Smc6 (structural maintenance of chromosomes 6) - Rat Genome Database
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Gene: Smc6 (structural maintenance of chromosomes 6) Rattus norvegicus
Analyze
Symbol: Smc6
Name: structural maintenance of chromosomes 6
RGD ID: 1311214
Description: Predicted to have ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including cellular senescence; positive regulation of chromosome segregation; and telomere maintenance via recombination. Predicted to localize to chromosome; mitotic spindle pole; and nuclear body. Orthologous to human SMC6 (structural maintenance of chromosomes 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; flutamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC313961; SMC6 structural maintenance of chromosomes 6-like 1; SMC6 structural maintenance of chromosomes 6-like 1 (yeast); Smc6l1; structural maintenance of chromosomes protein 6
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
mRatBN7.2633,978,730 - 34,033,201 (+)NCBI
Rnor_6.0 Ensembl636,941,233 - 36,995,138 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0636,941,233 - 36,995,920 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0646,691,346 - 46,746,033 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4634,710,177 - 34,763,158 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1634,718,849 - 34,765,945 (+)NCBI
Celera633,379,218 - 33,432,201 (+)NCBICelera
Cytogenetic Map6q15NCBI
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:11408570   PMID:17589526   PMID:18086888   PMID:25931565  


Genomics

Comparative Map Data
Smc6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2633,978,730 - 34,033,201 (+)NCBI
Rnor_6.0 Ensembl636,941,233 - 36,995,138 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0636,941,233 - 36,995,920 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0646,691,346 - 46,746,033 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4634,710,177 - 34,763,158 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1634,718,849 - 34,765,945 (+)NCBI
Celera633,379,218 - 33,432,201 (+)NCBICelera
Cytogenetic Map6q15NCBI
SMC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl217,663,812 - 17,800,242 (-)EnsemblGRCh38hg38GRCh38
GRCh38217,663,812 - 17,753,833 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37217,845,079 - 17,935,077 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36217,708,562 - 17,798,541 (-)NCBINCBI36hg18NCBI36
Build 34217,766,708 - 17,856,688NCBI
Celera217,724,884 - 17,815,383 (-)NCBI
Cytogenetic Map2p24.2NCBI
HuRef217,620,169 - 17,710,162 (-)NCBIHuRef
CHM1_1217,774,474 - 17,864,475 (-)NCBICHM1_1
Smc6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391211,315,887 - 11,369,786 (+)NCBIGRCm39mm39
GRCm39 Ensembl1211,315,887 - 11,369,786 (+)Ensembl
GRCm381211,265,886 - 11,319,785 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1211,265,886 - 11,319,785 (+)EnsemblGRCm38mm10GRCm38
MGSCv371211,272,692 - 11,326,591 (+)NCBIGRCm37mm9NCBIm37
MGSCv361211,292,229 - 11,346,128 (+)NCBImm8
Celera1211,610,123 - 11,665,032 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
Smc6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955469453,353 - 552,279 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955469456,023 - 552,794 (-)NCBIChiLan1.0ChiLan1.0
SMC6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A17,774,590 - 17,861,920 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A17,776,276 - 17,854,052 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A17,648,371 - 17,735,910 (-)NCBIMhudiblu_PPA_v0panPan3
SMC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1713,133,236 - 13,201,759 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11713,132,945 - 13,201,214 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Smc6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493649313,191,389 - 13,250,788 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMC6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3120,097,379 - 120,170,972 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13120,097,361 - 120,170,974 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23128,245,265 - 128,318,831 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMC6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11489,917,621 - 90,005,604 (+)NCBI
ChlSab1.1 Ensembl1489,917,518 - 90,000,088 (+)Ensembl
Smc6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624738612,758 - 689,191 (-)NCBI

Position Markers
RH143232  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0636,990,398 - 36,990,536NCBIRnor6.0
Rnor_5.0646,740,511 - 46,740,649UniSTSRnor5.0
RGSC_v3.4634,759,091 - 34,759,229UniSTSRGSC3.4
Celera633,428,134 - 33,428,272UniSTS
RH 3.4 Map6144.2UniSTS
Cytogenetic Map6q14UniSTS
RH143724  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0636,940,363 - 36,940,532NCBIRnor6.0
Rnor_5.0646,690,476 - 46,690,645UniSTSRnor5.0
RGSC_v3.4634,709,307 - 34,709,476UniSTSRGSC3.4
Celera633,378,348 - 33,378,517UniSTS
RH 3.4 Map6145.4UniSTS
Cytogenetic Map6q14UniSTS
BF387143  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0636,942,336 - 36,942,531NCBIRnor6.0
Rnor_5.0646,692,449 - 46,692,644UniSTSRnor5.0
RGSC_v3.4634,711,280 - 34,711,475UniSTSRGSC3.4
Celera633,380,321 - 33,380,516UniSTS
Cytogenetic Map6q14UniSTS
RH139846  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0636,995,549 - 36,995,730NCBIRnor6.0
Rnor_5.0646,745,662 - 46,745,843UniSTSRnor5.0
RGSC_v3.4634,764,242 - 34,764,423UniSTSRGSC3.4
Celera633,433,285 - 33,433,466UniSTS
RH 3.4 Map6143.8UniSTS
Cytogenetic Map6q14UniSTS
AA850777  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0636,994,124 - 36,994,317NCBIRnor6.0
Rnor_5.0646,744,237 - 46,744,430UniSTSRnor5.0
RGSC_v3.4634,762,817 - 34,763,010UniSTSRGSC3.4
Celera633,431,860 - 33,432,053UniSTS
RH 3.4 Map6144.5UniSTS
Cytogenetic Map6q14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
8693632Alc27Alcohol consumption QTL 272.20.791drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)63425776653855198Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63499565675623393Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63626028860606186Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:187
Count of miRNA genes:144
Interacting mature miRNAs:156
Transcripts:ENSRNOT00000007073
Prediction methods:Microtar, Miranda
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 41 57 41 19 41 8 10 74 35 41 11 8
Low 2 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007073   ⟹   ENSRNOP00000007073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl636,941,233 - 36,994,465 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083383   ⟹   ENSRNOP00000070408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl636,941,596 - 36,995,138 (+)Ensembl
RefSeq Acc Id: NM_001108014   ⟹   NP_001101484
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2633,978,766 - 34,031,746 (+)NCBI
Rnor_6.0636,941,233 - 36,994,465 (+)NCBI
Rnor_5.0646,691,346 - 46,746,033 (+)NCBI
RGSC_v3.4634,710,177 - 34,763,158 (+)RGD
Celera633,379,218 - 33,432,201 (+)RGD
Sequence:
RefSeq Acc Id: XM_006239898   ⟹   XP_006239960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2633,979,143 - 34,031,676 (+)NCBI
Rnor_6.0636,941,659 - 36,995,920 (+)NCBI
Rnor_5.0646,691,346 - 46,746,033 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039112188   ⟹   XP_038968116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2633,978,730 - 34,031,676 (+)NCBI
RefSeq Acc Id: XM_039112189   ⟹   XP_038968117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2633,986,772 - 34,031,676 (+)NCBI
RefSeq Acc Id: XM_039112190   ⟹   XP_038968118
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2634,000,158 - 34,033,201 (+)NCBI
RefSeq Acc Id: XM_039112191   ⟹   XP_038968119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2633,999,513 - 34,033,201 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101484   ⟸   NM_001108014
- UniProtKB: D4AB26 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239960   ⟸   XM_006239898
- Peptide Label: isoform X1
- UniProtKB: D4AB26 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070408   ⟸   ENSRNOT00000083383
RefSeq Acc Id: ENSRNOP00000007073   ⟸   ENSRNOT00000007073
RefSeq Acc Id: XP_038968116   ⟸   XM_039112188
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968117   ⟸   XM_039112189
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968119   ⟸   XM_039112191
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968118   ⟸   XM_039112190
- Peptide Label: isoform X3
Protein Domains
SMC_N

Transcriptome

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

Promoters
RGD ID:13694494
Promoter ID:EPDNEW_R5019
Type:initiation region
Name:Smc6_1
Description:structural maintenance of chromosomes 6
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_6.0636,941,218 - 36,941,278EPDNEW

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 46699393 46699394 C A snv SBN/Ygl (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311214 AgrOrtholog
Ensembl Genes ENSRNOG00000004908 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007073 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070408 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007073 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083383 UniProtKB/TrEMBL
InterPro P-loop_NTPase UniProtKB/TrEMBL
  RecF/RecN/SMC_N UniProtKB/TrEMBL
KEGG Report rno:313961 UniProtKB/TrEMBL
NCBI Gene 313961 ENTREZGENE
Pfam SMC_N UniProtKB/TrEMBL
PhenoGen Smc6 PhenoGen
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt D4AB26 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-05-05 Smc6  structural maintenance of chromosomes 6  Smc6l1  SMC6 structural maintenance of chromosomes 6-like 1 (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Smc6l1  SMC6 structural maintenance of chromosomes 6-like 1 (yeast)   Smc6l1_predicted  SMC6 structural maintenance of chromosomes 6-like 1 (yeast) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Smc6l1_predicted  SMC6 structural maintenance of chromosomes 6-like 1 (yeast) (predicted)      Symbol and Name status set to approved 70820 APPROVED