Smarca4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4) - Rat Genome Database

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Gene: Smarca4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4) Rattus norvegicus
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Symbol: Smarca4
Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
RGD ID: 621728
Description: Enables chromatin binding activity. Involved in chromatin organization; negative regulation of transcription, DNA-templated; and spermatid development. Located in nucleus. 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; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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; transcription activator BRG1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2820,167,717 - 20,258,975 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl820,167,717 - 20,258,975 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (EXP)
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)
bicalutamide  (ISO)
bisphenol A  (EXP)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
chloroprene  (EXP)
choline  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cyproconazole  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
diarsenic trioxide  (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)
fulvestrant  (ISO)
gallic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glucose  (ISO)
hexadecanoic acid  (ISO)
hydrazine  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP,ISO)
methylseleninic acid  (ISO)
motexafin gadolinium  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
phenobarbital  (EXP,ISO)
poly(propylene imine) macromolecule  (ISO)
promegestone  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP,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  (IBA,IDA,IEA,ISO)
coronary vasculature development  (ISO)
definitive erythrocyte differentiation  (ISO)
DNA methylation on cytosine within a CG sequence  (ISO)
DNA methylation-dependent heterochromatin assembly  (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)
hindbrain development  (ISO)
histone H3 acetylation  (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 transcription by RNA polymerase II  (ISO)
negative regulation of transcription, DNA-templated  (IEA,IMP,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 DNA binding  (ISO)
positive regulation of DNA-binding transcription factor activity  (IEA,ISO)
positive regulation of glucose mediated signaling pathway  (IEA,ISO)
positive regulation of pri-miRNA transcription by RNA polymerase II  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IBA,ISO,ISS)
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I  (IEA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of Wnt signaling pathway  (IEA,ISO)
regulation of cell migration  (ISO)
RNA polymerase I preinitiation complex assembly  (IEA)
spermatid development  (IEP)
stem cell population maintenance  (ISO)
vasculogenesis  (ISO)
ventricular septum development  (ISO)

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

References

References - curated
1. Battaglioli E, etal., J Biol Chem. 2002 Oct 25;277(43):41038-45. Epub 2002 Aug 20.
2. Dhar S, etal., J Biol Chem. 2012 Feb 24;287(9):6387-405. doi: 10.1074/jbc.M111.288167. Epub 2012 Jan 3.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Gebuhr TC, etal., J Exp Med 2003 Dec 15;198(12):1937-49.
5. Gordon MD and Nusse R, J Biol Chem. 2006 Aug 11;281(32):22429-33. Epub 2006 Jun 22.
6. Hargreaves DC and Crabtree GR, Cell Res. 2011 Mar;21(3):396-420. doi: 10.1038/cr.2011.32. Epub 2011 Mar 1.
7. Inayoshi Y, etal., J Biochem. 2006 Feb;139(2):177-88.
8. Jenkins BD, etal., Trends Endocrinol Metab. 2001 Apr;12(3):122-6.
9. Kadoch C and Crabtree GR, Cell. 2013 Mar 28;153(1):71-85. doi: 10.1016/j.cell.2013.02.036.
10. Medina PP, etal., Genes Chromosomes Cancer. 2004 Oct;41(2):170-7.
11. Mehrotra A, etal., J Cell Physiol. 2013 Dec;228(12):2337-42. doi: 10.1002/jcp.24404.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. OMIM Disease Annotation Pipeline
15. Ostlund Farrants AK, etal., Mol Cell Biol 1997 Feb;17(2):895-905.
16. Qiu Z and Ghosh A, Neuron. 2008 Dec 10;60(5):775-87. doi: 10.1016/j.neuron.2008.09.040.
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. 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. Shain AH and Pollack JR, PLoS One. 2013;8(1):e55119. doi: 10.1371/journal.pone.0055119. Epub 2013 Jan 23.
22. Sun A, etal., Prostate. 2007 Feb 1;67(2):203-13.
23. Valdman A, etal., Int J Oncol. 2003 May;22(5):1003-7.
24. Wang W, etal., EMBO J. 1996 Oct 1;15(19):5370-82.
25. Xu J, etal., J Diabetes Res. 2013;2013:716219. doi: 10.1155/2013/716219. Epub 2013 Jun 18.
26. Yu Y, etal., Cell. 2013 Jan 17;152(1-2):248-61. doi: 10.1016/j.cell.2012.12.006.
27. 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:16322236   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  


