Smc2 (structural maintenance of chromosomes 2) - Rat Genome Database
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Gene: Smc2 (structural maintenance of chromosomes 2) Rattus norvegicus
Analyze
Symbol: Smc2
Name: structural maintenance of chromosomes 2
RGD ID: 1305227
Description: Predicted to have chromatin binding activity and single-stranded DNA binding activity. Predicted to be involved in chromosome organization and meiotic chromosome segregation. Predicted to localize to chromosome; cytoplasm; and nuclear lumen. Orthologous to human SMC2 (structural maintenance of chromosomes 2); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-diaminodiphenylmethane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CAP-E; CAPE; chromosome-associated protein E; LOC362519; SMC2 structural maintenance of chromosomes 2-like 1; SMC2 structural maintenance of chromosomes 2-like 1 (yeast); Smc2l1; structural maintenance of chromosomes protein 2
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
mRatBN7.2566,806,882 - 66,853,478 (+)NCBI
Rnor_6.0 Ensembl568,717,519 - 68,763,850 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0568,717,509 - 68,764,080 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0573,151,967 - 73,198,538 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4569,561,142 - 69,607,373 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1569,566,160 - 69,612,480 (+)NCBI
Celera560,812,631 - 60,858,839 (-)NCBICelera
Cytogenetic Map5q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-butoxyethanol  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
azathioprine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (EXP)
doxorubicin  (ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
levetiracetam  (EXP)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenytoin  (EXP)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
quercetin  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
senecionine  (EXP)
Senkirkine  (EXP)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
topotecan  (EXP)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:9789013   PMID:10958694   PMID:11136719   PMID:12589063   PMID:14660695   PMID:19056867   PMID:20139420   PMID:21795393   PMID:23531880   PMID:25474630  


Genomics

Comparative Map Data
Smc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2566,806,882 - 66,853,478 (+)NCBI
Rnor_6.0 Ensembl568,717,519 - 68,763,850 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0568,717,509 - 68,764,080 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0573,151,967 - 73,198,538 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4569,561,142 - 69,607,373 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1569,566,160 - 69,612,480 (+)NCBI
Celera560,812,631 - 60,858,839 (-)NCBICelera
Cytogenetic Map5q23NCBI
SMC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9104,094,260 - 104,141,419 (+)EnsemblGRCh38hg38GRCh38
GRCh389104,093,760 - 104,141,419 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379106,856,590 - 106,903,700 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369105,896,362 - 105,943,521 (+)NCBINCBI36hg18NCBI36
Build 349103,936,161 - 103,981,492NCBI
Celera977,361,453 - 77,408,608 (+)NCBI
Cytogenetic Map9q31.1NCBI
HuRef976,458,199 - 76,505,354 (+)NCBIHuRef
CHM1_19107,002,961 - 107,050,087 (+)NCBICHM1_1
Smc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39452,438,966 - 52,488,365 (+)NCBIGRCm39mm39
GRCm39 Ensembl452,439,243 - 52,488,260 (+)Ensembl
GRCm38452,439,221 - 52,488,365 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl452,439,243 - 52,488,260 (+)EnsemblGRCm38mm10GRCm38
MGSCv37452,452,121 - 52,501,132 (+)NCBIGRCm37mm9NCBIm37
MGSCv36452,460,349 - 52,509,360 (+)NCBImm8
Celera452,415,636 - 52,464,543 (+)NCBICelera
Cytogenetic Map4B2NCBI
cM Map428.31NCBI
Smc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541922,245,843 - 22,294,508 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541922,245,843 - 22,294,508 (-)NCBIChiLan1.0ChiLan1.0
SMC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19103,402,526 - 103,449,949 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9103,402,967 - 103,449,949 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0975,273,163 - 75,323,486 (+)NCBIMhudiblu_PPA_v0panPan3
SMC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1160,091,457 - 60,151,442 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11160,091,728 - 60,155,295 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Smc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936793909,663 - 958,883 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1245,410,146 - 245,484,780 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11245,409,559 - 245,459,032 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21274,583,155 - 274,632,093 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMC2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11235,377,381 - 35,423,218 (-)NCBI
ChlSab1.1 Ensembl1235,374,947 - 35,423,364 (-)Ensembl
Smc2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247587,267,024 - 7,318,930 (-)NCBI

Position Markers
Fin16  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0568,763,643 - 68,763,779NCBIRnor6.0
Rnor_5.0573,198,101 - 73,198,237UniSTSRnor5.0
RGSC_v3.4569,607,156 - 69,607,292UniSTSRGSC3.4
Celera560,812,712 - 60,812,848UniSTS
Cytogenetic Map5q23UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51884791376608178Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52907889974078899Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52907889974078899Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52964166174641661Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52964166174641661Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531926122136640934Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53440240979402409Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53440240979402409Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53440240979402409Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)535225432108092802Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)535661945117554267Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53578875670742105Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535788756147487820Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54440427689432042Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)544404276134502294Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54872203893587756Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)551418671147487820Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)55180442696804426Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)55180442696804426Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55330956898309568Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)555903593100903593Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)556902367101902367Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)556991667137729065Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)560072951133313852Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)561086525149030144Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)56108665393273130Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)561086653117554114Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)561612600102331727Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)565696672129038896Rat
1598814Mcs13Mammary carcinoma susceptibility QTL 130.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)56839509671941113Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:158
Count of miRNA genes:114
Interacting mature miRNAs:135
Transcripts:ENSRNOT00000066226
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 27 39 25 19 25 1 1 73 25 37 11 1
Low 16 18 16 16 7 9 1 10 4 7
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001108666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AI639509 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BE119797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF396223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ202586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB719228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB729201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB762997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO388936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR471273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CV074555 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EV770551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225518 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000066226   ⟹   ENSRNOP00000061673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl568,717,519 - 68,763,850 (+)Ensembl
RefSeq Acc Id: NM_001108666   ⟹   NP_001102136
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2566,807,011 - 66,853,242 (+)NCBI
Rnor_6.0568,717,629 - 68,763,860 (+)NCBI
Rnor_5.0573,151,967 - 73,198,538 (+)NCBI
RGSC_v3.4569,561,142 - 69,607,373 (+)RGD
Celera560,812,631 - 60,858,839 (-)RGD
Sequence:
RefSeq Acc Id: XM_006238165   ⟹   XP_006238227
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2566,806,882 - 66,853,478 (+)NCBI
Rnor_6.0568,717,509 - 68,764,080 (+)NCBI
Rnor_5.0573,151,967 - 73,198,538 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102136 (Get FASTA)   NCBI Sequence Viewer  
  XP_006238227 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL78166 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102136   ⟸   NM_001108666
- UniProtKB: D4A5Q2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238227   ⟸   XM_006238165
- Peptide Label: isoform X1
- UniProtKB: D4A5Q2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061673   ⟸   ENSRNOT00000066226
Protein Domains
SMC hinge

Transcriptome

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

Promoters
RGD ID:13693738
Promoter ID:EPDNEW_R4262
Type:multiple initiation site
Name:Smc2_1
Description:structural maintenance of chromosomes 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_6.0568,717,537 - 68,717,597EPDNEW

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)
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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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 68750460 68750461 T A snv SHRSP/Gcrc (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305227 AgrOrtholog
Ensembl Genes ENSRNOG00000022325 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061673 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066226 ENTREZGENE, UniProtKB/TrEMBL
InterPro P-loop_NTPase UniProtKB/TrEMBL
  RecF/RecN/SMC_N UniProtKB/TrEMBL
  SMC UniProtKB/TrEMBL
  Smc2_ABC UniProtKB/TrEMBL
  SMC_hinge UniProtKB/TrEMBL
  SMC_hinge_sf UniProtKB/TrEMBL
KEGG Report rno:362519 UniProtKB/TrEMBL
NCBI Gene 362519 ENTREZGENE
Pfam SMC_hinge UniProtKB/TrEMBL
  SMC_N UniProtKB/TrEMBL
PhenoGen Smc2 PhenoGen
PIRSF SMC UniProtKB/TrEMBL
SMART SMC_hinge UniProtKB/TrEMBL
Superfamily-SCOP SMC_hinge UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt D4A5Q2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Smc2  structural maintenance of chromosomes 2  Smc2l1_predicted  SMC2 structural maintenance of chromosomes 2-like 1 (yeast) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Smc2l1_predicted  SMC2 structural maintenance of chromosomes 2-like 1 (yeast) (predicted)      Symbol and Name status set to approved 70820 APPROVED