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 enable several functions, including beta-tubulin binding activity; dynein complex binding activity; and mediator complex binding activity. Involved in meiotic cell cycle. Located in basement membrane and synaptonemal complex. Human ortholog(s) of this gene implicated in Cornelia de Lange syndrome 3; hepatocellular carcinoma; and intellectual disability. Orthologous to human SMC3 (structural maintenance of chromosomes 3); PARTICIPATES IN cell cycle pathway, mitotic; INTERACTS WITH (+)-pilocarpine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81262,606,731 - 262,649,832 (+)NCBIGRCr8
mRatBN7.21252,601,422 - 252,644,522 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1252,601,753 - 252,644,522 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1260,791,015 - 260,833,731 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01267,497,086 - 267,539,800 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01260,152,142 - 260,195,192 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-demecolcine  (ISO)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
afimoxifene  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
benzatropine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
busulfan  (ISO)
cadmium sulfate  (ISO)
caffeine  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
clofarabine  (ISO)
clozapine  (ISO)
coumarin  (ISO)
Cuprizon  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
deguelin  (ISO)
diazinon  (EXP)
dicrotophos  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
fenpyroximate  (ISO)
fenvalerate  (EXP)
flavonoids  (EXP)
folic acid  (ISO)
FR900359  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
Lasiocarpine  (ISO)
lead diacetate  (EXP)
methamphetamine  (EXP)
methylmercury chloride  (ISO)
miconazole  (ISO)
monocrotaline  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel dichloride  (EXP)
oxybenzone  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenethyl isothiocyanate  (EXP)
phenytoin  (ISO)
phosphorus atom  (ISO)
phosphorus(.)  (ISO)
picoxystrobin  (ISO)
piroxicam  (ISO)
pyrethrins  (EXP)
quercetin  (ISO)
resveratrol  (EXP,ISO)
riddelliine  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
taurine  (ISO)
tebufenpyrad  (ISO)
testosterone  (ISO)
testosterone enanthate  (ISO)
thapsigargin  (ISO)
torcetrapib  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
troglitazone  (ISO)
tungsten  (ISO)

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

References - curated
# Reference Title Reference Citation
1. Perlecan and basement membrane-chondroitin sulfate proteoglycan (bamacan) are two basement membrane chondroitin/dermatan sulfate proteoglycans in the Engelbreth-Holm-Swarm tumor matrix. Couchman JR, etal., J Biol Chem. 1996 Apr 19;271(16):9595-602.
2. CDK13 RNA Over-Editing Mediated by ADAR1 Associates with Poor Prognosis of Hepatocellular Carcinoma Patients. Dong X, etal., Cell Physiol Biochem. 2018;47(6):2602-2612. doi: 10.1159/000491656. Epub 2018 Jul 11.
3. Association of mammalian SMC1 and SMC3 proteins with meiotic chromosomes and synaptonemal complexes. Eijpe M, etal., J Cell Sci 2000 Feb;113 ( Pt 4):673-82.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. De novo heterozygous mutations in SMC3 cause a range of Cornelia de Lange syndrome-overlapping phenotypes. Gil-Rodríguez MC, etal., Hum Mutat. 2015 Apr;36(4):454-62. doi: 10.1002/humu.22761. Epub 2015 Mar 17.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Comprehensive gene review and curation RGD comprehensive gene curation
14. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
15. cDNA cloning of the basement membrane chondroitin sulfate proteoglycan core protein, bamacan: a five domain structure including coiled-coil motifs. Wu RR and Couchman JR, J Cell Biol 1997 Jan 27;136(2):433-44.
Additional References at PubMed
PMID:8889548   PMID:9789013   PMID:10375619   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:23242214   PMID:31505169  


Genomics

Comparative Map Data
Smc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81262,606,731 - 262,649,832 (+)NCBIGRCr8
mRatBN7.21252,601,422 - 252,644,522 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1252,601,753 - 252,644,522 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1260,791,015 - 260,833,731 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01267,497,086 - 267,539,800 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01260,152,142 - 260,195,192 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh3810110,567,695 - 110,606,048 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl10110,567,684 - 110,606,048 (+)EnsemblGRCh38hg38GRCh38
GRCh3710112,327,453 - 112,365,806 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3610112,317,439 - 112,354,382 (+)NCBINCBI36Build 36hg18NCBI36
Build 3410112,317,473 - 112,354,380NCBI
Celera10106,059,046 - 106,095,991 (+)NCBICelera
Cytogenetic Map10q25.2NCBI
HuRef10105,957,043 - 105,993,961 (+)NCBIHuRef
CHM1_110112,609,271 - 112,646,175 (+)NCBICHM1_1
T2T-CHM13v2.010111,451,468 - 111,489,803 (+)NCBIT2T-CHM13v2.0
Smc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391953,588,827 - 53,634,262 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1953,588,829 - 53,634,264 (+)EnsemblGRCm39 Ensembl
GRCm381953,600,396 - 53,645,831 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1953,600,398 - 53,645,833 (+)EnsemblGRCm38mm10GRCm38
MGSCv371953,674,886 - 53,720,321 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361953,653,759 - 53,698,460 (+)NCBIMGSCv36mm8
Celera1955,793,196 - 55,838,677 (+)NCBICelera
Cytogenetic Map19D2NCBI
cM Map1948.13NCBI
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
NHGRI_mPanPan1-v28122,450,881 - 122,488,731 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan110122,456,339 - 122,494,067 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v010107,164,086 - 107,201,220 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.110110,613,824 - 110,650,923 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10110,613,824 - 110,653,075 (+)Ensemblpanpan1.1panPan2
SMC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12821,889,690 - 21,928,367 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2821,889,662 - 21,928,034 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2822,041,009 - 22,080,134 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02822,416,380 - 22,455,786 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2822,416,380 - 22,455,779 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12821,973,911 - 22,012,990 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02821,979,557 - 22,018,930 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02822,114,201 - 22,153,585 (+)NCBIUU_Cfam_GSD_1.0
Smc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721324,122,824 - 24,157,519 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364861,408,045 - 1,435,875 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364861,409,757 - 1,436,206 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14120,969,631 - 121,021,497 (+)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.19103,506,779 - 103,543,836 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl9103,506,689 - 103,545,523 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604864,709,561 - 64,746,712 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473735,694,566 - 35,730,829 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473735,698,722 - 35,730,854 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smc3
152 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
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)1218748008257976495Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
1581544Rf52Renal function QTL 520.05urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
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)1233948574260522016Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1238699859259647894Rat
1598839Rf56Renal function QTL 56renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1245907761257976495Rat

Markers in Region
BE121234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21252,601,570 - 252,601,730 (+)MAPPERmRatBN7.2
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
RH 3.4 Map11673.1UniSTS
Cytogenetic Map1q55UniSTS


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
  XM_039109434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide 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
  JAXUCZ010000001 (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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1252,601,753 - 252,643,816 (+)Ensembl
Rnor_6.0 Ensembl1274,309,758 - 274,352,838 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000054686   ⟹   ENSRNOP00000051571
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1252,601,753 - 252,644,522 (+)Ensembl
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
GRCr81262,607,091 - 262,649,832 (+)NCBI
mRatBN7.21252,601,779 - 252,644,522 (+)NCBI
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:
RefSeq Acc Id: XM_039109434   ⟹   XP_038965362
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81262,606,731 - 262,649,832 (+)NCBI
mRatBN7.21252,601,422 - 252,644,522 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_113771   ⟸   NM_031583
- UniProtKB: P97690 (UniProtKB/Swiss-Prot),   A6JHW2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019560   ⟸   ENSRNOT00000019560
RefSeq Acc Id: ENSRNOP00000051571   ⟸   ENSRNOT00000054686
RefSeq Acc Id: XP_038965362   ⟸   XM_039109434
- Peptide Label: isoform X1
- UniProtKB: P97690 (UniProtKB/Swiss-Prot)
Protein Domains
SMC hinge

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P97690-F1-model_v2 AlphaFold P97690 1-1191 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:62006 AgrOrtholog
BioCyc Gene G2FUF-55381 BioCyc
Ensembl Genes ENSRNOG00000014173 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019560.8 UniProtKB/TrEMBL
  ENSRNOT00000054686 ENTREZGENE
  ENSRNOT00000054686.3 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.1490 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.20.1060.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.70.1620 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, 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
PANTHER STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 UniProtKB/Swiss-Prot
  STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 UniProtKB/Swiss-Prot
  STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 UniProtKB/TrEMBL
  STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 UniProtKB/TrEMBL
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
RatGTEx ENSRNOG00000014173 RatGTEx
SMART SMC_hinge UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF75553 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC229437
UniProt A6JHW2 ENTREZGENE, UniProtKB/TrEMBL
  D4A1B9_RAT 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