Smarce1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1) - Rat Genome Database

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Gene: Smarce1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1) Rattus norvegicus
Analyze
Symbol: Smarce1
Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1
RGD ID: 1304726
Description: Predicted to enable N-acetyltransferase activity; RNA binding activity; and nuclear receptor binding activity. Involved in negative regulation of DNA-templated transcription and spermatid development. Predicted to be located in nucleoplasm. Predicted to be part of SWI/SNF complex; nBAF complex; and npBAF complex. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 5; familial meningioma; and meningioma. Orthologous to human SMARCE1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1); PARTICIPATES IN SWI/SNF family mediated chromatin remodeling pathway; INTERACTS WITH 6-propyl-2-thiouracil; benzo[a]pyrene; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BAF57; BRG1-associated factor 57; LOC303518; RGD1304726; similar to RIKEN cDNA 6330509G02; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Smarce1-ps10   Smarce1-ps6  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81084,655,468 - 84,678,259 (-)NCBIGRCr8
mRatBN7.21084,159,270 - 84,180,547 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1084,159,275 - 84,179,989 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1089,103,140 - 89,123,847 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01088,601,260 - 88,621,968 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01083,993,326 - 84,013,905 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01087,116,827 - 87,138,890 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1087,116,827 - 87,137,965 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01086,912,863 - 86,934,554 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41088,104,643 - 88,127,707 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11927,930,282 - 27,931,646 (-)NCBI
Celera1082,899,032 - 82,919,746 (-)NCBICelera
Cytogenetic Map10q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nBAF complex  (ISO)
npBAF complex  (ISO)
nucleoplasm  (ISO)
nucleus  (IEA,ISO)
SWI/SNF complex  (IBA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. 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.
5. N-terminally truncated BAF57 isoforms contribute to the diversity of SWI/SNF complexes in neurons. Kazantseva A, etal., J Neurochem. 2009 May;109(3):807-18. doi: 10.1111/j.1471-4159.2009.06005.x. Epub 2009 Feb 20.
6. Targeted next-generation sequencing for differential diagnosis of neurofibromatosis type 2, schwannomatosis, and meningiomatosis. Louvrier C, etal., Neuro Oncol. 2018 Jun 18;20(7):917-929. doi: 10.1093/neuonc/noy009.
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. 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.
Additional References at PubMed
PMID:8804307   PMID:8895581   PMID:11078522   PMID:11726552   PMID:12368262   PMID:12477932   PMID:12917342   PMID:16217013   PMID:16287714   PMID:17363140   PMID:17640523   PMID:19781646  
PMID:21936910   PMID:24335282   PMID:31505169  


Genomics

Comparative Map Data
Smarce1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81084,655,468 - 84,678,259 (-)NCBIGRCr8
mRatBN7.21084,159,270 - 84,180,547 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1084,159,275 - 84,179,989 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1089,103,140 - 89,123,847 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01088,601,260 - 88,621,968 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01083,993,326 - 84,013,905 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01087,116,827 - 87,138,890 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1087,116,827 - 87,137,965 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01086,912,863 - 86,934,554 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41088,104,643 - 88,127,707 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11927,930,282 - 27,931,646 (-)NCBI
Celera1082,899,032 - 82,919,746 (-)NCBICelera
Cytogenetic Map10q31NCBI
SMARCE1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381740,624,962 - 40,647,818 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1740,624,962 - 40,648,654 (-)EnsemblGRCh38hg38GRCh38
GRCh371738,781,214 - 38,804,070 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361736,037,498 - 36,057,629 (-)NCBINCBI36Build 36hg18NCBI36
Build 341736,037,505 - 36,057,629NCBI
Celera1735,445,555 - 35,465,686 (-)NCBICelera
Cytogenetic Map17q21.2NCBI
HuRef1734,578,544 - 34,598,673 (-)NCBIHuRef
CHM1_11739,019,316 - 39,039,446 (-)NCBICHM1_1
T2T-CHM13v2.01741,489,340 - 41,512,196 (-)NCBIT2T-CHM13v2.0
Smarce1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391199,099,873 - 99,121,843 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1199,099,873 - 99,121,843 (-)EnsemblGRCm39 Ensembl
GRCm381199,209,047 - 99,231,017 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1199,209,047 - 99,231,017 (-)EnsemblGRCm38mm10GRCm38
MGSCv371199,070,361 - 99,092,331 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361199,025,137 - 99,047,107 (-)NCBIMGSCv36mm8
Celera11108,876,605 - 108,898,195 (-)NCBICelera
Cytogenetic Map11DNCBI
cM Map1162.92NCBI
Smarce1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545115,129,132 - 15,147,488 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545115,129,619 - 15,147,487 (-)NCBIChiLan1.0ChiLan1.0
SMARCE1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21924,301,208 - 24,322,471 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11726,192,677 - 26,217,200 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01716,633,982 - 16,660,502 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11716,860,098 - 16,884,946 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1716,860,400 - 16,884,946 (+)Ensemblpanpan1.1panPan2
SMARCE1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1922,015,402 - 22,036,424 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl922,015,600 - 22,035,442 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha921,488,381 - 21,509,366 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0922,808,541 - 22,829,536 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl922,808,728 - 22,829,536 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1921,582,974 - 21,603,940 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0921,841,783 - 21,862,772 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0921,966,284 - 21,987,292 (+)NCBIUU_Cfam_GSD_1.0
Smarce1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560221,415,651 - 21,435,591 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649015,638,526 - 15,659,706 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649015,638,546 - 15,659,372 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMARCE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1221,786,897 - 21,807,162 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11221,784,410 - 21,807,170 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21222,164,830 - 22,178,344 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMARCE1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11665,539,138 - 65,559,810 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1665,541,513 - 65,561,401 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607736,419,335 - 36,441,630 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smarce1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247952,714,525 - 2,729,961 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247952,712,524 - 2,730,028 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smarce1
111 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:29
Count of miRNA genes:22
Interacting mature miRNAs:29
Transcripts:ENSRNOT00000014230
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
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107563188787055282Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
724516Uae17Urinary albumin excretion QTL 173.6urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)107821062285220348Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)107889965587307728Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)107981378985160854Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108051528791230079Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108256485692369470Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108400727295933025Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108400727295933025Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108402232193995963Rat

Markers in Region
RH140914  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21084,159,357 - 84,159,555 (+)MAPPERmRatBN7.2
Rnor_6.01087,116,915 - 87,117,112NCBIRnor6.0
Rnor_5.01086,912,951 - 86,913,148UniSTSRnor5.0
RGSC_v3.41088,104,731 - 88,104,928UniSTSRGSC3.4
Celera1082,899,120 - 82,899,317UniSTS
RH 3.4 Map10859.5UniSTS
Cytogenetic Map10q32.1UniSTS
RH137042  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21084,159,290 - 84,159,507 (+)MAPPERmRatBN7.2
Rnor_6.01087,116,848 - 87,117,064NCBIRnor6.0
Rnor_5.01086,912,884 - 86,913,100UniSTSRnor5.0
RGSC_v3.41088,104,664 - 88,104,880UniSTSRGSC3.4
Celera1082,899,053 - 82,899,269UniSTS
RH 3.4 Map10858.8UniSTS
Cytogenetic Map10q32.1UniSTS
RH138775  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21084,181,723 - 84,181,910 (+)MAPPERmRatBN7.2
Rnor_6.01087,139,692 - 87,139,878NCBIRnor6.0
Rnor_5.01086,935,729 - 86,935,915UniSTSRnor5.0
RGSC_v3.41088,129,440 - 88,129,626UniSTSRGSC3.4
Celera1082,921,457 - 82,921,643UniSTS
RH 3.4 Map10860.5UniSTS
Cytogenetic Map10q32.1UniSTS


