Otx1 (orthodenticle homeobox 1) - Rat Genome Database

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Gene: Otx1 (orthodenticle homeobox 1) Rattus norvegicus
Analyze
Symbol: Otx1
Name: orthodenticle homeobox 1
RGD ID: 3237
Description: Predicted to have 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 brain development; inner ear morphogenesis; and positive regulation of transcription by RNA polymerase II. Predicted to localize to nucleus. Orthologous to human OTX1 (orthodenticle homeobox 1); INTERACTS WITH bisphenol A; ethanol; paracetamol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: homeobox protein OTX1; homeobox protein OTX1-like; LOC100364498; Orthodenticle (Drosophila) homolog 1; orthodenticle homolog 1 (Drosophila); OTX1X
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21496,082,151 - 96,089,161 (-)NCBI
Rnor_6.0 Ensembl14106,861,676 - 106,864,892 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.014106,861,556 - 106,864,933 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.014106,926,505 - 106,929,875 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414102,721,413 - 102,724,748 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114102,740,623 - 102,743,959 (-)NCBI
Celera1495,081,129 - 95,084,585 (-)NCBICelera
Cytogenetic Map14q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:8613727   PMID:10225993   PMID:15105370   PMID:15201224   PMID:15917450   PMID:18849347   PMID:20816794  


Genomics

Comparative Map Data
Otx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21496,082,151 - 96,089,161 (-)NCBI
Rnor_6.0 Ensembl14106,861,676 - 106,864,892 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.014106,861,556 - 106,864,933 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.014106,926,505 - 106,929,875 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414102,721,413 - 102,724,748 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114102,740,623 - 102,743,959 (-)NCBI
Celera1495,081,129 - 95,084,585 (-)NCBICelera
Cytogenetic Map14q22NCBI
OTX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl263,050,057 - 63,057,836 (+)EnsemblGRCh38hg38GRCh38
GRCh38263,049,735 - 63,057,831 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37263,276,870 - 63,284,966 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36263,131,469 - 63,137,818 (+)NCBINCBI36hg18NCBI36
Build 34263,189,615 - 63,195,961NCBI
Celera263,122,518 - 63,128,867 (+)NCBI
Cytogenetic Map2p15NCBI
HuRef263,016,136 - 63,023,910 (+)NCBIHuRef
CHM1_1263,207,478 - 63,215,248 (+)NCBICHM1_1
Otx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391121,944,764 - 21,954,044 (-)NCBIGRCm39mm39
GRCm39 Ensembl1121,944,764 - 21,952,897 (-)Ensembl
GRCm381121,994,764 - 22,001,651 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1121,994,764 - 22,002,897 (-)EnsemblGRCm38mm10GRCm38
MGSCv371121,894,767 - 21,901,654 (-)NCBIGRCm37mm9NCBIm37
MGSCv361121,894,767 - 21,901,654 (-)NCBImm8
Celera1124,135,716 - 24,142,604 (-)NCBICelera
Cytogenetic Map11A3.2NCBI
cM Map1114.1NCBI
Otx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542421,140,038 - 21,146,694 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542421,140,038 - 21,147,268 (-)NCBIChiLan1.0ChiLan1.0
OTX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A64,255,217 - 64,262,221 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A64,255,217 - 64,262,221 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A63,125,700 - 63,133,702 (+)NCBIMhudiblu_PPA_v0panPan3
OTX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11062,830,515 - 62,836,449 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1062,830,187 - 62,837,172 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1062,717,998 - 62,724,904 (+)NCBI
ROS_Cfam_1.01063,837,537 - 63,844,443 (+)NCBI
UMICH_Zoey_3.11063,520,614 - 63,527,516 (+)NCBI
UNSW_CanFamBas_1.01063,823,813 - 63,830,718 (+)NCBI
UU_Cfam_GSD_1.01064,121,011 - 64,127,929 (+)NCBI
Otx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629220,382,689 - 20,389,733 (-)NCBI
SpeTri2.0NW_0049364918,181,600 - 8,188,600 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OTX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl378,895,882 - 78,903,217 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1378,895,142 - 78,903,045 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2382,961,896 - 82,968,756 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OTX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11443,959,586 - 43,967,194 (-)NCBI
ChlSab1.1 Ensembl1443,961,534 - 43,964,879 (-)Ensembl
Vero_WHO_p1.0NW_02366604567,875,707 - 67,882,786 (+)NCBI
Otx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476210,379,775 - 10,388,262 (-)NCBI

Position Markers
RH131109  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21496,082,210 - 96,082,430 (+)MAPPER
Rnor_6.014106,860,290 - 106,860,509NCBIRnor6.0
Rnor_5.014106,925,239 - 106,925,458UniSTSRnor5.0
RGSC_v3.414102,720,147 - 102,720,366UniSTSRGSC3.4
Celera1495,079,863 - 95,080,082UniSTS
RH 3.4 Map14762.2UniSTS
Cytogenetic Map14q22UniSTS
RH94705  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21496,083,516 - 96,083,616 (+)MAPPER
Rnor_6.014106,861,596 - 106,861,695NCBIRnor6.0
Rnor_5.014106,926,545 - 106,926,644UniSTSRnor5.0
RGSC_v3.414102,721,453 - 102,721,552UniSTSRGSC3.4
Celera1495,081,169 - 95,081,268UniSTS
Cytogenetic Map14q22UniSTS
Otx1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21496,085,870 - 96,086,900 (+)MAPPER
Rnor_6.014106,863,863 - 106,864,892NCBIRnor6.0
Rnor_5.014106,928,805 - 106,929,834UniSTSRnor5.0
RGSC_v3.414102,723,678 - 102,724,707UniSTSRGSC3.4
Celera1495,083,515 - 95,084,544UniSTS
Cytogenetic Map14q22UniSTS
UniSTS:470671  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1495,081,564 - 95,081,657UniSTS
Cytogenetic Map14q22UniSTS
Otx1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21496,085,801 - 96,085,888 (+)MAPPER
Rnor_6.014106,863,794 - 106,863,880NCBIRnor6.0
Rnor_5.014106,928,736 - 106,928,822UniSTSRnor5.0
RGSC_v3.414102,723,609 - 102,723,695UniSTSRGSC3.4
Celera1495,083,446 - 95,083,532UniSTS
Cytogenetic Map14q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1478446303110402569Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1480049285115493446Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1480049285115493446Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:34
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000011668
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

circulatory system nervous system reproductive system respiratory system
High
Medium 36
Low 28 4 1
Below cutoff 12 6 10 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000090664   ⟹   ENSRNOP00000072147
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl14106,861,676 - 106,864,892 (-)Ensembl
RefSeq Acc Id: NM_013109   ⟹   NP_037241
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21496,083,477 - 96,086,941 (-)NCBI
Rnor_6.014106,861,556 - 106,864,933 (-)NCBI
Rnor_5.014106,926,505 - 106,929,875 (-)NCBI
RGSC_v3.414102,721,413 - 102,724,748 (-)RGD
Celera1495,081,129 - 95,084,585 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091639   ⟹   XP_038947567
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21496,082,151 - 96,089,161 (-)NCBI
RefSeq Acc Id: XM_039091640   ⟹   XP_038947568
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21496,082,151 - 96,089,161 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_037241   ⟸   NM_013109
- UniProtKB: Q63410 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072147   ⟸   ENSRNOT00000090664
RefSeq Acc Id: XP_038947567   ⟸   XM_039091639
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947568   ⟸   XM_039091640
- Peptide Label: isoform X1
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 (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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 (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
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
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 (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 (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3237 AgrOrtholog
Ensembl Genes ENSRNOG00000059469 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000072147 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000090664 UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Otx1_TF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Otx_TF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Otx_TF_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25646 UniProtKB/Swiss-Prot
NCBI Gene 25646 ENTREZGENE
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_Otx UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Otx1 PhenoGen
PRINTS OTX1HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OTXHOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC219556
UniProt A0A0G2K288_RAT UniProtKB/TrEMBL
  OTX1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q64203 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-04-12 Otx1  orthodenticle homeobox 1  LOC100364498  homeobox protein OTX1-like  Data Merged 737654 PROVISIONAL
2010-05-05 LOC100364498  homeobox protein OTX1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-09-24 Otx1  orthodenticle homeobox 1  Otx1  orthodenticle homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Otx1  Orthodenticle (Drosophila) homolog 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization prenatally localized to the cytoplasm but is translocated to the nucleus in first week of postnatal life 727353