Satb1 (SATB homeobox 1) - Rat Genome Database

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Gene: Satb1 (SATB homeobox 1) Rattus norvegicus
Analyze
Symbol: Satb1
Name: SATB homeobox 1
RGD ID: 1305561
Description: Predicted to have DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Predicted to be involved in several processes, including T cell activation; chromatin organization; and negative regulation of transcription by RNA polymerase II. Predicted to localize to PML body; heterochromatin; and nuclear matrix. Orthologous to human SATB1 (SATB homeobox 1); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,7-dihydropurine-6-thione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DNA-binding protein SATB1; LOC316164; special AT-rich sequence binding protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.294,677,817 - 4,773,061 (-)NCBI
Rnor_6.0 Ensembl92,190,915 - 2,274,629 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.092,181,135 - 2,277,949 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.092,129,797 - 2,224,329 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.493,307,651 - 3,391,348 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.193,307,650 - 3,391,345 (+)NCBI
Celera91,577,500 - 1,650,421 (-)NCBICelera
Cytogenetic Map9q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,7-dihydropurine-6-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acetamide  (EXP)
acetazolamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
arsenous acid  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
cisplatin  (ISO)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
entinostat  (ISO)
ethanol  (ISO)
folic acid  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
hydroquinone  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mercaptopurine  (EXP)
methylmercury chloride  (ISO)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
potassium chromate  (ISO)
purine-6-thiol  (EXP)
retinyl acetate  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
tungsten  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)

References

Additional References at PubMed
PMID:8114718   PMID:10716941   PMID:12477932   PMID:12692553   PMID:15814699   PMID:15851481   PMID:18408014   PMID:21930775   PMID:25896016   PMID:29506055   PMID:30024617   PMID:33011339  


Genomics

Comparative Map Data
Satb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.294,677,817 - 4,773,061 (-)NCBI
Rnor_6.0 Ensembl92,190,915 - 2,274,629 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.092,181,135 - 2,277,949 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.092,129,797 - 2,224,329 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.493,307,651 - 3,391,348 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.193,307,650 - 3,391,345 (+)NCBI
Celera91,577,500 - 1,650,421 (-)NCBICelera
Cytogenetic Map9q11NCBI
SATB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl318,345,377 - 18,445,588 (-)EnsemblGRCh38hg38GRCh38
GRCh38318,345,377 - 18,445,592 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37318,386,869 - 18,487,084 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36318,364,438 - 18,440,344 (-)NCBINCBI36hg18NCBI36
Build 34318,364,438 - 18,440,344NCBI
Celera318,327,413 - 18,424,451 (-)NCBI
Cytogenetic Map3p24.3NCBI
HuRef318,323,695 - 18,414,820 (-)NCBIHuRef
CHM1_1318,339,776 - 18,439,941 (-)NCBICHM1_1
Satb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391752,043,215 - 52,140,318 (-)NCBIGRCm39mm39
GRCm39 Ensembl1752,043,215 - 52,140,318 (-)Ensembl
GRCm381751,736,187 - 51,833,290 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1751,736,187 - 51,833,290 (-)EnsemblGRCm38mm10GRCm38
MGSCv371751,875,512 - 51,972,615 (-)NCBIGRCm37mm9NCBIm37
MGSCv361751,204,398 - 51,297,562 (-)NCBImm8
Celera1755,200,882 - 55,296,979 (-)NCBICelera
Cytogenetic Map17CNCBI
Satb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543010,587,539 - 10,683,887 (-)NCBIChiLan1.0ChiLan1.0
SATB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1318,602,204 - 18,700,696 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl318,602,204 - 18,681,211 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0318,267,819 - 18,368,924 (-)NCBIMhudiblu_PPA_v0panPan3
SATB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12324,614,198 - 24,692,254 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2324,593,489 - 24,690,977 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2324,628,318 - 24,729,971 (+)NCBI
ROS_Cfam_1.02325,080,231 - 25,182,042 (+)NCBI
UMICH_Zoey_3.12324,802,248 - 24,903,924 (+)NCBI
UNSW_CanFamBas_1.02324,862,371 - 24,964,041 (+)NCBI
UU_Cfam_GSD_1.02325,107,820 - 25,209,575 (+)NCBI
Satb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118177,766,685 - 177,862,478 (-)NCBI
SpeTri2.0NW_00493647310,906,059 - 11,001,007 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SATB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl135,314,358 - 5,417,591 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1135,315,985 - 5,410,686 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2136,018,336 - 6,115,617 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SATB1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11563,163,989 - 63,263,122 (-)NCBI
ChlSab1.1 Ensembl1563,170,243 - 63,263,149 (-)Ensembl
Vero_WHO_p1.0NW_02366604136,170,384 - 36,269,846 (-)NCBI
Satb1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248213,723,609 - 3,820,921 (-)NCBI