Genomics

Comparative Map Data
Smarca4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2820,167,717 - 20,258,975 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl820,167,717 - 20,258,975 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl1910,960,932 - 11,079,426 (+)EnsemblGRCh38hg38GRCh38
GRCh381910,960,999 - 11,062,277 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371911,071,706 - 11,172,949 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,932,606 - 11,033,953 (+)NCBINCBI36hg18NCBI36
Build 341910,932,605 - 11,033,953NCBI
Celera1910,966,440 - 11,067,798 (+)NCBI
Cytogenetic Map19p13.2NCBI
HuRef1910,649,456 - 10,749,943 (+)NCBIHuRef
CHM1_11911,072,949 - 11,174,225 (+)NCBICHM1_1
Smarca4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39921,527,377 - 21,615,526 (+)NCBIGRCm39mm39
GRCm39 Ensembl921,527,465 - 21,615,526 (+)Ensembl
GRCm38921,616,106 - 21,704,230 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,616,169 - 21,704,230 (+)EnsemblGRCm38mm10GRCm38
MGSCv37921,420,613 - 21,508,674 (+)NCBIGRCm37mm9NCBIm37
MGSCv36921,366,571 - 21,453,769 (+)NCBImm8
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
PanPan1.11911,250,006 - 11,334,952 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1911,250,006 - 11,334,952 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01910,515,216 - 10,616,155 (+)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.02050,696,689 - 50,790,220 (-)NCBI
UMICH_Zoey_3.12049,906,864 - 50,000,228 (-)NCBI
UNSW_CanFamBas_1.02050,333,903 - 50,427,442 (-)NCBI
UU_Cfam_GSD_1.02050,576,222 - 50,669,723 (-)NCBI
Smarca4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,107,992 - 209,201,474 (-)NCBI
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 - 69,810,298 (+)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 (+)NCBI
Vero_WHO_p1.0NW_0236660749,892,049 - 9,994,184 (-)NCBI
Smarca4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248282,893,075 - 2,985,968 (+)NCBI

Position Markers
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


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

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.


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_134368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242596 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242597 (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_006242600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242601 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080751 (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
  JACYVU010000190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X99723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000013165   ⟹   ENSRNOP00000013166
RefSeq Status:
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
RefSeq Acc Id: ENSRNOT00000097065   ⟹   ENSRNOP00000081001
RefSeq Status:
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
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_006242596   ⟹   XP_006242658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_006242597   ⟹   XP_006242659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_006242598   ⟹   XP_006242660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_006242600   ⟹   XP_006242662
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_017595429   ⟹   XP_017450918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,168,198 - 20,258,975 (+)NCBI
Rnor_6.0822,648,754 - 22,739,468 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039080750   ⟹   XP_038936678
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,174,365 - 20,258,975 (+)NCBI
RefSeq Acc Id: XM_039080751   ⟹   XP_038936679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,167,720 - 20,234,712 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_599195   ⟸   NM_134368
- UniProtKB: G3V790 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242658   ⟸   XM_006242596
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006242659   ⟸   XM_006242597
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006242660   ⟸   XM_006242598
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006242661   ⟸   XM_006242599
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006242662   ⟸   XM_006242600
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006242663   ⟸   XM_006242601
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017450918   ⟸   XM_017595429
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000013166   ⟸   ENSRNOT00000013165
RefSeq Acc Id: XP_038936679   ⟸   XM_039080751
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038936678   ⟸   XM_039080750
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000081001   ⟸   ENSRNOT00000097065
Protein Domains
Bromo   Helicase ATP-binding   Helicase C-terminal   HSA   QLQ

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621728 AgrOrtholog
Ensembl Genes ENSRNOG00000009271 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013166 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013165 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.920.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.20.28.130 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.10810 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_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171379 UniProtKB/TrEMBL
NCBI Gene 171379 ENTREZGENE
PANTHER PTHR10799:SF76 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
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 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
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