Smc3 (structural maintenance of chromosomes 3) - Rat Genome Database
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Gene: Smc3 (structural maintenance of chromosomes 3) Rattus norvegicus
Analyze
Symbol: Smc3
Name: structural maintenance of chromosomes 3
RGD ID: 62006
Description: Predicted to have several functions, including beta-tubulin binding activity; dynein complex binding activity; and mediator complex binding activity. Predicted to be involved in several processes, including mitotic spindle assembly; regulation of DNA replication; and sister chromatid cohesion. Localizes to basement membrane. Human ortholog(s) of this gene implicated in Cornelia de Lange syndrome 3. Orthologous to human SMC3 (structural maintenance of chromosomes 3); PARTICIPATES IN cell cycle pathway, mitotic; INTERACTS WITH (+)-pilocarpine; 17alpha-ethynylestradiol; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: bamacan; basement membrane chondroitin sulfate proteoglycan; basement membrane-associated chondroitin proteoglycan; chondroitin sulfate proteoglycan 6; chromosome segregation protein SmcD; Cspg6; SMC protein 3; SMC-3; structural maintenace of chromosomes 3; structural maintenance of chromosomes protein 3
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
Rnor_6.01274,310,120 - 274,352,856 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1274,309,758 - 274,352,854 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01281,719,796 - 281,762,532 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41259,822,480 - 259,865,602 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11260,033,557 - 260,076,645 (+)NCBI
Celera1248,320,880 - 248,363,620 (+)NCBICelera
Cytogenetic Map1q55NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8889548   PMID:9789013   PMID:10375619   PMID:10652260   PMID:11590136   PMID:12498344   PMID:12651860   PMID:12759374   PMID:15870106   PMID:15917200   PMID:16682347   PMID:19094982  
PMID:19444697   PMID:19907496   PMID:20720539   PMID:21242291   PMID:21527826   PMID:21743440   PMID:22164254   PMID:22415368   PMID:22628566   PMID:22711701   PMID:31505169  


Genomics

Comparative Map Data
Smc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01274,310,120 - 274,352,856 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1274,309,758 - 274,352,854 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01281,719,796 - 281,762,532 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41259,822,480 - 259,865,602 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11260,033,557 - 260,076,645 (+)NCBI
Celera1248,320,880 - 248,363,620 (+)NCBICelera
Cytogenetic Map1q55NCBI
SMC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl10110,567,691 - 110,604,636 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl10110,567,695 - 110,606,048 (+)EnsemblGRCh38hg38GRCh38
GRCh3810110,567,695 - 110,606,048 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3710112,327,449 - 112,364,392 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3610112,317,439 - 112,354,382 (+)NCBINCBI36hg18NCBI36
Build 3410112,317,473 - 112,354,380NCBI
Celera10106,059,046 - 106,095,991 (+)NCBI
Cytogenetic Map10q25.2NCBI
HuRef10105,957,043 - 105,993,961 (+)NCBIHuRef
CHM1_110112,609,271 - 112,646,175 (+)NCBICHM1_1
Smc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391953,588,827 - 53,634,262 (+)NCBIGRCm39mm39
GRCm381953,600,396 - 53,645,831 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1953,600,398 - 53,645,833 (+)EnsemblGRCm38mm10GRCm38
MGSCv371953,674,886 - 53,720,321 (+)NCBIGRCm37mm9NCBIm37
MGSCv361953,653,759 - 53,698,460 (+)NCBImm8
Celera1955,793,196 - 55,838,677 (+)NCBICelera
Cytogenetic Map19D2NCBI
Smc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955485815,281 - 848,561 (-)NCBIChiLan1.0ChiLan1.0
SMC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.110110,613,824 - 110,650,923 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10110,613,824 - 110,653,075 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v010107,164,086 - 107,201,220 (+)NCBIMhudiblu_PPA_v0panPan3
SMC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2821,889,662 - 21,928,034 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12821,889,690 - 21,928,367 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Smc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364861,409,757 - 1,436,206 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14120,969,632 - 121,008,924 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114120,969,629 - 121,008,924 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214131,854,806 - 131,894,120 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMC3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.19103,506,779 - 103,543,836 (+)NCBI
ChlSab1.1 Ensembl9103,506,689 - 103,545,523 (+)Ensembl
Smc3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473735,698,722 - 35,730,854 (-)NCBI

Position Markers
BE121234  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01274,309,912 - 274,310,071NCBIRnor6.0
Rnor_5.01281,719,588 - 281,719,747UniSTSRnor5.0
RGSC_v3.41259,822,272 - 259,822,431UniSTSRGSC3.4
Celera1248,320,672 - 248,320,831UniSTS
Cytogenetic Map1q55UniSTS
RH 3.4 Map11673.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1236795785281795785Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1245529606282763074Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1236265430281265430Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1156446196274977688Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1238830534278228767Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1243272341282763074Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1244401175282365384Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1235850810280850810Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1244992467282365384Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1252955158280632620Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1258132568282763074Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1167394665278228889Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1252948438281795785Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1241482188281795785Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1191825895279986079Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1255728828282763074Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1238824734279986079Rat
1598839Rf56Renal function QTL 56renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1266793821279986079Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1259295704282763074Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1258709726281795785Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1244401175282365384Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1217054291281795785Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1244087148282763074Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1213476630278978026Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1196395041282763074Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1249206242281795785Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1192639698278228889Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1161784169278228889Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1192639698278228889Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1236795785281795785Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1163796316282763074Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1230420627282645769Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1236265430281265430Rat
7387289Uae45Urinary albumin excretion QTL 452.860.0021urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1244148899282763074Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1242302911282763074Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:132
Count of miRNA genes:54
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000019560, ENSRNOT00000054686
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 42 56 40 19 40 8 10 74 35 41 11 8
Low 1 1 1 1 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031583 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAHX01000809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01000810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC110709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BE109731 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF396983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BP486487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BP499171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA509998 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA511001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO395251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EV773232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EV776219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231827 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U82626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000019560   ⟹   ENSRNOP00000019560
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1274,309,758 - 274,352,838 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000054686   ⟹   ENSRNOP00000051571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1274,310,153 - 274,352,854 (+)Ensembl
RefSeq Acc Id: NM_031583   ⟹   NP_113771
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01274,310,120 - 274,352,856 (+)NCBI
Rnor_5.01281,719,796 - 281,762,532 (+)NCBI
RGSC_v3.41259,822,480 - 259,865,602 (+)RGD
Celera1248,320,880 - 248,363,620 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_113771 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB96342 (Get FASTA)   NCBI Sequence Viewer  
  EDL94436 (Get FASTA)   NCBI Sequence Viewer  
  EDL94437 (Get FASTA)   NCBI Sequence Viewer  
  EDL94438 (Get FASTA)   NCBI Sequence Viewer  
  P97690 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_113771   ⟸   NM_031583
- UniProtKB: D4A1B9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019560   ⟸   ENSRNOT00000019560
RefSeq Acc Id: ENSRNOP00000051571   ⟸   ENSRNOT00000054686
Protein Domains
SMC hinge

Transcriptome

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

Promoters
RGD ID:13690997
Promoter ID:EPDNEW_R1518
Type:initiation region
Name:Smc3_1
Description:structural maintenance of chromosomes 3
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_6.01274,310,087 - 274,310,147EPDNEW

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)
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
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
1 281759351 281759352 C T snv COP/CrCrl (MCW & UW), ZFDM (KyushuU), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), FHL/EurMcwi (MCW)
1 281759366 281759367 T C snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), ZFDM (KyushuU)
1 281762119 281762120 G A snv ACI/EurMcwi (MCW), ZFDM (KyushuU), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SDLEF7/Barth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 274349675 274349676 C T snv COP/CrCrl (MCW & UW), WKY/Gcrc (RGD), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), CDR, CDS, ACI/EurMcwi (RGD), BBDP/Wor (RGD), LE/Stm (RGD), LEW/Crl (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), FHL/EurMcwi (MCW)
1 274349690 274349691 T C snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), CDR, CDS, ACI/N (MCW), MR/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), LE/Stm (RGD), LEW/Crl (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), WKY/Gcrc (RGD)
1 274352443 274352444 G A snv ACI/EurMcwi (MCW), SHRSP/Gcrc (RGD), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), CDS, ACI/N (MCW), Buf/N (MCW), M520/N (MCW), MR/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), LE/Stm (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), SBH/Ygl (RGD), SHR/NHsd (RGD), COP/CrCrl (MCW & UW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 259862421 259862422 C T snv COP/CrCrl (MCW & UW)
1 259862436 259862437 T C snv ACI/N (KNAW), SS/JrHsdMcwi (MDC), FHH/EurMcwi (MCW), HCR/1Mco (UMich), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), ACI/EurMcwi (MCW), WN/N (KNAW), MR/N (KNAW), LE/Stm (KNAW)
1 259865189 259865190 G A snv FHH/EurMcwi (MCW), HCR/1Mco (UMich), ACI/N (KNAW), ACI/EurMcwi (MCW), GH/OmrMcwi (MCW), BUF/N (KNAW), COP/CrCrl (MCW & UW), M520/N (KNAW), FHL/EurMcwi (MCW), LE/Stm (KNAW), MR/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:62006 AgrOrtholog
Ensembl Genes ENSRNOG00000014173 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019560 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000051571 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019560 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000054686 UniProtKB/TrEMBL
InterPro P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RecF/RecN/SMC_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMC3_ABC_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMC_hinge UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMC_hinge_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29486 UniProtKB/TrEMBL
NCBI Gene 29486 ENTREZGENE
Pfam SMC_hinge UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMC_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Smc3 PhenoGen
PIRSF SMC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SMC_hinge UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF75553 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC229437
UniGene Rn.11074 ENTREZGENE
UniProt D4A1B9 ENTREZGENE, UniProtKB/TrEMBL
  F1LQB2_RAT UniProtKB/TrEMBL
  P97690 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Smc3  structural maintenance of chromosomes 3  Smc3  structural maintenace of chromosomes 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-18 Smc3  structural maintenace of chromosomes 3  Cspg6  chondroitin sulfate proteoglycan 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Cspg6  chondroitin sulfate proteoglycan 6      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to basement membranes 61563
gene_domains contains a five domain structure including globular domains, a coiled-coil, three potential N-linked glycosylation sites, and three predicted chondroitin chain substitution sites 61563