Smarca4 (SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4) - Rat Genome Database

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Gene: Smarca4 (SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4) Rattus norvegicus
Analyze
Symbol: Smarca4
Name: SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4 (Ensembl:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4)
RGD ID: 621728
Description: Enables chromatin binding activity. Involved in negative regulation of DNA-templated transcription; nucleosome disassembly; and spermatid development. Part of SWI/SNF complex. Used to study cocaine dependence. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 4; hepatocellular carcinoma; lung non-small cell carcinoma; and rhabdoid tumor predisposition syndrome 2. Orthologous to human SMARCA4 (SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4); PARTICIPATES IN altered SWI/SNF family mediated chromatin remodeling pathway; cortisol signaling pathway; histone modification pathway; INTERACTS WITH 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: ATP-dependent helicase SMARCA4; BAF190A; brg-1; BRG1-associated factor 190A; protein brahma homolog 1; SNF2-beta; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4; transcription activator BRG1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8828,438,370 - 28,535,071 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl828,443,810 - 28,535,070 (+)EnsemblGRCr8
mRatBN7.2820,167,717 - 20,258,975 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,167,717 - 20,258,975 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx824,200,412 - 24,292,032 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0822,495,960 - 22,587,578 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0820,397,343 - 20,488,586 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,648,323 - 22,739,468 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,648,323 - 22,739,468 (+)Ensemblrn6Rnor6.0
Rnor_5.0822,702,277 - 22,793,519 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4820,720,915 - 20,812,157 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera821,558,796 - 21,650,002 (+)NCBICelera
RGSC_v3.1820,787,909 - 20,796,297 (+)NCBI
Cytogenetic Map8q13NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
beta-lapachone  (ISO)
bicalutamide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
C60 fullerene  (EXP)
caffeine  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
choline  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
coumarin  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cyproconazole  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenvalerate  (EXP)
finasteride  (EXP)
flutamide  (EXP)
FR900359  (ISO)
fulvestrant  (ISO)
gallic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glucose  (ISO)
graphene oxide  (ISO)
hexadecanoic acid  (ISO)
hydrazine  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methapyrilene  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP,ISO)
methylseleninic acid  (ISO)
motexafin gadolinium  (ISO)
nitrates  (ISO)
nobiletin  (ISO)
okadaic acid  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
poly(propylene imine) macromolecule  (ISO)
promegestone  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (EXP,ISO)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
trichloroethene  (EXP)
triphenyl phosphate  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc acetate  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aorta development  (ISO)
aortic smooth muscle cell differentiation  (ISO)
blastocyst growth  (ISO)
blastocyst hatching  (ISO)
blood vessel development  (ISO)
cell morphogenesis  (ISO)
cellular response to glucose stimulus  (IEP)
chromatin organization  (IEA)
chromatin remodeling  (IDA,IEA,ISO)
coronary vasculature development  (ISO)
definitive erythrocyte differentiation  (ISO)
DNA-templated transcription  (IEA)
embryonic hindlimb morphogenesis  (ISO)
embryonic organ morphogenesis  (ISO)
epidermis morphogenesis  (ISO)
extracellular matrix organization  (ISO)
forebrain development  (ISO)
gene expression  (ISO)
glial cell fate determination  (ISO)
heart development  (ISO)
heart trabecula formation  (ISO)
heterochromatin formation  (IBA)
hindbrain development  (ISO)
host-mediated activation of viral transcription  (IEA,ISO)
in utero embryonic development  (ISO)
keratinocyte differentiation  (ISO)
lens fiber cell development  (ISO)
liver development  (ISO)
negative regulation of androgen receptor signaling pathway  (IEA,ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cell growth  (IEA,ISO)
negative regulation of DNA-templated transcription  (IEA,IMP,ISO)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of reactive oxygen species biosynthetic process  (IMP)
negative regulation of transcription by RNA polymerase II  (ISO)
nervous system development  (IEA,ISO)
neural retina development  (IEA,ISO)
neurogenesis  (ISO)
nucleosome disassembly  (IDA,IEA,ISO)
nucleosome organization  (IEA)
oligodendrocyte development  (IMP)
outflow tract morphogenesis  (ISO)
pharyngeal arch artery morphogenesis  (ISO)
positive regulation of cell differentiation  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cell size  (IMP)
positive regulation of cold-induced thermogenesis  (ISO)
positive regulation of DNA-templated transcription  (IEA,ISO)
positive regulation of glucose mediated signaling pathway  (IEA,ISO)
positive regulation of macrophage fusion  (IMP)
positive regulation of miRNA transcription  (IEA,ISO)
positive regulation of myelination  (IMP)
positive regulation of signal transduction by p53 class mediator  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IBA,IEA,ISO,ISS)
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I  (IEA,ISO)
positive regulation of Wnt signaling pathway  (IEA,ISO)
regulation of cell migration  (ISO)
regulation of DNA-templated transcription  (IEA)
RNA polymerase I preinitiation complex assembly  (IEA)
spermatid development  (IEP)
stem cell population maintenance  (ISO)
transcription initiation-coupled chromatin remodeling  (ISO)
vasculogenesis  (ISO)
ventricular septum development  (ISO)

Cellular Component
chromatin  (IBA,IEA,ISO)
euchromatin  (ISO)
fibrillar center  (IEA,ISO)
nBAF complex  (ISO,ISS)
npBAF complex  (IEA,ISO,ISS)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO,TAS)
nucleus  (IBA,IEA,ISO)
perichromatin fibrils  (ISO)
SWI/SNF complex  (IDA,IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. REST repression of neuronal genes requires components of the hSWI.SNF complex. Battaglioli E, etal., J Biol Chem. 2002 Oct 25;277(43):41038-45. Epub 2002 Aug 20.
2. Insights into role of bromodomain, testis-specific (Brdt) in acetylated histone H4-dependent chromatin remodeling in mammalian spermiogenesis. Dhar S, etal., J Biol Chem. 2012 Feb 24;287(9):6387-405. doi: 10.1074/jbc.M111.288167. Epub 2012 Jan 3.
3. 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.
4. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. Gebuhr TC, etal., J Exp Med 2003 Dec 15;198(12):1937-49.
5. Wnt signaling: multiple pathways, multiple receptors, and multiple transcription factors. Gordon MD and Nusse R, J Biol Chem. 2006 Aug 11;281(32):22429-33. Epub 2006 Jun 22.
6. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Hargreaves DC and Crabtree GR, Cell Res. 2011 Mar;21(3):396-420. doi: 10.1038/cr.2011.32. Epub 2011 Mar 1.
7. Mammalian chromatin remodeling complex SWI/SNF is essential for enhanced expression of the albumin gene during liver development. Inayoshi Y, etal., J Biochem. 2006 Feb;139(2):177-88.
8. Novel glucocorticoid receptor coactivator effector mechanisms. Jenkins BD, etal., Trends Endocrinol Metab. 2001 Apr;12(3):122-6.
9. Reversible disruption of mSWI/SNF (BAF) complexes by the SS18-SSX oncogenic fusion in synovial sarcoma. Kadoch C and Crabtree GR, Cell. 2013 Mar 28;153(1):71-85. doi: 10.1016/j.cell.2013.02.036.
10. IUGR increases chromatin-remodeling factor Brg1 expression and binding to GR exon 1.7 promoter in newborn male rat hippocampus. Ke X, etal., Am J Physiol Regul Integr Comp Physiol. 2015 Jul 15;309(2):R119-27. doi: 10.1152/ajpregu.00495.2014. Epub 2015 May 13.
11. Genetic and epigenetic screening for gene alterations of the chromatin-remodeling factor, SMARCA4/BRG1, in lung tumors. Medina PP, etal., Genes Chromosomes Cancer. 2004 Oct;41(2):170-7.
12. SWI/SNF chromatin remodeling enzymes are associated with cardiac hypertrophy in a genetic rat model of hypertension. Mehrotra A, etal., J Cell Physiol. 2013 Dec;228(12):2337-42. doi: 10.1002/jcp.24404.
13. MITF interacts with the SWI/SNF subunit, BRG1, to promote GATA4 expression in cardiac hypertrophy. Mehta G, etal., J Mol Cell Cardiol. 2015 Nov;88:101-10. doi: 10.1016/j.yjmcc.2015.09.010. Epub 2015 Sep 24.
14. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
15. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
17. Glucocorticoid receptor-glucocorticoid response element binding stimulates nucleosome disruption by the SWI/SNF complex. Ostlund Farrants AK, etal., Mol Cell Biol 1997 Feb;17(2):895-905.
18. A calcium-dependent switch in a CREST-BRG1 complex regulates activity-dependent gene expression. Qiu Z and Ghosh A, Neuron. 2008 Dec 10;60(5):775-87. doi: 10.1016/j.neuron.2008.09.040.
19. GOA pipeline RGD automated data pipeline
20. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
22. Integrating phosphoproteome and transcriptome reveals new determinants of macrophage multinucleation. Rotival M, etal., Mol Cell Proteomics. 2015 Mar;14(3):484-98. doi: 10.1074/mcp.M114.043836. Epub 2014 Dec 22.
23. The bromodomain: From epigenome reader to druggable target. Sanchez R, etal., Biochim Biophys Acta. 2014 Aug;1839(8):676-685. doi: 10.1016/j.bbagrm.2014.03.011. Epub 2014 Mar 28.
24. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. Shain AH and Pollack JR, PLoS One. 2013;8(1):e55119. doi: 10.1371/journal.pone.0055119. Epub 2013 Jan 23.
25. Aberrant expression of SWI/SNF catalytic subunits BRG1/BRM is associated with tumor development and increased invasiveness in prostate cancers. Sun A, etal., Prostate. 2007 Feb 1;67(2):203-13.
26. Upregulation of heme oxygenase-1 by Brahma-related gene 1 through Nrf2 signaling confers protective effect against high glucose-induced oxidative damage of retinal ganglion cells. Sun W, etal., Eur J Pharmacol. 2020 May 15;875:173038. doi: 10.1016/j.ejphar.2020.173038. Epub 2020 Feb 24.
27. Mutation analysis of the BRG1 gene in prostate cancer clinical samples. Valdman A, etal., Int J Oncol. 2003 May;22(5):1003-7.
28. Label-free quantitative proteomics identifies Smarca4 is involved in vascular calcification. Wang C, etal., Ren Fail. 2019 Nov;41(1):220-228. doi: 10.1080/0886022X.2019.1591997.
29. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. Wang W, etal., EMBO J. 1996 Oct 1;15(19):5370-82.
30. BRG1 in the Nucleus Accumbens Regulates Cocaine-Seeking Behavior. Wang ZJ, etal., Biol Psychiatry. 2016 Nov 1;80(9):652-660. doi: 10.1016/j.biopsych.2016.04.020. Epub 2016 May 6.
31. Antioxidant N-acetylcysteine attenuates the reduction of Brg1 protein expression in the myocardium of type 1 diabetic rats. Xu J, etal., J Diabetes Res. 2013;2013:716219. doi: 10.1155/2013/716219. Epub 2013 Jun 18.
32. Olig2 targets chromatin remodelers to enhancers to initiate oligodendrocyte differentiation. Yu Y, etal., Cell. 2013 Jan 17;152(1-2):248-61. doi: 10.1016/j.cell.2012.12.006.
33. Overexpression of Brg1 alleviates high glucose-induced retinal ganglion cell apoptosis though regulating Notch/Hes1 signaling. Zhang X, etal., Biochem Biophys Res Commun. 2019 Jul 5;514(4):1160-1166. doi: 10.1016/j.bbrc.2019.05.069. Epub 2019 May 15.
34. Genetic variant in SWI/SNF complexes influences hepatocellular carcinoma risk: a new clue for the contribution of chromatin remodeling in carcinogenesis. Zhong R, etal., Sci Rep. 2014 Feb 21;4:4147. doi: 10.1038/srep04147.
Additional References at PubMed
PMID:8208605   PMID:8232556   PMID:8804307   PMID:9603422   PMID:10318760   PMID:10943845   PMID:11078522   PMID:11163203   PMID:11726552   PMID:11950834   PMID:12065415   PMID:12368262  
PMID:12477932   PMID:12917342   PMID:15565649   PMID:15767674   PMID:15774904   PMID:16192310   PMID:16217013   PMID:16245309   PMID:16287714   PMID:16330018   PMID:16687403   PMID:16787967  
PMID:16880268   PMID:17074803   PMID:17582821   PMID:17640523   PMID:17666433   PMID:17938176   PMID:18267097   PMID:18487222   PMID:18816825   PMID:19342595   PMID:19571879   PMID:19946888  
PMID:20176728   PMID:20418909   PMID:21118511   PMID:22162999   PMID:22368283   PMID:22513373   PMID:22664934   PMID:23319608   PMID:23785148   PMID:24335282   PMID:25119045   PMID:25569094  
PMID:25633415   PMID:25807483   PMID:26138476   PMID:26582913   PMID:29374058   PMID:31939625   PMID:32987653   PMID:38679350  


Genomics

Comparative Map Data
Smarca4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8828,438,370 - 28,535,071 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl828,443,810 - 28,535,070 (+)EnsemblGRCr8
mRatBN7.2820,167,717 - 20,258,975 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,167,717 - 20,258,975 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx824,200,412 - 24,292,032 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0822,495,960 - 22,587,578 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0820,397,343 - 20,488,586 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,648,323 - 22,739,468 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,648,323 - 22,739,468 (+)Ensemblrn6Rnor6.0
Rnor_5.0822,702,277 - 22,793,519 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4820,720,915 - 20,812,157 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera821,558,796 - 21,650,002 (+)NCBICelera
RGSC_v3.1820,787,909 - 20,796,297 (+)NCBI
Cytogenetic Map8q13NCBI
SMARCA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381910,961,030 - 11,062,273 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1910,960,824 - 11,079,426 (+)Ensemblhg38GRCh38
GRCh371911,071,706 - 11,172,949 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,932,606 - 11,033,953 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341910,932,605 - 11,033,953NCBI
Celera1910,966,440 - 11,067,798 (+)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef1910,649,456 - 10,749,943 (+)NCBIHuRef
CHM1_11911,072,949 - 11,174,225 (+)NCBICHM1_1
T2T-CHM13v2.01911,088,037 - 11,189,277 (+)NCBIT2T-CHM13v2.0
Smarca4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39921,527,377 - 21,615,526 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl921,527,465 - 21,615,526 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38921,616,106 - 21,704,230 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,616,169 - 21,704,230 (+)Ensemblmm10GRCm38
MGSCv37921,420,613 - 21,508,674 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36921,366,571 - 21,453,769 (+)NCBIMGSCv36mm8
Celera918,885,790 - 18,973,851 (+)NCBICelera
Cytogenetic Map9A3NCBI
cM Map97.84NCBI
Smarca4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554952,021,566 - 2,105,397 (+)Ensembl
ChiLan1.0NW_0049554952,021,671 - 2,105,155 (+)NCBIChiLan1.0ChiLan1.0
SMARCA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22015,881,885 - 15,982,873 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11914,880,580 - 14,981,524 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01910,515,216 - 10,616,155 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11911,250,006 - 11,334,952 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1911,250,006 - 11,334,952 (+)EnsemblpanPan2panpan1.1
SMARCA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12050,175,489 - 50,268,865 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2050,175,687 - 50,268,836 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2050,049,076 - 50,142,476 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02050,696,689 - 50,790,220 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2050,696,700 - 50,790,215 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12049,906,864 - 50,000,228 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02050,333,903 - 50,427,442 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02050,576,222 - 50,669,723 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Smarca4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,107,992 - 209,201,474 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366591,169,792 - 1,249,213 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366591,152,846 - 1,246,718 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMARCA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl269,662,238 - 69,810,295 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1269,717,175 - 69,810,301 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2270,151,823 - 70,182,978 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMARCA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.169,943,162 - 10,044,476 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660749,892,049 - 9,994,184 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smarca4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248282,893,096 - 2,985,968 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248282,893,075 - 2,985,968 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Smarca4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1817,885,953 - 17,977,507 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Smarca4
779 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:71
Interacting mature miRNAs:82
Transcripts:ENSRNOT00000013165
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

Markers in Region
AI111450  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,258,676 - 20,258,891 (+)MAPPERmRatBN7.2
Rnor_6.0822,739,170 - 22,739,384NCBIRnor6.0
Rnor_5.0822,793,221 - 22,793,435UniSTSRnor5.0
RGSC_v3.4820,811,859 - 20,812,073UniSTSRGSC3.4
Celera821,649,704 - 21,649,918UniSTS
Cytogenetic Map8q13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_134368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242601 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063264830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063264831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063264832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063264833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063264834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063264835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063264836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC120728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ504723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC169035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X99723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000013165   ⟹   ENSRNOP00000013166
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl828,443,869 - 28,535,068 (+)Ensembl
mRatBN7.2 Ensembl820,167,717 - 20,258,975 (+)Ensembl
Rnor_6.0 Ensembl822,648,323 - 22,739,468 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000097065   ⟹   ENSRNOP00000081001
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl828,443,819 - 28,533,092 (+)Ensembl
mRatBN7.2 Ensembl820,167,717 - 20,256,996 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000140415   ⟹   ENSRNOP00000107457
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl828,443,810 - 28,535,070 (+)Ensembl
RefSeq Acc Id: NM_134368   ⟹   NP_599195
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,443,819 - 28,535,071 (+)NCBI
mRatBN7.2820,167,717 - 20,258,975 (+)NCBI
Rnor_6.0822,648,323 - 22,739,468 (+)NCBI
Rnor_5.0822,702,277 - 22,793,519 (+)NCBI
RGSC_v3.4820,720,915 - 20,812,157 (+)RGD
Celera821,558,796 - 21,650,002 (+)RGD
Sequence:
RefSeq Acc Id: XM_006242598   ⟹   XP_006242660
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,438,370 - 28,535,068 (+)NCBI
mRatBN7.2820,167,720 - 20,258,975 (+)NCBI
Rnor_6.0822,648,326 - 22,739,468 (+)NCBI
Rnor_5.0822,702,277 - 22,793,519 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006242599   ⟹   XP_006242661
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,438,370 - 28,535,068 (+)NCBI
mRatBN7.2820,167,720 - 20,258,975 (+)NCBI
Rnor_6.0822,648,326 - 22,739,468 (+)NCBI
Rnor_5.0822,702,277 - 22,793,519 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006242601   ⟹   XP_006242663
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,438,370 - 28,535,068 (+)NCBI
mRatBN7.2820,167,720 - 20,258,975 (+)NCBI
Rnor_6.0822,648,326 - 22,739,468 (+)NCBI
Rnor_5.0822,702,277 - 22,793,519 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063264830   ⟹   XP_063120900
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,438,370 - 28,535,068 (+)NCBI
RefSeq Acc Id: XM_063264831   ⟹   XP_063120901
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,444,515 - 28,535,068 (+)NCBI
RefSeq Acc Id: XM_063264832   ⟹   XP_063120902
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,438,370 - 28,535,068 (+)NCBI
RefSeq Acc Id: XM_063264833   ⟹   XP_063120903
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,438,370 - 28,535,068 (+)NCBI
RefSeq Acc Id: XM_063264834   ⟹   XP_063120904
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,438,370 - 28,535,068 (+)NCBI
RefSeq Acc Id: XM_063264835   ⟹   XP_063120905
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,444,252 - 28,535,068 (+)NCBI
RefSeq Acc Id: XM_063264836   ⟹   XP_063120906
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,444,515 - 28,535,068 (+)NCBI
RefSeq Acc Id: NP_599195   ⟸   NM_134368
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242660   ⟸   XM_006242598
- Peptide Label: isoform X3
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot),   G3V790 (UniProtKB/TrEMBL),   A6JNT8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242661   ⟸   XM_006242599
- Peptide Label: isoform X4
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242663   ⟸   XM_006242601
- Peptide Label: isoform X7
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot),   A6JNT9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000013166   ⟸   ENSRNOT00000013165
Ensembl Acc Id: ENSRNOP00000081001   ⟸   ENSRNOT00000097065
RefSeq Acc Id: XP_063120900   ⟸   XM_063264830
- Peptide Label: isoform X1
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063120902   ⟸   XM_063264832
- Peptide Label: isoform X2
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063120903   ⟸   XM_063264833
- Peptide Label: isoform X5
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063120904   ⟸   XM_063264834
- Peptide Label: isoform X6
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063120905   ⟸   XM_063264835
- Peptide Label: isoform X1
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063120906   ⟸   XM_063264836
- Peptide Label: isoform X1
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063120901   ⟸   XM_063264831
- Peptide Label: isoform X1
- UniProtKB: Q8K1P7 (UniProtKB/Swiss-Prot)
Ensembl Acc Id: ENSRNOP00000107457   ⟸   ENSRNOT00000140415
Protein Domains
Bromo   Helicase ATP-binding   Helicase C-terminal   HSA   QLQ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8K1P7-F1-model_v2 AlphaFold Q8K1P7 1-1613 view protein structure

Transcriptome

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

Promoters
RGD ID:13695785
Promoter ID:EPDNEW_R6310
Type:initiation region
Name:Smarca4_1
Description:SWI/SNF related, matrix associated, actin dependent regulatorof chromatin, subfamily a, member 4
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_6.0822,648,490 - 22,648,550EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621728 AgrOrtholog
BioCyc Gene G2FUF-31412 BioCyc
Ensembl Genes ENSRNOG00000009271 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000013165 ENTREZGENE
  ENSRNOT00000097065 ENTREZGENE
  ENSRNOT00000140415 ENTREZGENE
Gene3D-CATH 1.20.5.170 UniProtKB/Swiss-Prot
  1.20.920.10 UniProtKB/Swiss-Prot
  3.40.5.120 UniProtKB/Swiss-Prot
  3.40.50.10810 UniProtKB/Swiss-Prot
  3.40.50.300 UniProtKB/Swiss-Prot
InterPro BRG1 UniProtKB/Swiss-Prot
  BRK_domain UniProtKB/Swiss-Prot
  BRK_sf UniProtKB/Swiss-Prot
  Bromodomain UniProtKB/Swiss-Prot
  Bromodomain-like_sf UniProtKB/Swiss-Prot
  Bromodomain_CS UniProtKB/Swiss-Prot
  Gln-Leu-Gln_QLQ UniProtKB/Swiss-Prot
  Helicase_ATP-bd UniProtKB/Swiss-Prot
  Helicase_C UniProtKB/Swiss-Prot
  HSA_dom UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
  SnAC UniProtKB/Swiss-Prot
  SNF2-like_sf UniProtKB/Swiss-Prot
  SNF2/RAD54-like_C UniProtKB/Swiss-Prot
  SNF2_N UniProtKB/Swiss-Prot
NCBI Gene 171379 ENTREZGENE
PANTHER SNF2/RAD54 HELICASE FAMILY UniProtKB/Swiss-Prot
Pfam BRK UniProtKB/Swiss-Prot
  Bromodomain UniProtKB/Swiss-Prot
  Helicase_C UniProtKB/Swiss-Prot
  HSA UniProtKB/Swiss-Prot
  QLQ UniProtKB/Swiss-Prot
  SnAC UniProtKB/Swiss-Prot
  SNF2_N UniProtKB/Swiss-Prot
PhenoGen Smarca4 PhenoGen
PRINTS BROMODOMAIN UniProtKB/Swiss-Prot
PROSITE BROMODOMAIN_1 UniProtKB/Swiss-Prot
  BROMODOMAIN_2 UniProtKB/Swiss-Prot
  HELICASE_ATP_BIND_1 UniProtKB/Swiss-Prot
  HELICASE_CTER UniProtKB/Swiss-Prot
  HSA UniProtKB/Swiss-Prot
  QLQ UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000009271 RatGTEx
SMART BRK UniProtKB/Swiss-Prot
  BROMO UniProtKB/Swiss-Prot
  DEXDc UniProtKB/Swiss-Prot
  HELICc UniProtKB/Swiss-Prot
  HSA UniProtKB/Swiss-Prot
  QLQ UniProtKB/Swiss-Prot
  SnAC UniProtKB/Swiss-Prot
Superfamily-SCOP SSF160481 UniProtKB/Swiss-Prot
  SSF47370 UniProtKB/Swiss-Prot
  SSF52540 UniProtKB/Swiss-Prot
UniProt A0A8I6G5D7_RAT UniProtKB/TrEMBL
  A0ABK0LZQ0_RAT UniProtKB/TrEMBL
  A6JNT8 ENTREZGENE, UniProtKB/TrEMBL
  A6JNT9 ENTREZGENE, UniProtKB/TrEMBL
  B5DFE9_RAT UniProtKB/TrEMBL
  G3V790 ENTREZGENE, UniProtKB/TrEMBL
  Q8K1P7 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-11-08 Smarca4  SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4  Smarca4  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Smarca4  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Smarca4  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4      Symbol and Name status set to provisional 70820 PROVISIONAL