214,986,146 - 15,382,687 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D9Rat28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,973,326 - 176,973,650 (+)MAPPERmRatBN7.2
Rnor_6.04178,253,454 - 178,253,777NCBIRnor6.0
Rnor_5.04242,456,468 - 242,456,791UniSTSRnor5.0
RGSC_v3.44181,645,676 - 181,646,000RGDRGSC3.4
RGSC_v3.44181,645,677 - 181,646,000UniSTSRGSC3.4
RGSC_v3.14181,890,801 - 181,891,124RGD
Celera4165,498,972 - 165,499,295UniSTS
RH 3.4 Map41062.3RGD
RH 3.4 Map41062.3UniSTS
Cytogenetic Map4q44UniSTS
D4Got154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,951,334 - 176,951,490 (+)MAPPERmRatBN7.2
Rnor_6.04178,231,463 - 178,231,618NCBIRnor6.0
Rnor_5.04242,434,477 - 242,434,632UniSTSRnor5.0
RGSC_v3.44181,623,685 - 181,623,841RGDRGSC3.4
RGSC_v3.44181,623,686 - 181,623,841UniSTSRGSC3.4
RGSC_v3.14181,868,810 - 181,868,965RGD
Celera4165,476,979 - 165,477,134UniSTS
RH 3.4 Map41013.5RGD
RH 3.4 Map41013.5UniSTS
RH 2.0 Map41105.3RGD
Cytogenetic Map4q44UniSTS
BE108803  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,860,248 - 176,860,432 (+)MAPPERmRatBN7.2
Rnor_6.04178,141,125 - 178,141,308NCBIRnor6.0
Rnor_5.04242,344,099 - 242,344,282UniSTSRnor5.0
RGSC_v3.44180,472,699 - 180,472,882UniSTSRGSC3.4
Celera4165,387,487 - 165,387,670UniSTS
RH 3.4 Map41057.9UniSTS
Cytogenetic Map4q44UniSTS
RH134712  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,786,011 - 176,786,169 (+)MAPPERmRatBN7.2
Rnor_6.04178,066,907 - 178,067,064NCBIRnor6.0
Rnor_5.04242,270,935 - 242,271,092UniSTSRnor5.0
RGSC_v3.44180,399,064 - 180,399,221UniSTSRGSC3.4
Celera4165,313,400 - 165,313,557UniSTS
RH 3.4 Map41057.9UniSTS
Cytogenetic Map4q44UniSTS
Sox5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,786,012 - 176,786,632 (+)MAPPERmRatBN7.2
Rnor_6.04178,066,908 - 178,067,527NCBIRnor6.0
Rnor_5.04242,270,936 - 242,271,555UniSTSRnor5.0
RGSC_v3.44180,399,065 - 180,399,684UniSTSRGSC3.4
Celera4165,313,401 - 165,314,020UniSTS
Cytogenetic Map4q44UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:114
Count of miRNA genes:90
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000020729
Prediction methods:Microtar, 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

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 6 6 6 47 11 2
Low 2 41 51 35 19 35 7 7 27 35 30 9 7
Below cutoff 1 2 1 4 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001271267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592402 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592403 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592405 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592406 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592407 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592408 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592409 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106953 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB073719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC121477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC086415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000020729   ⟹   ENSRNOP00000020729
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4176,785,892 - 177,736,852 (-)Ensembl
Rnor_6.0 Ensembl4178,067,051 - 178,168,690 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000055542   ⟹   ENSRNOP00000052404
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4176,785,892 - 177,159,525 (-)Ensembl
Rnor_6.0 Ensembl4178,066,787 - 178,441,547 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087434   ⟹   ENSRNOP00000073853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4176,785,892 - 177,208,076 (-)Ensembl
Rnor_6.0 Ensembl4178,066,165 - 178,441,547 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096663   ⟹   ENSRNOP00000079278
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4176,785,892 - 177,736,852 (-)Ensembl
RefSeq Acc Id: NM_001271267   ⟹   NP_001258196
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,785,886 - 177,159,525 (-)NCBI
Rnor_6.04178,066,781 - 178,441,547 (-)NCBI
Rnor_5.04242,266,295 - 243,221,217 (-)NCBI
Celera4165,313,274 - 165,629,808 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237604   ⟹   XP_006237666
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,576 (-)NCBI
Rnor_6.04178,062,267 - 178,441,601 (-)NCBI
Rnor_5.04242,266,295 - 243,221,217 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763349   ⟹   XP_008761571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,641 (-)NCBI
Rnor_6.04178,062,267 - 178,441,669 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763350   ⟹   XP_008761572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,715 - 176,893,809 (-)NCBI
Rnor_6.04178,062,267 - 178,174,280 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592402   ⟹   XP_017447891
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,736,833 (-)NCBI
Rnor_6.04178,062,267 - 179,031,991 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592404   ⟹   XP_017447893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,154,286 (-)NCBI
Rnor_6.04178,062,267 - 178,436,745 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592405   ⟹   XP_017447894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,641 (-)NCBI
Rnor_6.04178,062,267 - 178,441,669 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592406   ⟹   XP_017447895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,736,831 (-)NCBI
Rnor_6.04178,062,267 - 179,031,991 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592407   ⟹   XP_017447896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,575 (-)NCBI
Rnor_6.04178,062,267 - 178,441,601 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592408   ⟹   XP_017447897
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,641 (-)NCBI
Rnor_6.04178,062,267 - 178,441,669 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592409   ⟹   XP_017447898
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 176,889,262 (-)NCBI
Rnor_6.04178,062,267 - 178,169,792 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592410   ⟹   XP_017447899
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,715 - 176,893,809 (-)NCBI
Rnor_6.04178,062,267 - 178,174,275 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039106952   ⟹   XP_038962880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,237,409 (-)NCBI
RefSeq Acc Id: XM_039106953   ⟹   XP_038962881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,736,833 (-)NCBI
RefSeq Acc Id: XM_039106955   ⟹   XP_038962883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 176,889,262 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001258196   ⟸   NM_001271267
- UniProtKB: F1M8W4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237666   ⟸   XM_006237604
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008761571   ⟸   XM_008763349
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008761572   ⟸   XM_008763350
- Peptide Label: isoform X12
- UniProtKB: Q5U1X4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447895   ⟸   XM_017592406
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017447891   ⟸   XM_017592402
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017447897   ⟸   XM_017592408
- Peptide Label: isoform X8
- UniProtKB: A0A0G2K6K9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447894   ⟸   XM_017592405
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017447896   ⟸   XM_017592407
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017447893   ⟸   XM_017592404
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017447899   ⟸   XM_017592410
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017447898   ⟸   XM_017592409
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000052404   ⟸   ENSRNOT00000055542
RefSeq Acc Id: ENSRNOP00000073853   ⟸   ENSRNOT00000087434
RefSeq Acc Id: ENSRNOP00000020729   ⟸   ENSRNOT00000020729
RefSeq Acc Id: XP_038962881   ⟸   XM_039106953
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038962880   ⟸   XM_039106952
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038962883   ⟸   XM_039106955
- Peptide Label: isoform X11
RefSeq Acc Id: ENSRNOP00000079278   ⟸   ENSRNOT00000096663
Protein Domains
HMG box

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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NRrrc (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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (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)
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)
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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)
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: 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)
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: SBN/Ygl sequenced by MCW
SBN/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
SHR/NHsd (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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620471 AgrOrtholog
Ensembl Genes ENSRNOG00000027869 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020729 UniProtKB/Swiss-Prot
  ENSRNOP00000052404 UniProtKB/Swiss-Prot
  ENSRNOP00000073853 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020729 UniProtKB/Swiss-Prot
  ENSRNOT00000055542 UniProtKB/Swiss-Prot
  ENSRNOT00000087434 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7131922 IMAGE-MGC_LOAD
InterPro HMG_box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:140587 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105885 IMAGE-MGC_LOAD
NCBI Gene 140587 ENTREZGENE
Pfam HMG_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sox5 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K6K9 ENTREZGENE, UniProtKB/TrEMBL
  F1M8W4 ENTREZGENE
  Q5U1X4 ENTREZGENE
  SOX5_RAT UniProtKB/Swiss-Prot
UniProt Secondary F1LQN4 UniProtKB/Swiss-Prot
  Q5U1X4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Sox5  SRY-box transcription factor 5  Sox5  SRY box 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Sox5  SRY box 5  Sox5  SRY (sex determining region Y)-box 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Sox5  SRY (sex determining region Y)-box 5  Sox5l1  SRY-box containing gene 5-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-04-17 Sox5l1  SRY-box containing gene 5-like 1  Sox5  SRY (sex determining region Y)-box 5  Data Merged 737654 PROVISIONAL
2010-04-20 Sox5  SRY (sex determining region Y)-box 5  LOC312831  similar to SRY (sex determining region Y)-box 5 isoform a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC312831  similar to SRY (sex determining region Y)-box 5 isoform a      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-07-08 Sox5  SRY-box containing gene 5    SRY (sex determining region Y)-box 5  Name updated 1299863 APPROVED
2002-08-07 Sox5  SRY (sex determining region Y)-box 5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference