Otx2 (orthodenticle homeobox 2) - Rat Genome Database

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Gene: Otx2 (orthodenticle homeobox 2) Rattus norvegicus
Analyze
Symbol: Otx2
Name: orthodenticle homeobox 2
RGD ID: 1305705
Description: Predicted to enable DNA-binding transcription activator 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 neuron differentiation; positive regulation of gastrulation; and regulation of transcription, DNA-templated. Predicted to act upstream of or within several processes, including cellular response to leukemia inhibitory factor; nervous system development; and regionalization. Predicted to be located in cytoplasm and growth cone. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in panhypopituitarism and syndromic microphthalmia 5. Orthologous to human OTX2 (orthodenticle homeobox 2); INTERACTS WITH (R)-lipoic acid; 6-propyl-2-thiouracil; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: homeobox Otx2; homeobox protein OTX2; homeobox protein OTX2-like; LOC100911492; LOC305858; orthodenticle homolog 2; orthodenticle homolog 2 (Drosophila)
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
mRatBN7.21521,942,233 - 21,953,034 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1521,943,191 - 21,953,416 (-)Ensembl
Rnor_6.01525,500,037 - 25,511,619 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1525,502,019 - 25,505,691 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1525,517,721 - 25,521,393 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01529,425,136 - 29,435,678 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41524,622,851 - 24,632,435 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11524,638,550 - 24,643,418 (-)NCBI
Celera1522,321,144 - 22,330,728 (-)NCBICelera
Cytogenetic Map15p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:8613727   PMID:9501024   PMID:10225993   PMID:10891582   PMID:11291865   PMID:11412024   PMID:11731459   PMID:12559959   PMID:12652306   PMID:14625556   PMID:15105370   PMID:15201223  
PMID:15201224   PMID:15888661   PMID:15890343   PMID:15917450   PMID:16267555   PMID:16339193   PMID:16539743   PMID:17499638   PMID:17936272   PMID:19592574   PMID:19796622   PMID:19951692  
PMID:20439489   PMID:20530484   PMID:20816794   PMID:22992956   PMID:23056351   PMID:24399192   PMID:26166575   PMID:26494787   PMID:26985665   PMID:30451368   PMID:30803008  


Genomics

Comparative Map Data
Otx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21521,942,233 - 21,953,034 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1521,943,191 - 21,953,416 (-)Ensembl
Rnor_6.01525,500,037 - 25,511,619 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1525,502,019 - 25,505,691 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1525,517,721 - 25,521,393 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01529,425,136 - 29,435,678 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41524,622,851 - 24,632,435 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11524,638,550 - 24,643,418 (-)NCBI
Celera1522,321,144 - 22,330,728 (-)NCBICelera
Cytogenetic Map15p14NCBI
OTX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1456,799,905 - 56,816,693 (-)EnsemblGRCh38hg38GRCh38
GRCh381456,799,905 - 56,810,479 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371457,266,623 - 57,277,197 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361456,337,178 - 56,346,937 (-)NCBINCBI36hg18NCBI36
Build 341456,337,179 - 56,342,098NCBI
Celera1437,316,938 - 37,326,697 (-)NCBI
Cytogenetic Map14q22.3NCBI
HuRef1437,431,939 - 37,441,708 (-)NCBIHuRef
CHM1_11457,206,163 - 57,215,915 (-)NCBICHM1_1
Otx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391448,894,238 - 48,905,101 (-)NCBIGRCm39mm39
GRCm39 Ensembl1448,895,134 - 48,911,276 (-)Ensembl
GRCm381448,656,781 - 48,667,644 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1448,657,677 - 48,673,819 (-)EnsemblGRCm38mm10GRCm38
MGSCv371449,277,846 - 49,282,547 (-)NCBIGRCm37mm9NCBIm37
MGSCv361447,579,630 - 47,587,057 (-)NCBImm8
Celera1444,858,278 - 44,862,991 (-)NCBICelera
Cytogenetic Map14C1NCBI
cM Map1425.36NCBI
Otx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546610,755,012 - 10,765,095 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546610,755,143 - 10,764,957 (-)NCBIChiLan1.0ChiLan1.0
OTX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11455,641,349 - 55,651,012 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1455,641,349 - 55,651,012 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01437,370,926 - 37,381,610 (-)NCBIMhudiblu_PPA_v0panPan3
OTX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1832,435,169 - 32,445,093 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl832,435,863 - 32,445,446 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha832,203,297 - 32,213,040 (-)NCBI
ROS_Cfam_1.0832,685,680 - 32,695,437 (-)NCBI
UMICH_Zoey_3.1832,288,616 - 32,298,366 (-)NCBI
UNSW_CanFamBas_1.0832,364,566 - 32,374,316 (-)NCBI
UU_Cfam_GSD_1.0832,740,360 - 32,750,115 (-)NCBI
Otx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864072,742,666 - 72,758,575 (+)NCBI
SpeTri2.0NW_0049364951,433,124 - 1,449,409 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OTX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1186,028,575 - 186,038,229 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11186,028,575 - 186,039,026 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21206,642,523 - 206,650,665 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OTX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12433,975,043 - 33,984,816 (-)NCBI
Vero_WHO_p1.0NW_02366605322,189,742 - 22,199,522 (-)NCBI
Otx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248841,830,645 - 1,840,213 (-)NCBI

Position Markers
BB256399  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21521,943,228 - 21,943,332 (+)MAPPERmRatBN7.2
Rnor_6.01525,516,735 - 25,516,838NCBIRnor6.0
Rnor_6.01525,501,033 - 25,501,136NCBIRnor6.0
Rnor_5.01529,426,132 - 29,426,235UniSTSRnor5.0
Rnor_5.01529,441,040 - 29,441,143UniSTSRnor5.0
RGSC_v3.41524,622,889 - 24,622,992UniSTSRGSC3.4
Celera1522,321,182 - 22,321,285UniSTS
Cytogenetic Map15p14UniSTS
PMC263842P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21521,944,349 - 21,944,558 (+)MAPPERmRatBN7.2
Rnor_6.01525,517,856 - 25,518,064NCBIRnor6.0
Rnor_6.01525,502,154 - 25,502,362NCBIRnor6.0
Rnor_5.01529,427,253 - 29,427,461UniSTSRnor5.0
Rnor_5.01529,442,161 - 29,442,369UniSTSRnor5.0
RGSC_v3.41524,624,010 - 24,624,218UniSTSRGSC3.4
Celera1522,322,303 - 22,322,511UniSTS
Cytogenetic Map15p14UniSTS
PMC304098P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21521,944,347 - 21,944,558 (+)MAPPERmRatBN7.2
Rnor_6.01525,517,854 - 25,518,064NCBIRnor6.0
Rnor_6.01525,502,152 - 25,502,362NCBIRnor6.0
Rnor_5.01529,427,251 - 29,427,461UniSTSRnor5.0
Rnor_5.01529,442,159 - 29,442,369UniSTSRnor5.0
RGSC_v3.41524,624,008 - 24,624,218UniSTSRGSC3.4
Celera1522,322,301 - 22,322,511UniSTS
Cytogenetic Map15p14UniSTS
RH136748  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21521,943,229 - 21,943,414 (+)MAPPERmRatBN7.2
Rnor_6.01525,516,736 - 25,516,920NCBIRnor6.0
Rnor_6.01525,501,034 - 25,501,218NCBIRnor6.0
Rnor_5.01529,426,133 - 29,426,317UniSTSRnor5.0
Rnor_5.01529,441,041 - 29,441,225UniSTSRnor5.0
RGSC_v3.41524,622,890 - 24,623,074UniSTSRGSC3.4
Celera1522,321,183 - 22,321,367UniSTS
Cytogenetic Map15p14UniSTS
Otx2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21521,946,668 - 21,947,881 (+)MAPPERmRatBN7.2
Rnor_6.01525,520,175 - 25,521,387NCBIRnor6.0
Rnor_6.01525,504,473 - 25,505,685NCBIRnor6.0
Rnor_5.01529,429,572 - 29,430,784UniSTSRnor5.0
Rnor_5.01529,444,480 - 29,445,692UniSTSRnor5.0
RGSC_v3.41524,626,329 - 24,627,541UniSTSRGSC3.4
Celera1522,324,622 - 22,325,834UniSTS
Cytogenetic Map15p14UniSTS
OTX2_1019  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21521,943,622 - 21,944,540 (+)MAPPERmRatBN7.2
Rnor_6.01525,517,129 - 25,518,046NCBIRnor6.0
Rnor_6.01525,501,427 - 25,502,344NCBIRnor6.0
Rnor_5.01529,426,526 - 29,427,443UniSTSRnor5.0
Rnor_5.01529,441,434 - 29,442,351UniSTSRnor5.0
RGSC_v3.41524,623,283 - 24,624,200UniSTSRGSC3.4
Celera1522,321,576 - 22,322,493UniSTS
Cytogenetic Map15p14UniSTS
Otx2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21521,944,058 - 21,944,513 (+)MAPPERmRatBN7.2
Rnor_6.01525,517,565 - 25,518,019NCBIRnor6.0
Rnor_6.01525,501,863 - 25,502,317NCBIRnor6.0
Rnor_5.01529,426,962 - 29,427,416UniSTSRnor5.0
Rnor_5.01529,441,870 - 29,442,324UniSTSRnor5.0
RGSC_v3.41524,623,719 - 24,624,173UniSTSRGSC3.4
Celera1522,322,012 - 22,322,466UniSTS
Cytogenetic Map15p14UniSTS
Otx2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21521,944,058 - 21,944,160 (+)MAPPERmRatBN7.2
Rnor_6.01525,517,565 - 25,517,666NCBIRnor6.0
Rnor_6.01525,501,863 - 25,501,964NCBIRnor6.0
Rnor_5.01529,426,962 - 29,427,063UniSTSRnor5.0
Rnor_5.01529,441,870 - 29,441,971UniSTSRnor5.0
RGSC_v3.41524,623,719 - 24,623,820UniSTSRGSC3.4
Celera1522,322,012 - 22,322,113UniSTS
Cytogenetic Map15p14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15226636822711984Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151448116528469888Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:501
Count of miRNA genes:243
Interacting mature miRNAs:301
Transcripts:ENSRNOT00000018109, ENSRNOT00000074488
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


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001100566 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599668 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599675 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599681 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599682 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001841259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CB580080 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S81922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000074488   ⟹   ENSRNOP00000064262
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1521,943,191 - 21,953,416 (-)Ensembl
Rnor_6.0 Ensembl1525,502,019 - 25,505,691 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085910   ⟹   ENSRNOP00000073390
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1521,943,191 - 21,952,778 (-)Ensembl
Rnor_6.0 Ensembl1525,517,721 - 25,521,393 (-)Ensembl
RefSeq Acc Id: NM_001100566   ⟹   NP_001094036
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21521,943,191 - 21,952,778 (-)NCBI
Rnor_6.01525,500,995 - 25,510,579 (-)NCBI
Rnor_5.01529,425,136 - 29,435,678 (-)NCBI
RGSC_v3.41524,622,851 - 24,632,435 (-)RGD
Celera1522,321,144 - 22,330,728 (-)RGD
Sequence:
RefSeq Acc Id: XM_006251838   ⟹   XP_006251900
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21521,942,233 - 21,953,028 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039093283   ⟹   XP_038949211
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21521,942,233 - 21,953,034 (-)NCBI
RefSeq Acc Id: XM_039093284   ⟹   XP_038949212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21521,942,233 - 21,952,226 (-)NCBI
RefSeq Acc Id: XM_039093285   ⟹   XP_038949213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21521,942,233 - 21,953,028 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001094036   ⟸   NM_001100566
- UniProtKB: F2Z3S7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064262   ⟸   ENSRNOT00000074488
RefSeq Acc Id: XP_038949211   ⟸   XM_039093283
- Peptide Label: isoform X1
RefSeq Acc Id: XP_006251900   ⟸   XM_006251838
- Peptide Label: isoform X2
- UniProtKB: F2Z3S7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038949213   ⟸   XM_039093285
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949212   ⟸   XM_039093284
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000073390   ⟸   ENSRNOT00000085910
Protein Domains
Homeobox

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)
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)
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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)
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
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)
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
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)
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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/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
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)
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
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)
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
LEXF11/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
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)
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
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)
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
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)
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/RijCrl (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: 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:1305705 AgrOrtholog
  RGD:6492889 AgrOrtholog
Ensembl Genes ENSRNOG00000048322 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000056186 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000065063 Ensembl
Ensembl Protein ENSRNOP00000064262 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073390 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074488 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085910 UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Otx2_TF UniProtKB/TrEMBL
  Otx_TF UniProtKB/TrEMBL
  Otx_TF_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:305858 UniProtKB/TrEMBL
NCBI Gene 305858 ENTREZGENE
Pfam Homeobox UniProtKB/TrEMBL
  TF_Otx UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Otx2 PhenoGen
PRINTS OTX2HOMEOBOX UniProtKB/TrEMBL
  OTXHOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt F2Z3S7 ENTREZGENE, UniProtKB/TrEMBL
  OTX2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Otx2  orthodenticle homeobox 2  LOC100911492  homeobox protein OTX2-like  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100911492  homeobox protein OTX2-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-04-23 Otx2  orthodenticle homeobox 2  Otx2  orthodenticle homolog 2 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Otx2  orthodenticle homolog 2 (Drosophila)  Otx2_predicted  orthodenticle homolog 2 (Drosophila) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Otx2_predicted  orthodenticle homolog 2 (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED