Sim1 (SIM bHLH transcription factor 1) - Rat Genome Database

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Gene: Sim1 (SIM bHLH transcription factor 1) Rattus norvegicus
Analyze
Symbol: Sim1
Name: SIM bHLH transcription factor 1
RGD ID: 1309949
Description: Predicted to have DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in regulation of transcription by RNA polymerase II and ureteric bud development. Predicted to localize to nucleus. Human ortholog(s) of this gene implicated in obesity. Orthologous to human SIM1 (SIM bHLH transcription factor 1); INTERACTS WITH bisphenol A; gentamycin; vinclozolin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC309888; MGC189161; single-minded 1; single-minded family bHLH transcription factor 1; single-minded homolog 1; single-minded homolog 1 (Drosophila)
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
mRatBN7.22053,827,601 - 53,907,219 (+)NCBI
Rnor_6.0 Ensembl2055,594,676 - 55,673,995 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02055,590,810 - 55,674,002 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02057,192,734 - 57,274,564 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42054,908,178 - 54,988,099 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12054,937,202 - 55,012,573 (+)NCBI
Celera2046,257,466 - 46,336,238 (-)NCBICelera
Cytogenetic Map20q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:8927054   PMID:11782478   PMID:12477932   PMID:16545622   PMID:27782878  


Genomics

Comparative Map Data
Sim1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22053,827,601 - 53,907,219 (+)NCBI
Rnor_6.0 Ensembl2055,594,676 - 55,673,995 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02055,590,810 - 55,674,002 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02057,192,734 - 57,274,564 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42054,908,178 - 54,988,099 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12054,937,202 - 55,012,573 (+)NCBI
Celera2046,257,466 - 46,336,238 (-)NCBICelera
Cytogenetic Map20q13NCBI
SIM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6100,385,009 - 100,464,921 (-)EnsemblGRCh38hg38GRCh38
GRCh386100,385,009 - 100,464,929 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376100,832,885 - 100,912,797 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366100,943,471 - 101,018,272 (-)NCBINCBI36hg18NCBI36
Build 346100,943,470 - 101,018,272NCBI
Celera6101,480,981 - 101,555,761 (-)NCBI
Cytogenetic Map6q16.3NCBI
HuRef698,275,663 - 98,350,456 (-)NCBIHuRef
CHM1_16101,098,793 - 101,173,570 (-)NCBICHM1_1
Sim1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391050,770,794 - 50,865,252 (+)NCBIGRCm39mm39
GRCm39 Ensembl1050,770,850 - 50,865,248 (+)Ensembl
GRCm381050,894,698 - 50,989,156 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1050,894,754 - 50,989,152 (+)EnsemblGRCm38mm10GRCm38
MGSCv371050,615,457 - 50,708,958 (+)NCBIGRCm37mm9NCBIm37
MGSCv361050,584,066 - 50,677,567 (+)NCBImm8
Celera1051,744,683 - 51,838,475 (+)NCBICelera
Cytogenetic Map10B3NCBI
cM Map1024.87NCBI
Sim1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541126,173,009 - 26,259,752 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541126,173,009 - 26,256,545 (-)NCBIChiLan1.0ChiLan1.0
SIM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16102,104,462 - 102,181,062 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6102,104,783 - 102,181,062 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0698,221,476 - 98,301,215 (-)NCBIMhudiblu_PPA_v0panPan3
SIM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11258,480,744 - 58,552,126 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1258,485,823 - 58,553,192 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1258,239,464 - 58,312,667 (-)NCBI
ROS_Cfam_1.01259,313,324 - 59,386,528 (-)NCBI
UMICH_Zoey_3.11258,666,215 - 58,739,215 (-)NCBI
UNSW_CanFamBas_1.01258,507,210 - 58,580,362 (-)NCBI
UU_Cfam_GSD_1.01258,747,572 - 58,820,839 (-)NCBI
Sim1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494693,381,896 - 93,456,539 (-)NCBI
SpeTri2.0NW_0049366511,841,040 - 1,911,944 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl167,214,337 - 67,294,397 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1167,213,685 - 67,294,455 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2176,000,269 - 76,071,230 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SIM1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11373,451,838 - 73,527,733 (+)NCBI
ChlSab1.1 Ensembl1373,453,800 - 73,527,198 (+)Ensembl
Vero_WHO_p1.0NW_02366604045,749,767 - 45,824,784 (+)NCBI
Sim1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248104,479,589 - 4,558,735 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:541
Count of miRNA genes:251
Interacting mature miRNAs:351
Transcripts:ENSRNOT00000057010
Prediction methods:Miranda, 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 32
Low 7 10 7 7 53 3 22 9 7
Below cutoff 2 10 21 12 8 12 1 4 11 12 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000057010   ⟹   ENSRNOP00000053843
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2055,594,676 - 55,673,995 (+)Ensembl
RefSeq Acc Id: NM_001107641   ⟹   NP_001101111
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22053,828,364 - 53,907,212 (+)NCBI
Rnor_6.02055,594,676 - 55,673,995 (+)NCBI
Rnor_5.02057,192,734 - 57,274,564 (+)NCBI
RGSC_v3.42054,908,178 - 54,988,099 (+)RGD
Celera2046,257,466 - 46,336,238 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256604   ⟹   XP_006256666
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22053,827,601 - 53,907,219 (+)NCBI
Rnor_6.02055,593,907 - 55,674,002 (+)NCBI
Rnor_5.02057,192,734 - 57,274,564 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772994   ⟹   XP_008771216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02055,593,770 - 55,674,002 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772995   ⟹   XP_008771217
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02055,590,810 - 55,674,002 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772996   ⟹   XP_008771218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02055,594,203 - 55,674,002 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772998   ⟹   XP_008771220
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02055,607,277 - 55,669,243 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101111 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256666 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99652 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101111   ⟸   NM_001107641
- UniProtKB: D3ZMU8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256666   ⟸   XM_006256604
- Peptide Label: isoform X1
- UniProtKB: D3ZMU8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771217   ⟸   XM_008772995
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771216   ⟸   XM_008772994
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771218   ⟸   XM_008772996
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771220   ⟸   XM_008772998
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000053843   ⟸   ENSRNOT00000057010
Protein Domains
bHLH   PAS   Single-minded C-terminal

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)
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)
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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:1309949 AgrOrtholog
Ensembl Genes ENSRNOG00000037600 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000053843 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057010 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
  PAC UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
  PAS-like_dom_sf UniProtKB/TrEMBL
  PAS_fold UniProtKB/TrEMBL
  PAS_fold_3 UniProtKB/TrEMBL
  SIM_C UniProtKB/TrEMBL
KEGG Report rno:309888 UniProtKB/TrEMBL
NCBI Gene 309888 ENTREZGENE
Pfam HLH UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
  PAS_3 UniProtKB/TrEMBL
  SIM_C UniProtKB/TrEMBL
PhenoGen Sim1 PhenoGen
PROSITE HLH UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
  SIM_C UniProtKB/TrEMBL
SMART HLH UniProtKB/TrEMBL
  PAC UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
  SSF55785 UniProtKB/TrEMBL
UniProt D3ZMU8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-04-27 Sim1  SIM bHLH transcription factor 1  Sim1  single-minded family bHLH transcription factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-11-11 Sim1  single-minded family bHLH transcription factor 1  Sim1  single-minded homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Sim1  single-minded homolog 1 (Drosophila)  Sim1_predicted  single-minded 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Sim1_predicted  single-minded 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED