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 enable 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 act upstream of or within regulation of DNA-templated transcription. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in obesity. Orthologous to human SIM1 (SIM bHLH transcription factor 1); INTERACTS WITH bisphenol A; gentamycin; paracetamol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously 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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82055,409,814 - 55,489,450 (+)NCBIGRCr8
mRatBN7.22053,827,601 - 53,907,219 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2053,828,364 - 53,907,212 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2055,543,215 - 55,626,456 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02055,192,931 - 55,276,173 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02055,885,015 - 55,963,896 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02055,590,810 - 55,674,002 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2055,594,676 - 55,673,995 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02057,192,734 - 57,274,564 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42054,908,178 - 54,988,099 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
nucleus  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Profound obesity associated with a balanced translocation that disrupts the SIM1 gene. Holder JL Jr, etal., Hum Mol Genet. 2000 Jan 1;9(1):101-8.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
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
GRCr82055,409,814 - 55,489,450 (+)NCBIGRCr8
mRatBN7.22053,827,601 - 53,907,219 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2053,828,364 - 53,907,212 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2055,543,215 - 55,626,456 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02055,192,931 - 55,276,173 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02055,885,015 - 55,963,896 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02055,590,810 - 55,674,002 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2055,594,676 - 55,673,995 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02057,192,734 - 57,274,564 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42054,908,178 - 54,988,099 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh386100,385,009 - 100,464,921 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6100,385,009 - 100,464,921 (-)EnsemblGRCh38hg38GRCh38
GRCh376100,832,885 - 100,912,797 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366100,943,471 - 101,018,272 (-)NCBINCBI36Build 36hg18NCBI36
Build 346100,943,470 - 101,018,272NCBI
Celera6101,480,981 - 101,555,761 (-)NCBICelera
Cytogenetic Map6q16.3NCBI
HuRef698,275,663 - 98,350,456 (-)NCBIHuRef
CHM1_16101,098,793 - 101,173,570 (-)NCBICHM1_1
T2T-CHM13v2.06101,558,767 - 101,638,670 (-)NCBIT2T-CHM13v2.0
Sim1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391050,770,794 - 50,865,252 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1050,770,850 - 50,865,248 (+)EnsemblGRCm39 Ensembl
GRCm381050,894,698 - 50,989,156 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1050,894,754 - 50,989,152 (+)EnsemblGRCm38mm10GRCm38
MGSCv371050,615,457 - 50,708,958 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361050,584,066 - 50,677,567 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v25120,431,444 - 120,506,816 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16118,308,628 - 118,388,705 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0698,221,476 - 98,301,215 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16102,104,462 - 102,181,062 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6102,104,783 - 102,181,062 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01259,313,324 - 59,386,528 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1259,319,037 - 59,386,575 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11258,666,215 - 58,739,215 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01258,507,210 - 58,580,362 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01258,747,572 - 58,820,839 (-)NCBIUU_Cfam_GSD_1.0
Sim1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494693,381,896 - 93,456,539 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366511,841,054 - 1,911,944 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11373,451,838 - 73,527,733 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1373,453,800 - 73,527,198 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604045,749,767 - 45,824,784 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sim1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248104,479,589 - 4,558,434 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248104,479,589 - 4,558,735 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sim1
458 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat


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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2053,828,364 - 53,907,212 (+)Ensembl
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
GRCr82055,410,577 - 55,489,449 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82055,409,814 - 55,489,450 (+)NCBI
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:
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  
Ensembl Protein ENSRNOP00000053843
  ENSRNOP00000053843.2
Reference Protein Sequences
RefSeq Acc Id: NP_001101111   ⟸   NM_001107641
- UniProtKB: D3ZMU8 (UniProtKB/TrEMBL),   A6K6T3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256666   ⟸   XM_006256604
- Peptide Label: isoform X1
- UniProtKB: D3ZMU8 (UniProtKB/TrEMBL),   A6K6T3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000053843   ⟸   ENSRNOT00000057010
Protein Domains
bHLH   PAS   Single-minded C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZMU8-F1-model_v2 AlphaFold D3ZMU8 1-765 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309949 AgrOrtholog
BioCyc Gene G2FUF-3228 BioCyc
Ensembl Genes ENSRNOG00000037600 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057010 ENTREZGENE
  ENSRNOT00000057010.3 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
  PAS domain 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
PANTHER HYPOXIA-INDUCIBLE FACTOR 1 ALPHA UniProtKB/TrEMBL
  SINGLE-MINDED HOMOLOG 1 UniProtKB/TrEMBL
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
RatGTEx ENSRNOG00000037600 RatGTEx
SMART HLH UniProtKB/TrEMBL
  PAC UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
  SSF55785 UniProtKB/TrEMBL
UniProt A6K6T3 ENTREZGENE, UniProtKB/TrEMBL
  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