Position Markers
U05252  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.294,681,268 - 4,681,425 (-)MAPPER
Rnor_6.092,274,328 - 2,274,484NCBIRnor6.0
Rnor_5.092,221,688 - 2,221,844UniSTSRnor5.0
RGSC_v3.493,391,044 - 3,391,200UniSTSRGSC3.4
Celera91,577,648 - 1,577,804UniSTS
Cytogenetic Map9q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9116520166Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9190783415555026Rat
631533Iresp3Immunoglobin response QTL316.2blood immunoglobulin E amount (VT:0002492)serum total immunoglobulin E level (CMO:0001542)920055833309921Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:449
Count of miRNA genes:237
Interacting mature miRNAs:281
Transcripts:ENSRNOT00000017556
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 2 26 18 2 19 2 8 11 74 18 33 11 8
Low 1 17 36 36 36 17 8
Below cutoff 3 3 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001012129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC085814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000017556   ⟹   ENSRNOP00000017557
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl92,202,511 - 2,274,629 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077417   ⟹   ENSRNOP00000070853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl92,190,915 - 2,272,687 (+)Ensembl
RefSeq Acc Id: NM_001012129   ⟹   NP_001012129
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,681,121 - 4,753,251 (-)NCBI
Rnor_6.092,202,511 - 2,274,632 (+)NCBI
Rnor_5.092,129,797 - 2,224,329 (+)NCBI
RGSC_v3.493,307,651 - 3,391,348 (+)RGD
Celera91,577,500 - 1,650,421 (-)RGD
Sequence:
RefSeq Acc Id: XM_006244219   ⟹   XP_006244281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,680,283 - 4,753,160 (-)NCBI
Rnor_6.092,202,396 - 2,277,949 (+)NCBI
Rnor_5.092,129,797 - 2,224,329 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244221   ⟹   XP_006244283
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.092,181,135 - 2,277,949 (+)NCBI
Rnor_5.092,129,797 - 2,224,329 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766761   ⟹   XP_008764983
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.092,191,060 - 2,277,949 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766762   ⟹   XP_008764984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.092,181,135 - 2,277,949 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766763   ⟹   XP_008764985
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.092,181,135 - 2,277,949 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596404   ⟹   XP_017451893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.092,181,365 - 2,277,949 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083475   ⟹   XP_038939403
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,680,283 - 4,753,160 (-)NCBI
RefSeq Acc Id: XM_039083476   ⟹   XP_038939404
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,680,283 - 4,773,061 (-)NCBI
RefSeq Acc Id: XM_039083477   ⟹   XP_038939405
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,677,817 - 4,767,091 (-)NCBI
RefSeq Acc Id: XM_039083478   ⟹   XP_038939406
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,677,817 - 4,761,541 (-)NCBI
RefSeq Acc Id: XM_039083479   ⟹   XP_038939407
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,680,283 - 4,753,145 (-)NCBI
RefSeq Acc Id: XM_039083480   ⟹   XP_038939408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,680,283 - 4,753,160 (-)NCBI
RefSeq Acc Id: XM_039083481   ⟹   XP_038939409
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,680,283 - 4,753,160 (-)NCBI
RefSeq Acc Id: XM_039083482   ⟹   XP_038939410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.294,680,283 - 4,753,160 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001012129   ⟸   NM_001012129
- UniProtKB: Q5U2Y2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244283   ⟸   XM_006244221
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006244281   ⟸   XM_006244219
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008764984   ⟸   XM_008766762
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008764985   ⟸   XM_008766763
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008764983   ⟸   XM_008766761
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451893   ⟸   XM_017596404
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000070853   ⟸   ENSRNOT00000077417
RefSeq Acc Id: ENSRNOP00000017557   ⟸   ENSRNOT00000017556
RefSeq Acc Id: XP_038939405   ⟸   XM_039083477
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939406   ⟸   XM_039083478
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939404   ⟸   XM_039083476
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939410   ⟸   XM_039083482
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038939409   ⟸   XM_039083481
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038939408   ⟸   XM_039083480
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038939403   ⟸   XM_039083475
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939407   ⟸   XM_039083479
- Peptide Label: isoform X1
Protein Domains
CUT   Homeobox

Transcriptome

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

Promoters
RGD ID:13696419
Promoter ID:EPDNEW_R6944
Type:single initiation site
Name:Satb1_1
Description:SATB homeobox 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.092,202,430 - 2,202,490EPDNEW

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)
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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
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)
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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
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)
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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
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/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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305561 AgrOrtholog
Ensembl Genes ENSRNOG00000012942 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017557 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070853 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017556 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077417 UniProtKB/TrEMBL
Gene3D-CATH 1.10.260.40 UniProtKB/TrEMBL
  1.10.260.70 UniProtKB/TrEMBL
  3.10.20.710 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123102 IMAGE-MGC_LOAD
InterPro CUTL UniProtKB/TrEMBL
  Hmoeo_CUT UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Lambda_DNA-bd UniProtKB/TrEMBL
  SATB1/SATB2 UniProtKB/TrEMBL
  SATB_CUTL_sf UniProtKB/TrEMBL
  SATB_ULD_sf UniProtKB/TrEMBL
  ULD UniProtKB/TrEMBL
KEGG Report rno:316164 UniProtKB/TrEMBL
MGC_CLONE MGC:94048 IMAGE-MGC_LOAD
NCBI Gene 316164 ENTREZGENE
PANTHER PTHR15116 UniProtKB/TrEMBL
Pfam CUT UniProtKB/TrEMBL
  CUTL UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  ULD UniProtKB/TrEMBL
PhenoGen Satb1 PhenoGen
PROSITE CUT UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART CUT UniProtKB/TrEMBL
  HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
  Lambda_like_DNA UniProtKB/TrEMBL
UniProt A0A0G2JYZ8_RAT UniProtKB/TrEMBL
  Q5U2Y2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-18 Satb1  SATB homeobox 1  Satb1  special AT-rich sequence binding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Satb1  special AT-rich sequence binding protein 1  Satb1_predicted  special AT-rich sequence binding protein 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Satb1_predicted  special AT-rich sequence binding protein 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED