Smarcc2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2) - Rat Genome Database

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Gene: Smarcc2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2) Rattus norvegicus
Analyze
Symbol: Smarcc2
Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2
RGD ID: 1597704
Description: Predicted to enable chromatin binding activity and histone binding activity. Involved in negative regulation of DNA-templated transcription. 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 8. Orthologous to human SMARCC2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2); PARTICIPATES IN SWI/SNF family mediated chromatin remodeling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; fenvalerate.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC685179; similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2; SWI/SNF complex subunit SMARCC2
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
mRatBN7.27881,844 - 910,090 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7881,421 - 909,978 (+)Ensembl
Rnor_6.072,875,898 - 2,905,463 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,875,909 - 2,904,453 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,851,993 - 2,880,204 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,743,425 - 1,771,951 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7754,570 - 783,204 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. 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.
3. 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.
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
8. 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.
9. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. Wang W, etal., EMBO J. 1996 Oct 1;15(19):5370-82.
Additional References at PubMed
PMID:8804307   PMID:10078207   PMID:11018012   PMID:11078522   PMID:11726552   PMID:12368262   PMID:16217013   PMID:17640523   PMID:23643363   PMID:23785148   PMID:24335282   PMID:26514267  
PMID:31505169  


Genomics

Comparative Map Data
Smarcc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27881,844 - 910,090 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7881,421 - 909,978 (+)Ensembl
Rnor_6.072,875,898 - 2,905,463 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,875,909 - 2,904,453 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,851,993 - 2,880,204 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,743,425 - 1,771,951 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7754,570 - 783,204 (+)NCBICelera
Cytogenetic Map7q11NCBI
SMARCC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381256,162,359 - 56,189,483 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1256,162,359 - 56,189,567 (-)EnsemblGRCh38hg38GRCh38
GRCh371256,556,143 - 56,583,267 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361254,843,379 - 54,869,544 (-)NCBINCBI36hg18NCBI36
Build 341254,843,390 - 54,869,544NCBI
Celera1256,207,780 - 56,235,494 (-)NCBI
Cytogenetic Map12q13.2NCBI
HuRef1253,594,695 - 53,620,204 (-)NCBIHuRef
CHM1_11256,523,019 - 56,550,728 (-)NCBICHM1_1
T2T-CHM13v2.01256,129,971 - 56,157,086 (-)NCBI
Smarcc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,294,823 - 128,326,460 (+)NCBIGRCm39mm39
GRCm39 Ensembl10128,295,117 - 128,326,351 (+)Ensembl
GRCm3810128,459,182 - 128,490,591 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,459,248 - 128,490,482 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710127,896,292 - 127,927,230 (+)NCBIGRCm37mm9NCBIm37
MGSCv3610127,862,243 - 127,893,121 (+)NCBImm8
Celera10130,853,448 - 130,882,127 (+)NCBICelera
Cytogenetic Map10D3NCBI
Smarcc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554583,764,823 - 3,787,901 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554583,764,823 - 3,787,159 (-)NCBIChiLan1.0ChiLan1.0
SMARCC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11232,977,917 - 33,004,144 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1232,977,879 - 33,004,144 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01232,726,150 - 32,753,366 (+)NCBIMhudiblu_PPA_v0panPan3
SMARCC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110481,504 - 502,914 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl10481,817 - 501,551 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10545,013 - 566,990 (-)NCBI
ROS_Cfam_1.010490,173 - 512,172 (-)NCBI
ROS_Cfam_1.0 Ensembl10490,179 - 512,125 (-)Ensembl
UMICH_Zoey_3.110467,623 - 489,601 (-)NCBI
UNSW_CanFamBas_1.010710,697 - 732,674 (-)NCBI
UU_Cfam_GSD_1.010834,753 - 856,729 (-)NCBI
Smarcc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,277,454 - 58,298,490 (+)NCBI
SpeTri2.0NW_004936646571,745 - 594,365 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMARCC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,563,400 - 21,586,737 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,563,426 - 21,586,790 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2523,227,371 - 23,250,183 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMARCC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11152,103,075 - 52,131,070 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1152,104,345 - 52,131,079 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037193,853,224 - 193,881,291 (+)NCBIVero_WHO_p1.0
Smarcc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480211,821,615 - 11,845,403 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462480211,821,686 - 11,845,407 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:166
Count of miRNA genes:65
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000028244, ENSRNOT00000061933
Prediction methods:Microtar, 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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028244   ⟹   ENSRNOP00000028244
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7881,933 - 909,939 (+)Ensembl
Rnor_6.0 Ensembl72,875,909 - 2,904,453 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097786   ⟹   ENSRNOP00000091991
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7881,421 - 909,978 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100913   ⟹   ENSRNOP00000086212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7881,421 - 909,978 (+)Ensembl
RefSeq Acc Id: XM_001055673   ⟹   XP_001055673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27881,846 - 910,090 (+)NCBI
Rnor_6.072,875,900 - 2,905,463 (+)NCBI
Rnor_5.072,851,993 - 2,880,204 (+)NCBI
RGSC_v3.471,743,425 - 1,771,951 (+)RGD
Sequence:
RefSeq Acc Id: XM_001055738   ⟹   XP_001055738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27881,847 - 910,090 (+)NCBI
Rnor_6.072,875,900 - 2,905,463 (+)NCBI
Rnor_5.072,851,993 - 2,880,204 (+)NCBI
RGSC_v3.471,743,425 - 1,771,951 (+)RGD
Sequence:
RefSeq Acc Id: XM_001055795   ⟹   XP_001055795
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27881,846 - 910,090 (+)NCBI
Rnor_6.072,875,898 - 2,905,463 (+)NCBI
Rnor_5.072,851,993 - 2,880,204 (+)NCBI
RGSC_v3.471,743,425 - 1,771,951 (+)RGD
Sequence:
RefSeq Acc Id: XM_002729767   ⟹   XP_002729813
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27881,845 - 910,090 (+)NCBI
Rnor_6.072,875,898 - 2,905,463 (+)NCBI
Rnor_5.072,851,993 - 2,880,204 (+)NCBI
RGSC_v3.471,743,425 - 1,771,951 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240805   ⟹   XP_006240867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27881,844 - 910,090 (+)NCBI
Rnor_6.072,875,898 - 2,905,463 (+)NCBI
Rnor_5.072,851,993 - 2,880,204 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006240806   ⟹   XP_006240868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27881,844 - 910,090 (+)NCBI
Rnor_6.072,875,898 - 2,905,463 (+)NCBI
Rnor_5.072,851,993 - 2,880,204 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006240807   ⟹   XP_006240869
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27881,845 - 910,090 (+)NCBI
Rnor_6.072,875,898 - 2,905,463 (+)NCBI
Rnor_5.072,851,993 - 2,880,204 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039079999   ⟹   XP_038935927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27881,845 - 910,090 (+)NCBI
RefSeq Acc Id: XM_039080000   ⟹   XP_038935928
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27881,942 - 910,090 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_002729813   ⟸   XM_002729767
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_001055673   ⟸   XM_001055673
- Peptide Label: isoform X7
- UniProtKB: D4A510 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_001055795   ⟸   XM_001055795
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_001055738   ⟸   XM_001055738
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006240867   ⟸   XM_006240805
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006240868   ⟸   XM_006240806
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006240869   ⟸   XM_006240807
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000028244   ⟸   ENSRNOT00000028244
RefSeq Acc Id: XP_038935927   ⟸   XM_039079999
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038935928   ⟸   XM_039080000
- Peptide Label: isoform X8
RefSeq Acc Id: ENSRNOP00000091991   ⟸   ENSRNOT00000097786
RefSeq Acc Id: ENSRNOP00000086212   ⟸   ENSRNOT00000100913
Protein Domains
Myb-like   SANT   SWIRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A510-F1-model_v2 AlphaFold D4A510 1-1135 view protein structure

Transcriptome

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

Promoters
RGD ID:13694941
Promoter ID:EPDNEW_R5463
Type:multiple initiation site
Name:Smarcc2_1
Description:SWI/SNF related, matrix associated, actin dependent regulatorof chromatin, subfamily c, member 2
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_6.072,875,955 - 2,876,015EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
BUF/N (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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/Stm (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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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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
LEW/Crl (2019)
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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
LEXF10A/StmMcwi (2020)
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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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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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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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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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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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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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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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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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/NRrrcMcwi (2019)
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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
MR/N (2020)
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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
MWF/Hsd (2019)
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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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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
SHR/OlalpcvMcwi (2019)
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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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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
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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
WN/N (2020)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 2899523 2899524 C T snv WKY/NCrl (RGD)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 2874264 2874265 C T snv WKY/NCrl (KNAW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 1766007 1766008 C T snv WKY/NCrl (ICL)
7 1769147 1769148 A G snv HCR/2Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1597704 AgrOrtholog
BioCyc Gene G2FUF-35365 BioCyc
Ensembl Genes ENSRNOG00000031135 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000028244 ENTREZGENE
  ENSRNOP00000028244.8 UniProtKB/TrEMBL
  ENSRNOP00000086212 ENTREZGENE
  ENSRNOP00000086212.1 UniProtKB/TrEMBL
  ENSRNOP00000091991 ENTREZGENE
  ENSRNOP00000091991.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028244 ENTREZGENE
  ENSRNOT00000028244.8 UniProtKB/TrEMBL
  ENSRNOT00000097786 ENTREZGENE
  ENSRNOT00000097786.1 UniProtKB/TrEMBL
  ENSRNOT00000100913 ENTREZGENE
  ENSRNOT00000100913.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro BRCT_dom_sf UniProtKB/TrEMBL
  Chromodomain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Myb_dom UniProtKB/TrEMBL
  SANT_DNA-bd UniProtKB/TrEMBL
  SANT_eukarya UniProtKB/TrEMBL
  SMARCC2 UniProtKB/TrEMBL
  SMARCC_C UniProtKB/TrEMBL
  SMARCC_N UniProtKB/TrEMBL
  SWIRM UniProtKB/TrEMBL
  SWIRM-assoc UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:685179 UniProtKB/TrEMBL
NCBI Gene 685179 ENTREZGENE
PANTHER PTHR12802:SF105 UniProtKB/TrEMBL
Pfam Myb_DNA-binding UniProtKB/TrEMBL
  SWIRM UniProtKB/TrEMBL
  SWIRM-assoc_1 UniProtKB/TrEMBL
  SWIRM-assoc_2 UniProtKB/TrEMBL
  SWIRM-assoc_3 UniProtKB/TrEMBL
PhenoGen Smarcc2 PhenoGen
PROSITE MYB_LIKE UniProtKB/TrEMBL
  SANT UniProtKB/TrEMBL
  SWIRM UniProtKB/TrEMBL
SMART CHROMO UniProtKB/TrEMBL
  SANT UniProtKB/TrEMBL
Superfamily-SCOP BRCT UniProtKB/TrEMBL
  Homeodomain_like UniProtKB/TrEMBL
UniProt A0A8I6A5E1_RAT UniProtKB/TrEMBL
  A0A8I6AGR8_RAT UniProtKB/TrEMBL
  D4A510 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-21 Smarcc2  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2  LOC685179  similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC685179  similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2      Symbol and Name status set to provisional 70820 PROVISIONAL