Smarcb1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Smarcb1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1) Ictidomys tridecemlineatus
Analyze
Symbol: Smarcb1
Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
RGD ID: 12709305
Description: ENCODES a protein that exhibits RNA polymerase I core promoter sequence-specific DNA binding (ortholog); INVOLVED IN blastocyst development (ortholog); blastocyst hatching (ortholog); hepatocyte differentiation (ortholog); PARTICIPATES IN SWI/SNF family mediated chromatin remodeling pathway; ASSOCIATED WITH adenoid cystic carcinoma (ortholog); agammaglobulinemia 2 (ortholog); atypical teratoid rhabdoid tumor (ortholog); FOUND IN chromatin (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118141,445,150 - 141,477,819 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366191,275,362 - 1,308,913 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366191,276,239 - 1,308,945 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Smarcb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118141,445,150 - 141,477,819 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366191,275,362 - 1,308,913 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366191,276,239 - 1,308,945 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMARCB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382223,786,966 - 23,838,009 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2223,786,931 - 23,838,009 (+)EnsemblGRCh38hg38GRCh38
GRCh372224,129,153 - 24,180,196 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362222,459,150 - 22,506,705 (+)NCBINCBI36Build 36hg18NCBI36
Build 342222,453,703 - 22,501,258NCBI
Celera227,968,247 - 8,015,764 (+)NCBICelera
Cytogenetic Map22q11.23NCBI
HuRef227,117,207 - 7,164,626 (+)NCBIHuRef
CHM1_12224,141,393 - 24,188,920 (+)NCBICHM1_1
T2T-CHM13v2.02224,234,168 - 24,285,193 (+)NCBIT2T-CHM13v2.0
Smarcb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391075,732,603 - 75,757,448 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1075,732,603 - 75,757,451 (-)EnsemblGRCm39 Ensembl
GRCm381075,896,769 - 75,921,614 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1075,896,769 - 75,921,617 (-)EnsemblGRCm38mm10GRCm38
MGSCv371075,359,514 - 75,384,359 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361075,340,491 - 75,365,304 (-)NCBIMGSCv36mm8
Celera1076,941,458 - 76,966,299 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1038.61NCBI
Smarcb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82012,740,105 - 12,763,054 (+)NCBIGRCr8
mRatBN7.22012,741,164 - 12,763,616 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2012,741,477 - 12,763,620 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2013,448,137 - 13,470,241 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02012,809,058 - 12,831,162 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02013,280,851 - 13,302,955 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02013,679,955 - 13,702,821 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2013,680,716 - 13,704,931 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02015,836,242 - 15,858,384 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42013,140,331 - 13,162,437 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12013,140,557 - 13,162,664 (+)NCBI
Celera2014,232,795 - 14,254,901 (+)NCBICelera
Cytogenetic Map20p12NCBI
Smarcb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554558,415,839 - 8,457,097 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554558,420,263 - 8,457,105 (-)NCBIChiLan1.0ChiLan1.0
SMARCB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22333,515,250 - 33,565,294 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12236,255,101 - 36,301,814 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0224,542,764 - 4,589,461 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12222,627,950 - 22,673,921 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2222,627,982 - 22,673,921 (+)Ensemblpanpan1.1panPan2
SMARCB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12628,692,610 - 28,728,778 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2628,692,899 - 28,728,783 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2627,765,925 - 27,802,103 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02630,097,586 - 30,133,966 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2630,097,586 - 30,134,047 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12628,178,905 - 28,215,089 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02627,796,839 - 27,833,022 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02628,784,702 - 28,820,890 (-)NCBIUU_Cfam_GSD_1.0
SMARCB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1449,874,984 - 49,906,048 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11449,874,981 - 49,906,043 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21453,317,251 - 53,348,336 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMARCB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1196,902,985 - 6,945,111 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl196,902,951 - 6,944,784 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666100428,050 - 470,045 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smarcb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474710,361,260 - 10,396,719 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474710,362,149 - 10,396,580 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSSTOT00000012413   ⟹   ENSSTOP00000011122
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049366191,275,362 - 1,308,913 (-)Ensembl
RefSeq Acc Id: XM_005334471   ⟹   XP_005334528
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405118141,445,150 - 141,477,819 (+)NCBI
SpeTri2.0NW_0049366191,276,239 - 1,308,945 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005334472   ⟹   XP_005334529
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405118141,445,150 - 141,477,819 (+)NCBI
SpeTri2.0NW_0049366191,276,239 - 1,308,945 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005334528 (Get FASTA)   NCBI Sequence Viewer  
  XP_005334529 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000011122.3
GenBank Protein KAG3278767 (Get FASTA)   NCBI Sequence Viewer  
  KAG3278768 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_005334529   ⟸   XM_005334472
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_005334528   ⟸   XM_005334471
- Peptide Label: isoform X1
- UniProtKB: I3MJ39 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSTOP00000011122   ⟸   ENSSTOT00000012413
Protein Domains
SWI/SNF Subunit INI1 DNA binding


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000012408 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000012413.3 UniProtKB/TrEMBL
InterPro INI1_DNA-bd UniProtKB/TrEMBL
  Sfh1/SNF5 UniProtKB/TrEMBL
  SNF5 UniProtKB/TrEMBL
NCBI Gene Smarcb1 ENTREZGENE
PANTHER SNF5 UniProtKB/TrEMBL
  SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1 UniProtKB/TrEMBL
Pfam INI1_DNA-bd UniProtKB/TrEMBL
  SNF5 UniProtKB/TrEMBL
PIRSF SWI_SNF UniProtKB/TrEMBL
UniProt I3MJ39 ENTREZGENE, UniProtKB/TrEMBL