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. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 4; hepatocellular carcinoma; lung non-small cell carcinoma; and rhabdoid cancer. Orthologous to human SMARCA4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8828,438,370 - 28,535,071 (+)NCBIGRCr8
mRatBN7.2820,167,717 - 20,258,975 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,167,717 - 20,258,975 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx824,200,412 - 24,292,032 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0822,495,960 - 22,587,578 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0820,397,343 - 20,488,586 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,648,323 - 22,739,468 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,648,323 - 22,739,468 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,702,277 - 22,793,519 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4820,720,915 - 20,812,157 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1820,787,909 - 20,796,297 (+)NCBI
Celera821,558,796 - 21,650,002 (+)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)
bisphenol A  (EXP)
C60 fullerene  (EXP)
caffeine  (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)
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)
methapyrilene  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP,ISO)
methylseleninic acid  (ISO)
motexafin gadolinium  (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 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)
chromatin remodeling  (IDA,IEA,ISO)
coronary vasculature development  (ISO)
definitive erythrocyte differentiation  (ISO)
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)
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 transcription by RNA polymerase II  (ISO)
nervous system development  (ISO)
neural retina development  (IEA,ISO)
neurogenesis  (ISO)
nucleosome disassembly  (IDA,IEA,ISO)
outflow tract morphogenesis  (ISO)
pharyngeal arch artery morphogenesis  (ISO)
positive regulation by host of viral transcription  (IEA,ISO)
positive regulation of cell differentiation  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cold-induced thermogenesis  (ISO)
positive regulation of DNA-binding transcription factor activity  (ISO)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of glucose mediated signaling pathway  (IEA,ISO)
positive regulation of miRNA transcription  (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)
primitive erythrocyte differentiation  (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 by RNA polymerase II  (ISO)
transcription initiation-coupled chromatin remodeling  (ISO)
vasculogenesis  (ISO)
ventricular septum development  (ISO)

Cellular Component
chromatin  (IBA,ISO)
euchromatin  (ISO)
fibrillar center  (IEA,ISO)
male germ cell nucleus  (ISO)
nBAF complex  (ISO,ISS)
npBAF complex  (IEA,ISO,ISS)
nucleolus  (ISO)
nucleoplasm  (IEA,ISO,TAS)
nucleus  (IBA,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. 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.
11. 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.
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
15. 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.
16. 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.
17. GOA pipeline RGD automated data pipeline
18. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
20. 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.
21. 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.
22. 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.
23. Mutation analysis of the BRG1 gene in prostate cancer clinical samples. Valdman A, etal., Int J Oncol. 2003 May;22(5):1003-7.
24. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. Wang W, etal., EMBO J. 1996 Oct 1;15(19):5370-82.
25. 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.
26. 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.
27. 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:25532521  
PMID:25569094   PMID:25633415   PMID:25807483   PMID:25972460   PMID:26138476   PMID:26388265   PMID:26582913   PMID:27422367   PMID:29374058   PMID:30973285   PMID:31939625   PMID:32105681  
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 (+)NCBIGRCr8
mRatBN7.2820,167,717 - 20,258,975 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,167,717 - 20,258,975 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx824,200,412 - 24,292,032 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0822,495,960 - 22,587,578 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0820,397,343 - 20,488,586 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,648,323 - 22,739,468 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,648,323 - 22,739,468 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,702,277 - 22,793,519 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4820,720,915 - 20,812,157 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1820,787,909 - 20,796,297 (+)NCBI
Celera821,558,796 - 21,650,002 (+)NCBICelera
Cytogenetic Map8q13NCBI
SMARCA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381910,961,030 - 11,062,273 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1910,960,932 - 11,079,426 (+)EnsemblGRCh38hg38GRCh38
GRCh371911,071,706 - 11,172,949 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,932,606 - 11,033,953 (+)NCBINCBI36Build 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 Ensembl
GRCm38921,616,106 - 21,704,230 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,616,169 - 21,704,230 (+)EnsemblGRCm38mm10GRCm38
MGSCv37921,420,613 - 21,508,674 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2050,049,076 - 50,142,476 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02050,696,689 - 50,790,220 (-)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248282,893,075 - 2,985,968 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smarca4
259 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat

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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

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
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
mRatBN7.2 Ensembl820,167,717 - 20,256,996 (+)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
RefSeq Acc Id: XP_063120902   ⟸   XM_063264832
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063120903   ⟸   XM_063264833
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063120904   ⟸   XM_063264834
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063120905   ⟸   XM_063264835
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063120906   ⟸   XM_063264836
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063120901   ⟸   XM_063264831
- Peptide Label: isoform X1
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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013165.7 UniProtKB/TrEMBL
  ENSRNOT00000097065.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.20.920.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.5.120 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.10810 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro BRG1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BRK_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BRK_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Bromodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Bromodomain-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Bromodomain_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Gln-Leu-Gln_QLQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HSA_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SnAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2/RAD54-like_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 171379 ENTREZGENE
PANTHER PTHR10799:SF76 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2/RAD54 HELICASE FAMILY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam BRK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Bromodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HSA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  QLQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SnAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Smarca4 PhenoGen
PRINTS BROMODOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE BROMODOMAIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BROMODOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HSA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  QLQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009271 RatGTEx
SMART BRK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BROMO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEXDc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HSA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  QLQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SnAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF160481 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47370 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6G5D7_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