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 41 57 41 19 41 6 8 74 35 41 11 6
Low 2 2 3 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001024993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001399629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC096439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC091314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC092210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU327027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU327028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU327029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU327030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU327031 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000014230   ⟹   ENSRNOP00000014230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1084,159,275 - 84,179,989 (-)Ensembl
Rnor_6.0 Ensembl1087,117,887 - 87,136,026 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080617
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1087,126,966 - 87,137,965 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080836
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1087,117,888 - 87,137,965 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082494
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1087,126,966 - 87,137,965 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082605
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1087,121,344 - 87,128,924 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083233   ⟹   ENSRNOP00000074941
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1084,159,291 - 84,178,094 (-)Ensembl
Rnor_6.0 Ensembl1087,116,835 - 87,136,072 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085389
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1087,121,739 - 87,127,030 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086103
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1087,116,827 - 87,136,072 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087775
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1087,126,966 - 87,137,965 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089629
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1087,120,676 - 87,122,195 (-)Ensembl
RefSeq Acc Id: NM_001024993   ⟹   NP_001020164
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,655,468 - 84,676,173 (-)NCBI
mRatBN7.21084,159,270 - 84,179,977 (-)NCBI
Rnor_6.01087,116,827 - 87,137,959 (-)NCBI
Rnor_5.01086,912,863 - 86,934,554 (-)NCBI
RGSC_v3.41088,104,643 - 88,127,707 (-)RGD
Celera1082,899,032 - 82,919,746 (-)RGD
Sequence:
RefSeq Acc Id: NM_001399629   ⟹   NP_001386558
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,655,468 - 84,676,173 (-)NCBI
mRatBN7.21084,159,270 - 84,179,977 (-)NCBI
RefSeq Acc Id: XM_039086082   ⟹   XP_038942010
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,655,468 - 84,678,259 (-)NCBI
mRatBN7.21084,159,270 - 84,180,547 (-)NCBI
RefSeq Acc Id: XM_039086083   ⟹   XP_038942011
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,655,468 - 84,678,259 (-)NCBI
mRatBN7.21084,159,270 - 84,179,972 (-)NCBI
RefSeq Acc Id: XM_039086084   ⟹   XP_038942012
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,655,468 - 84,676,172 (-)NCBI
mRatBN7.21084,159,270 - 84,180,006 (-)NCBI
RefSeq Acc Id: XM_039086085   ⟹   XP_038942013
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,655,468 - 84,678,259 (-)NCBI
mRatBN7.21084,160,141 - 84,180,269 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001020164   ⟸   NM_001024993
- Peptide Label: isoform 2
- UniProtKB: C0IMX6 (UniProtKB/Swiss-Prot),   C0IMX5 (UniProtKB/Swiss-Prot),   C0IMX4 (UniProtKB/Swiss-Prot),   Q5BJV2 (UniProtKB/Swiss-Prot),   Q56A18 (UniProtKB/Swiss-Prot),   E9PU44 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000014230   ⟸   ENSRNOT00000014230
RefSeq Acc Id: ENSRNOP00000074941   ⟸   ENSRNOT00000083233
RefSeq Acc Id: XP_038942010   ⟸   XM_039086082
- Peptide Label: isoform X2
- UniProtKB: A6HIX0 (UniProtKB/TrEMBL),   E9PU44 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942012   ⟸   XM_039086084
- Peptide Label: isoform X2
- UniProtKB: A6HIX0 (UniProtKB/TrEMBL),   E9PU44 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942011   ⟸   XM_039086083
- Peptide Label: isoform X2
- UniProtKB: A6HIX0 (UniProtKB/TrEMBL),   E9PU44 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942013   ⟸   XM_039086085
- Peptide Label: isoform X1
- UniProtKB: E9PU44 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001386558   ⟸   NM_001399629
- Peptide Label: isoform 1
- UniProtKB: A6HIW9 (UniProtKB/TrEMBL)
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q56A18-F1-model_v2 AlphaFold Q56A18 1-376 view protein structure

Transcriptome

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

Promoters
RGD ID:13697682
Promoter ID:EPDNEW_R8203
Type:multiple initiation site
Name:Smarce1_1
Description:SWI/SNF related, matrix associated, actin dependent regulatorof chromatin, subfamily e, member 1
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_6.01087,137,947 - 87,138,007EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304726 AgrOrtholog
BioCyc Gene G2FUF-23318 BioCyc
Ensembl Genes ENSRNOG00000010676 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055033308 UniProtKB/Swiss-Prot
  ENSRNOG00060021983 UniProtKB/Swiss-Prot
  ENSRNOG00065026498 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014230 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000014230.8 UniProtKB/Swiss-Prot
  ENSRNOT00000083233 ENTREZGENE
  ENSRNOT00000083233.2 UniProtKB/TrEMBL
  ENSRNOT00055057573 UniProtKB/Swiss-Prot
  ENSRNOT00060038207 UniProtKB/Swiss-Prot
  ENSRNOT00065045922 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7311688 IMAGE-MGC_LOAD
  IMAGE:7312354 IMAGE-MGC_LOAD
InterPro HMG_box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:303518 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105577 IMAGE-MGC_LOAD
  MGC:109283 IMAGE-MGC_LOAD
NCBI Gene 303518 ENTREZGENE
PANTHER PTHR46232 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY E MEMBER 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Smarce1 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010676 RatGTEx
  ENSRNOG00055033308 RatGTEx
  ENSRNOG00060021983 RatGTEx
  ENSRNOG00065026498 RatGTEx
SMART HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K9C1_RAT UniProtKB/TrEMBL
  A6HIW9 ENTREZGENE, UniProtKB/TrEMBL
  A6HIX0 ENTREZGENE, UniProtKB/TrEMBL
  C0IMX4 ENTREZGENE
  C0IMX5 ENTREZGENE
  C0IMX6 ENTREZGENE
  E9PU44 ENTREZGENE, UniProtKB/TrEMBL
  Q56A18 ENTREZGENE
  Q5BJV2 ENTREZGENE
  SMCE1_RAT UniProtKB/Swiss-Prot
UniProt Secondary C0IMX4 UniProtKB/Swiss-Prot
  C0IMX5 UniProtKB/Swiss-Prot
  C0IMX6 UniProtKB/Swiss-Prot
  Q5BJV2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Smarce1  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1  RGD1304726  similar to RIKEN cDNA 6330509G02  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1304726  similar to RIKEN cDNA 6330509G02  RGD1304726_predicted  similar to RIKEN cDNA 6330509G02 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1304726_predicted  similar to RIKEN cDNA 6330509G02 (predicted)  LOC303518_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC303518_predicted  similar to RIKEN cDNA 6330509G02 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL