Smarcal1 (Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1) - Rat Genome Database

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Gene: Smarcal1 (Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1) Rattus norvegicus
Analyze
Symbol: Smarcal1
Name: Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1
RGD ID: 1306134
Description: Predicted to have DNA-dependent ATPase activity and annealing helicase activity. Predicted to be involved in DNA metabolic process and regulation of transcription by RNA polymerase II. Predicted to colocalize with DNA replication factor A complex. Human ortholog(s) of this gene implicated in Schimke immuno-osseous dysplasia. Orthologous to human SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: hepA-related protein; hypothetical protein LOC690314; LOC316477; LOC690314; sucrose nonfermenting protein 2-like 1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2974,239,718 - 74,286,156 (+)NCBI
Rnor_6.0 Ensembl979,944,132 - 79,990,229 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0979,943,775 - 79,990,230 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0979,716,012 - 79,762,216 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4971,780,870 - 71,827,780 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1971,930,360 - 71,974,752 (+)NCBI
Celera971,834,400 - 71,880,797 (+)NCBICelera
Cytogenetic Map9q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8702927   PMID:10857751   PMID:12477932   PMID:18974355   PMID:19793862   PMID:19793863   PMID:22705370   PMID:26089390  


Genomics

Comparative Map Data
Smarcal1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2974,239,718 - 74,286,156 (+)NCBI
Rnor_6.0 Ensembl979,944,132 - 79,990,229 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0979,943,775 - 79,990,230 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0979,716,012 - 79,762,216 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4971,780,870 - 71,827,780 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1971,930,360 - 71,974,752 (+)NCBI
Celera971,834,400 - 71,880,797 (+)NCBICelera
Cytogenetic Map9q33NCBI
SMARCAL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2216,412,414 - 216,483,053 (+)EnsemblGRCh38hg38GRCh38
GRCh382216,412,484 - 216,483,053 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372217,277,207 - 217,347,776 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362216,986,820 - 217,056,021 (+)NCBINCBI36hg18NCBI36
Build 342217,104,083 - 217,173,278NCBI
Celera2211,045,111 - 211,115,648 (+)NCBI
Cytogenetic Map2q35NCBI
HuRef2209,131,595 - 209,202,094 (+)NCBIHuRef
CHM1_12217,282,680 - 217,353,309 (+)NCBICHM1_1
Smarcal1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39172,575,593 - 72,675,949 (+)NCBIGRCm39mm39
GRCm39 Ensembl172,622,410 - 72,672,293 (+)Ensembl
GRCm38172,536,695 - 72,636,790 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl172,583,251 - 72,633,134 (+)EnsemblGRCm38mm10GRCm38
MGSCv37172,629,825 - 72,683,364 (+)NCBIGRCm37mm9NCBIm37
MGSCv36172,516,478 - 72,566,341 (+)NCBImm8
Celera173,151,284 - 73,205,338 (+)NCBICelera
Cytogenetic Map1C3NCBI
cM Map136.72NCBI
Smarcal1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545316,719,931 - 16,784,709 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545316,724,286 - 16,784,129 (-)NCBIChiLan1.0ChiLan1.0
SMARCAL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B222,276,294 - 222,347,258 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B222,276,353 - 222,347,258 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B103,672,934 - 103,743,802 (+)NCBIMhudiblu_PPA_v0panPan3
SMARCAL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13723,364,941 - 23,425,206 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3723,367,220 - 23,419,248 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3724,193,550 - 24,253,982 (+)NCBI
ROS_Cfam_1.03723,392,255 - 23,452,837 (+)NCBI
UMICH_Zoey_3.13723,277,174 - 23,331,540 (+)NCBI
UNSW_CanFamBas_1.03723,229,412 - 23,289,770 (+)NCBI
UU_Cfam_GSD_1.03723,247,796 - 23,308,267 (+)NCBI
Smarcal1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303171,702,084 - 171,797,210 (+)NCBI
SpeTri2.0NW_004936586828,661 - 887,988 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMARCAL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15118,629,238 - 118,687,940 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115118,627,734 - 118,688,005 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215131,503,125 - 131,506,635 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMARCAL1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110102,253,187 - 102,319,356 (+)NCBI
ChlSab1.1 Ensembl10102,255,453 - 102,319,330 (+)Ensembl
Smarcal1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248238,645,340 - 8,708,039 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96081029882732466Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96173092382890620Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:8
Count of miRNA genes:4
Interacting mature miRNAs:4
Transcripts:ENSRNOT00000022459, ENSRNOT00000071856
Prediction methods:Miranda, Rnahybrid
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 26 28 16 19 16 48 25 40 11
Low 17 29 25 25 8 11 26 10 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022459   ⟹   ENSRNOP00000022459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl979,944,155 - 79,990,219 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000071856   ⟹   ENSRNOP00000064323
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl979,944,132 - 79,990,229 (+)Ensembl
RefSeq Acc Id: NM_001108222   ⟹   NP_001101692
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,240,218 - 74,286,156 (+)NCBI
Rnor_6.0979,944,132 - 79,990,229 (+)NCBI
Rnor_5.0979,716,012 - 79,762,216 (+)NCBI
RGSC_v3.4971,780,870 - 71,827,780 (+)RGD
Celera971,834,400 - 71,880,797 (+)RGD
Sequence:
RefSeq Acc Id: XM_006245212   ⟹   XP_006245274
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,239,724 - 74,286,150 (+)NCBI
Rnor_6.0979,943,775 - 79,990,230 (+)NCBI
Rnor_5.0979,716,012 - 79,762,216 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006245213   ⟹   XP_006245275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,240,603 - 74,286,150 (+)NCBI
Rnor_6.0979,944,305 - 79,990,230 (+)NCBI
Rnor_5.0979,716,012 - 79,762,216 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767235   ⟹   XP_008765457
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,240,469 - 74,286,150 (+)NCBI
Rnor_6.0979,944,305 - 79,990,230 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767236   ⟹   XP_008765458
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,239,718 - 74,286,150 (+)NCBI
Rnor_6.0979,943,775 - 79,990,230 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596474   ⟹   XP_017451963
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,241,934 - 74,286,150 (+)NCBI
Rnor_6.0979,944,305 - 79,990,230 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083659   ⟹   XP_038939587
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,240,431 - 74,286,150 (+)NCBI
RefSeq Acc Id: XM_039083661   ⟹   XP_038939589
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,240,603 - 74,286,150 (+)NCBI
RefSeq Acc Id: XM_039083662   ⟹   XP_038939590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,239,728 - 74,286,150 (+)NCBI
RefSeq Acc Id: XM_039083663   ⟹   XP_038939591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2974,240,479 - 74,286,150 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101692   ⟸   NM_001108222
- UniProtKB: B4F769 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245274   ⟸   XM_006245212
- Peptide Label: isoform X1
- UniProtKB: B4F769 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245275   ⟸   XM_006245213
- Peptide Label: isoform X1
- UniProtKB: B4F769 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008765458   ⟸   XM_008767236
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008765457   ⟸   XM_008767235
- Peptide Label: isoform X1
- UniProtKB: B4F769 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017451963   ⟸   XM_017596474
- Peptide Label: isoform X1
- UniProtKB: B4F769 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022459   ⟸   ENSRNOT00000022459
RefSeq Acc Id: ENSRNOP00000064323   ⟸   ENSRNOT00000071856
RefSeq Acc Id: XP_038939590   ⟸   XM_039083662
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038939587   ⟸   XM_039083659
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038939591   ⟸   XM_039083663
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038939589   ⟸   XM_039083661
- Peptide Label: isoform X4
Transcriptome

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

Promoters
RGD ID:13696738
Promoter ID:EPDNEW_R7262
Type:multiple initiation site
Name:Smarcal1_1
Description:Swi/SNF related matrix associated, actin dependent regulatorof chromatin, subfamily a-like 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_6.0979,944,134 - 79,944,194EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
F344/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
F344/NRrrc (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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
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)
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
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
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)
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
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
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/Ox (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
LE/Stm (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
LEW/Crl (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
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
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
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
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
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
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 (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
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)
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
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
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 (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 (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
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 (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 (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/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 (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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306134 AgrOrtholog
Ensembl Genes ENSRNOG00000016503 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000022459 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000064323 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022459 UniProtKB/Swiss-Prot
  ENSRNOT00000071856 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.10810 UniProtKB/Swiss-Prot
InterPro HARP(SMARCAL1) UniProtKB/Swiss-Prot
  HARP_dom UniProtKB/Swiss-Prot
  Helicase_ATP-bd UniProtKB/Swiss-Prot
  Helicase_C UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
  SNF2-like_sf UniProtKB/Swiss-Prot
  SNF2_N UniProtKB/Swiss-Prot
KEGG Report rno:316477 UniProtKB/Swiss-Prot
NCBI Gene 316477 ENTREZGENE
PANTHER PTHR45766:SF3 UniProtKB/Swiss-Prot
Pfam HARP UniProtKB/Swiss-Prot
  Helicase_C UniProtKB/Swiss-Prot
  SNF2_N UniProtKB/Swiss-Prot
PhenoGen Smarcal1 PhenoGen
PROSITE HARP UniProtKB/Swiss-Prot
  HELICASE_ATP_BIND_1 UniProtKB/Swiss-Prot
  HELICASE_CTER UniProtKB/Swiss-Prot
SMART DEXDc UniProtKB/Swiss-Prot
  HELICc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
UniProt B4F769 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Smarcal1  Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1  LOC690314  hypothetical protein LOC690314  Data Merged 737654 PROVISIONAL
2008-04-30 Smarcal1  Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1   Smarcal1_predicted  Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1 (predicted)  'predicted' is removed 2292626 APPROVED
2008-01-09 LOC690314  hypothetical protein LOC690314  LOC679248  hypothetical protein LOC679248  Data Merged 1643240 APPROVED
2006-11-20 LOC690314  hypothetical protein LOC690314      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC679248  hypothetical protein LOC679248      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Smarcal1_predicted  Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED