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Gene: Smc3 (structural maintenance of chromosomes 3) Rattus norvegicus

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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

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	SMC3 (structural maintenance of chromosomes 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Smc3 (structural maintenance of chromosomes 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Smc3 (structural maintenance of chromosomes 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SMC3 (structural maintenance of chromosomes 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SMC3 (structural maintenance of chromosomes 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Smc3 (structural maintenance of chromosomes 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SMC3 (structural maintenance of chromosomes 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SMC3 (structural maintenance of chromosomes 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Smc3 (structural maintenance of chromosomes 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Smc3 (structural maintenance of chromosomes 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	LASP1 (LIM and SH3 protein 1)	HGNC	OMA
Alliance orthologs ³
Mus musculus (house mouse):	Smc3 (structural maintenance of chromosomes 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	SMC3 (structural maintenance of chromosomes 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	smc3 (structural maintenance of chromosomes 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	smc3 (structural maintenance of chromosomes 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	smc-3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	SMC3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SMC3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	smc3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	smc3	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	262,606,731 - 262,649,832 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	262,607,080 - 262,649,825 (+)	Ensembl				GRCr8
mRatBN7.2	1	252,601,422 - 252,644,522 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	252,601,753 - 252,644,522 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	260,791,015 - 260,833,731 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	267,497,086 - 267,539,800 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	260,152,142 - 260,195,192 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	274,310,120 - 274,352,856 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	274,309,758 - 274,352,854 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	281,719,796 - 281,762,532 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	259,822,480 - 259,865,602 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	248,320,880 - 248,363,620 (+)	NCBI		Celera
RGSC_v3.1	1	260,033,557 - 260,076,645 (+)	NCBI
Cytogenetic Map	1	q55	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autism spectrum disorder (ISO)

Cornelia de Lange syndrome (ISO)

Cornelia de Lange syndrome 1 (ISO)

Cornelia de Lange syndrome 3 (ISO,ISS)

Desbuquois dysplasia (ISO)

genetic disease (ISO)

hepatocellular carcinoma (ISO)

intellectual disability (ISO)

myeloid leukemia (ISO)

Neurodevelopmental Disorders (ISO)

neuromuscular disease (ISO)

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)

4,4'-sulfonyldiphenol (ISO)

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)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (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)

nitrates (ISO)

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)

triphenyl phosphate (ISO)

troglitazone (ISO)

tungsten (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell division (IEA)

chromosome organization (IEA)

DNA damage response (IEA)

DNA repair (IEA)

meiotic cell cycle (IEA,IEP,ISO,ISS)

mitotic sister chromatid cohesion (IBA)

mitotic spindle assembly (IEA,ISO)

regulation of DNA replication (IEA,ISO,ISS)

sister chromatid cohesion (IEA,ISO)

stem cell population maintenance (ISO)

Cellular Component

basement membrane (IDA,TAS)

chromatin (IEA,ISO,ISS)

chromosome (IEA)

chromosome, centromeric region (IEA)

cohesin complex (IEA,ISO)

lateral element (IEA,ISO)

meiotic cohesin complex (IEA,ISO,ISS)

mitotic cohesin complex (IBA,IEA,ISO)

mitotic spindle pole (IEA,ISO,ISS)

nuclear matrix (IEA,ISO,ISS)

nucleoplasm (IEA,ISO)

nucleus (IEA,ISO)

synaptonemal complex (IDA,IEA)

Molecular Function

ATP binding (IEA)

ATP hydrolysis activity (IEA)

beta-tubulin binding (IEA,ISO)

chromatin binding (IEA,ISO)

cis-regulatory region sequence-specific DNA binding (IEA,ISO)

double-stranded DNA binding (IBA)

dynein complex binding (IEA,ISO,ISS)

mediator complex binding (IEA,ISO)

nucleotide binding (IEA)

protein binding (ISO)

protein heterodimerization activity (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

cell cycle pathway, mitotic (IEA)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	262,606,731 - 262,649,832 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	262,607,080 - 262,649,825 (+)	Ensembl				GRCr8
mRatBN7.2	1	252,601,422 - 252,644,522 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	252,601,753 - 252,644,522 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	260,791,015 - 260,833,731 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	267,497,086 - 267,539,800 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	260,152,142 - 260,195,192 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	274,310,120 - 274,352,856 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	274,309,758 - 274,352,854 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	281,719,796 - 281,762,532 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	259,822,480 - 259,865,602 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	248,320,880 - 248,363,620 (+)	NCBI		Celera
RGSC_v3.1	1	260,033,557 - 260,076,645 (+)	NCBI
Cytogenetic Map	1	q55	NCBI

SMC3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	10	110,567,695 - 110,606,048 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	10	110,567,680 - 110,606,048 (+)	Ensembl			hg38	GRCh38
GRCh37	10	112,327,453 - 112,365,806 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	112,317,439 - 112,354,382 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	10	112,317,473 - 112,354,380	NCBI
Celera	10	106,059,046 - 106,095,991 (+)	NCBI		Celera
Cytogenetic Map	10	q25.2	NCBI
HuRef	10	105,957,043 - 105,993,961 (+)	NCBI		HuRef
CHM1_1	10	112,609,271 - 112,646,175 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	10	111,451,468 - 111,489,803 (+)	NCBI		T2T-CHM13v2.0

Smc3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	53,588,827 - 53,634,262 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	19	53,588,829 - 53,634,264 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	19	53,600,396 - 53,645,831 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	53,600,398 - 53,645,833 (+)	Ensembl			mm10	GRCm38
MGSCv37	19	53,674,886 - 53,720,321 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	19	53,653,759 - 53,698,460 (+)	NCBI		MGSCv36	mm8
Celera	19	55,793,196 - 55,838,677 (+)	NCBI		Celera
Cytogenetic Map	19	D2	NCBI
cM Map	19	48.13	NCBI

Smc3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955485	814,297 - 848,573 (-)	Ensembl
ChiLan1.0	NW_004955485	815,281 - 848,561 (-)	NCBI	ChiLan1.0	ChiLan1.0

SMC3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	8	122,450,881 - 122,488,731 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	10	122,456,339 - 122,494,067 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	10	107,164,086 - 107,201,220 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	10	110,613,824 - 110,650,923 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	10	110,613,824 - 110,653,075 (+)	Ensembl			panPan2	panpan1.1

SMC3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	28	21,889,690 - 21,928,367 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	28	21,889,662 - 21,928,034 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	28	22,041,009 - 22,080,134 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	28	22,416,380 - 22,455,786 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	28	22,416,380 - 22,455,779 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	28	21,973,911 - 22,012,990 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	28	21,979,557 - 22,018,930 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	28	22,114,201 - 22,153,585 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Smc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024407213	24,122,824 - 24,157,519 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936486	1,408,045 - 1,435,875 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936486	1,409,757 - 1,436,206 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SMC3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	120,969,631 - 121,021,497 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	14	120,969,629 - 121,008,924 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	131,854,806 - 131,894,120 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SMC3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	9	103,506,779 - 103,543,836 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	9	103,506,689 - 103,545,523 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666048	64,709,561 - 64,746,712 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Smc3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624737	35,694,566 - 35,730,829 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624737	35,698,722 - 35,730,854 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Smc3
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	2	53,025,829 - 53,068,102 (+)	NCBI		Rrattus_CSIRO_v1

miRNA Target Status (No longer updated)

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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	154961463	266453731	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	208479811	269633915	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	160573753	266453731	Rat
70211	Niddm24	Non-insulin dependent diabetes mellitus QTL 24	3.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	224633915	269633915	Rat
724552	Glom2	Glomerulus QTL 2	3.3	0.0001	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	1	232312773	270518180	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	186658830	266453731	Rat
61327	Eae7	Experimental allergic encephalomyelitis QTL 7	5.6		body mass (VT:0001259)	change in body weight (CMO:0002045)	1	226175591	270518180	Rat
1578775	Iddm21	Insulin dependent diabetes mellitus QTL 21	4.13		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	245782829	270518180	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	205233991	267096252	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	218829748	263829748	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	186658830	266453731	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	205233991	267096252	Rat
631837	Niddm35	Non-insulin dependent diabetes mellitus QTL 35		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	248619887	269633915	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	176288899	270518180	Rat
631836	Stl31	Serum triglyceride level QTL 31	4.64	5e-06	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	1	247133834	270518180	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	162548015	270518180	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	205233991	267096252	Rat
1598853	Memor3	Memory QTL 3	4.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	1	152919152	268496042	Rat
1600390	Niddm64	Non-insulin dependent diabetes mellitus QTL 64		0.003	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	257624997	270518180	Rat
1300108	Rf8	Renal function QTL 8	3.75		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	1	237995023	269633915	Rat
734767	Niddm57	Non-insulin dependent diabetes mellitus QTL 57			body mass (VT:0001259)	body weight (CMO:0000012)	1	233480549	270108840	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	160573753	266453731	Rat
631215	Stl8	Serum triglyceride level QTL 8	9.27	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	1	234540191	270518180	Rat
7387289	Uae45	Urinary albumin excretion QTL 45	2.86	0.0021	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	233204160	270518180	Rat
631843	Bw116	Body weight QTL 116	4.1	0.016	abdominal adipose amount (VT:1000220)	abdominal fat pad weight (CMO:0000088)	1	233480549	270108840	Rat
731175	Uae20	Urinary albumin excretion QTL 20	3.5	0.0018	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	207163993	269633915	Rat
1598839	Rf56	Renal function QTL 56			renal blood flow trait (VT:2000006)	ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)	1	255849111	270518180	Rat
1581544	Rf52	Renal function QTL 52		0.05	urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	1	241569529	269633915	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	160573753	266453731	Rat
631536	Lnnr2	Liver neoplastic nodule remodeling QTL 2	2.9	0.0005	liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)	1	243953669	270518180	Rat
734769	Niddm58	Non-insulin dependent diabetes mellitus QTL 58			body mass (VT:0001259)	body weight (CMO:0000012)	1	225108840	270108840	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	185857683	270518180	Rat
2302040	Pia35	Pristane induced arthritis QTL 35	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	226175591	270518180	Rat
631669	Iddm9	Insulin dependent diabetes mellitus QTL 9	2.8	0.039	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	233349180	270518180	Rat
1598821	Rf55	Renal function QTL 55	6.3		renal blood flow trait (VT:2000006)	ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)	1	228174566	270518180	Rat
724533	Rf51	Renal function QTL 51	5.3	0.0002	kidney plasma flow trait (VT:0005524)	renal plasma flow (CMO:0001914)	1	228180370	266453608	Rat

Markers in Region

BE121234

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	252,601,570 - 252,601,730 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	274,309,912 - 274,310,071	NCBI	Rnor6.0
Rnor_5.0	1	281,719,588 - 281,719,747	UniSTS	Rnor5.0
RGSC_v3.4	1	259,822,272 - 259,822,431	UniSTS	RGSC3.4
Celera	1	248,320,672 - 248,320,831	UniSTS
RH 3.4 Map	1	1673.1	UniSTS
Cytogenetic Map	1	q55	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

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

Ensembl Acc Id:

ENSRNOT00000019560 ⟹ ENSRNOP00000019560

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	262,607,080 - 262,649,126 (+)	Ensembl
mRatBN7.2 Ensembl	1	252,601,753 - 252,643,816 (+)	Ensembl
Rnor_6.0 Ensembl	1	274,309,758 - 274,352,838 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000054686 ⟹ ENSRNOP00000051571

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	262,607,080 - 262,649,825 (+)	Ensembl
mRatBN7.2 Ensembl	1	252,601,753 - 252,644,522 (+)	Ensembl
Rnor_6.0 Ensembl	1	274,310,153 - 274,352,854 (+)	Ensembl

RefSeq Acc Id:

NM_031583 ⟹ NP_113771

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	262,607,091 - 262,649,832 (+)	NCBI
mRatBN7.2	1	252,601,779 - 252,644,522 (+)	NCBI
Rnor_6.0	1	274,310,120 - 274,352,856 (+)	NCBI
Rnor_5.0	1	281,719,796 - 281,762,532 (+)	NCBI
RGSC_v3.4	1	259,822,480 - 259,865,602 (+)	RGD
Celera	1	248,320,880 - 248,363,620 (+)	RGD

Sequence:

show sequence

GGGGAGCGAGCGGGAGCGATCGGAACCCAGTGAGAGGGGCCGGTCTGCGTCTCTCCTGACCCTG
CCGCCGCGCTGTTGCGGTTCTGAGGTGAAGCTTTCCTCCTGCGGAGGGGCGCGGAGCCATGTAC
ATCAAGCAGGTGATTATCCAGGGCTTCCGAAGTTACCGAGATCAAACAATTGTAGATCCCTTCA
GTTCAAAACATAATGTTATTGTGGGCAGAAATGGATCTGGAAAAAGCAACTTTTTTTATGCAAT
CCAGTTTGTTCTCAGTGATGAATTTAGTCATCTTCGTCCAGAGCAGCGATTGGCTTTGTTGCAC
GAGGGTACAGGTCCTCGTGTTATTTCTGCTTTTGTGGAAATCATTTTTGACAATTCAGACAACC
GGTTACCAATTGATAAAGAGGAAGTTTCGCTTCGAAGAGTTATTGGTGCCAAAAAAGATCAGTA
TTTCCTAGATAAGAAGATGGTCACGAAAAATGATGTGATGAATCTCCTTGAAAGTGCTGGGTTT
TCGAGAAGTAATCCTTATTACATTGTTAAACAAGGAAAGATCAACCAAATGGCAACAGCACCGG
ATTCTCAGAGATTAAAGCTGTTGAGAGAAGTAGCTGGCACTCGAGTGTATGACGAGCGCAAAGA
GGAAAGCATCTCCCTGATGAAAGAAACAGAGGGCAAACGGGAAAAGATCAATGAGTTGTTAAAA
TACATTGAAGAGCGATTACATACTCTAGAGGAGGAGAAGGAGGAACTGGCCCAGTATCAGAAGT
GGGATAAAATGAGGCGTGCCCTGGAGTACACCATCTACAACCAGGAGCTCAACGAGACTCGCGC
CAAGCTTGATGAGCTTTCTGCTAAGCGAGAAACAAGCGGAGAGAAATCCAGACAATTAAGAGAT
GCCCAGCAGGATGCAAGAGATAAAATGGAGGATATTGAGCGCCAAGTTAGAGAACTGAAAACAA
AAATTTCAGCCATGAAAGAAGAAAAAGAACAGCTCAGTGCGGAGAGACAAGAGCAGATTAAGCA
AAGGACCAAGCTGGAGCTTAAAGCCAAGGACTTACAGGATGAGCTGGCAGGGAACAGTGAGCAG
CGGAAACGTTTATTAAAAGAAAGACAGAAGCTGCTTGAAAAAATAGAAGAAAAGCAGAAAGAAC
TGGCAGAAACAGAACCGAAATTCAACAGCGTAAAGGAAAAAGAAGAGCGAGGAATTGCTAGATT
GGCTCAAGCTACACAGGAAAGAACTGATCTTTATGCAAAGCAGGGTCGAGGAAGCCAGTTTACA
TCAAAAGAAGAAAGAGATAAGTGGATTAAGAAGGAACTGAAGTCTTTAGATCAGGCTATTAATG
ATAAGAAAAGACAGATTGCTGCTATACACAAGGATTTGGAGGATACCGAGGCCAATAAAGAGAA
AAATCTGGAGCAATATAATAAACTGGATCAGGATCTCAATGAAGTCAAAGCTCGAGTTGAAGAA
CTGGACAGAAAATATTATGAAGTGAAAAATAAGAAAGATGAACTACAAAGTGAAAGAAATTACT
TGTGGAGAGAGGAGAATGCAGAACAGCAAGCACTTGCCGCTAAGAGAGAAGACCTTGAGAAGAA
GCAGCAGCTTCTTAGAGCGGCAACAGGAAAGGCCATTTTAAATGGAATCGACAGCATTAACAAA
GTGTTAGACCATTTCCGGCGGAAGGGTATAAACCAGCATGTGCAAAATGGCTACCATGGCATCG
TGATGAATAACTTTGAGTGCGAACCAGCTTTCTATACTTGTGTGGAAGTCACTGCCGGTAACAG
GTTATTCTATCACATTGTCGATTCAGATGAAGTCAGCACGAAGATCTTAATGGAGTTCAATAAA
ATGAATCTTCCTGGAGAGGTGACTTTCCTGCCTCTTAACAAGTTAGATGTGAGGGACACTGCCT
ATCCTGAAACTAACGATGCTATTCCTATGATCAGTAAGCTGAGGTACAATCCCAGATTCGACAA
AGCTTTCAAACATGTGTTTGGAAAGACACTCATCTGTCGGAGCATGGAGGTTTCCACTCAGCTA
GCTCGTGCCTTCACTATGGACTGCATTACTCTGGAAGGTGATCAAGTCAGCCATCGAGGTGCTC
TGACTGGAGGCTATTACGACACAAGAAAGTCTCGCCTTGAGTTACAGAAGGATGTTAGGAAAGC
AGAGGAGGAGCTGGGTGAGCTCGAAGCTAAGCTCAATGAAAACCTGCGCAGAAACATTGAAAGG
ATTAATAATGAAATTGATCAATTGATGAACCAAATGCAGCAGATAGAGACCCAACAGAGAAAAT
TTAAAGCATCCAGAGATAGCATCTTATCAGAGATGAAGATGCTAAAAGAGAAGAGACAGCAGTC
AGAAAAGACCTTCATGCCAAAGCAACGCAGTTTGCAGAGTCTGGAGGCCAGTCTGCACGCTATG
GAGTCGACCAGAGAGTCGCTGAAGGCAGAGCTAGGGACAGATTTGCTCTCTCAGCTCAGCCTGG
AAGACCAGAAAAGAGTCGACGCACTGAATGACGAGATCCGGCAGCTTCAGCAGGAAAACAGACA
GCTGCTGAATGAAAGAATTAAACTAGAAGGCATTATTACTCGAGTAGAGACTTACCTCAATGAG
AATCTGAGGAAACGTCTGGACCAAGTAGAGCAGGAACTTAATGAACTGAGAGAGACAGAAGGTG
GCACTGTTCTTACTGCCACCACGTCAGAACTTGAAGCTATTAATAAAAGAGTGAAAGATACTAT
GGCAAGATCAGAAGATTTGGATAATTCCATTGACAAAACAGAAGCTGGAATTAAAGAGCTCCAG
AAAAGCATGGAGCGCTGGAAGAACATGGAGAAGGAGCACATGGATGCCATAAATCACGACACTA
AAGAGCTGGAGAAGATGACCAACCGACAGGGCATGCTGTTGAAGAAGAAAGAGGAGTGCATGAA
GAAGATCCGAGAGCTGGGGTCCCTTCCCCAGGAAGCATTTGAAAAGTACCAGACACTGAGCCTG
AAGCAGTTGTTTCGGAAACTTGAGCAGTGCAACACAGAGTTGAAGAAGTACAGCCATGTCAACA
AGAAGGCTCTGGACCAGTTTGTGAATTTCTCTGAGCAGAAGGAGAAACTGATAAAGCGACAGGA
AGAATTGGACAGGGGCTACAAGTCAATCATGGAGTTGATGAATGTACTCGAACTTAGAAAATAT
GAAGCTATCCAGTTAACCTTCAAACAGGTATCTAAGAACTTTAGTGAAGTTTTCCAGAAGTTGG
TACCTGGGGGAAAAGCGACCTTGGTGATGAAGAAAGGAGACGTGGAGGGCAGCCAGTCTCAGGA
CGAAGGAGAGGGGAGCGGCGAGAGCGAGAGGGGCTCTGGGTCACAAAGCAGCGTTCCATCAGTT
GACCAGTTCACAGGAGTCGGGATCAGGGTATCATTTACAGGAAAGCAAGGCGAGATGAGAGAAA
TGCAGCAGCTTTCAGGAGGGCAGAAGTCTCTGGTAGCCCTTGCTCTCATTTTTGCCATTCAGAA
GTGTGACCCTGCTCCTTTCTACCTGTTTGATGAGATCGACCAAGCTTTGGATGCTCAGCACAGA
AAAGCTGTGTCAGATATGATTATGGAACTAGCTGTACACGCCCAGTTTATCACTACCACTTTTA
GGCCTGAACTGCTTGAGTCTGCTGATAAATTCTACGGTGTAAAGTTCAGAAATAAGGTTAGTCA
CATCGACGTGATCACAGCAGAGATGGCCAAAGACTTTGTAGAAGACGATACCACGCATGGTTAA
CTGAAAGATAACGCCTGCCGTCTTGGAAGATGTGTATAGTAATGTGGTCCGTACCTGGGAACTG
TAAATTTTAAAAATAATAATTGGTTATTACTGAGTTTTTGGATTTAGAATACACAGTCCTTTTA
TACTTGTCTTTGTATTTTATAAGCTCCCCTGTAATGTTACATTTCTACGTATAGTCGAGGAATT
TTATTTCCTACACGACTTTTTGTAAGTGTCCTCCTATTTTAAATCTTTTGAGATTCTAAATATT
CCCAATTATTTTATAGCTTCTATTAAATAATTGGTTTGTGACTAACTTAGTGTAAATGTGGCCT
TTTGTCTTTGTAATTGTTAGAAACATTCAATAAATATTTTGCATAAGAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039109434 ⟹ XP_038965362

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	262,606,731 - 262,649,832 (+)	NCBI
mRatBN7.2	1	252,601,422 - 252,644,522 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_113771	(Get FASTA)	NCBI Sequence Viewer
	XP_038965362	(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
Ensembl Protein	ENSRNOP00000051571
GenBank Protein	P97690	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_113771 ⟸ NM_031583

- UniProtKB:

P97690 (UniProtKB/Swiss-Prot), A6JHW2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MYIKQVIIQGFRSYRDQTIVDPFSSKHNVIVGRNGSGKSNFFYAIQFVLSDEFSHLRPEQRLAL
LHEGTGPRVISAFVEIIFDNSDNRLPIDKEEVSLRRVIGAKKDQYFLDKKMVTKNDVMNLLESA
GFSRSNPYYIVKQGKINQMATAPDSQRLKLLREVAGTRVYDERKEESISLMKETEGKREKINEL
LKYIEERLHTLEEEKEELAQYQKWDKMRRALEYTIYNQELNETRAKLDELSAKRETSGEKSRQL
RDAQQDARDKMEDIERQVRELKTKISAMKEEKEQLSAERQEQIKQRTKLELKAKDLQDELAGNS
EQRKRLLKERQKLLEKIEEKQKELAETEPKFNSVKEKEERGIARLAQATQERTDLYAKQGRGSQ
FTSKEERDKWIKKELKSLDQAINDKKRQIAAIHKDLEDTEANKEKNLEQYNKLDQDLNEVKARV
EELDRKYYEVKNKKDELQSERNYLWREENAEQQALAAKREDLEKKQQLLRAATGKAILNGIDSI
NKVLDHFRRKGINQHVQNGYHGIVMNNFECEPAFYTCVEVTAGNRLFYHIVDSDEVSTKILMEF
NKMNLPGEVTFLPLNKLDVRDTAYPETNDAIPMISKLRYNPRFDKAFKHVFGKTLICRSMEVST
QLARAFTMDCITLEGDQVSHRGALTGGYYDTRKSRLELQKDVRKAEEELGELEAKLNENLRRNI
ERINNEIDQLMNQMQQIETQQRKFKASRDSILSEMKMLKEKRQQSEKTFMPKQRSLQSLEASLH
AMESTRESLKAELGTDLLSQLSLEDQKRVDALNDEIRQLQQENRQLLNERIKLEGIITRVETYL
NENLRKRLDQVEQELNELRETEGGTVLTATTSELEAINKRVKDTMARSEDLDNSIDKTEAGIKE
LQKSMERWKNMEKEHMDAINHDTKELEKMTNRQGMLLKKKEECMKKIRELGSLPQEAFEKYQTL
SLKQLFRKLEQCNTELKKYSHVNKKALDQFVNFSEQKEKLIKRQEELDRGYKSIMELMNVLELR
KYEAIQLTFKQVSKNFSEVFQKLVPGGKATLVMKKGDVEGSQSQDEGEGSGESERGSGSQSSVP
SVDQFTGVGIRVSFTGKQGEMREMQQLSGGQKSLVALALIFAIQKCDPAPFYLFDEIDQALDAQ
HRKAVSDMIMELAVHAQFITTTFRPELLESADKFYGVKFRNKVSHIDVITAEMAKDFVEDDTTH
G

hide sequence

Ensembl Acc Id:

ENSRNOP00000019560 ⟸ ENSRNOT00000019560

Ensembl 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	274,310,087 - 274,310,147	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:62006	AgrOrtholog
BioCyc Gene	G2FUF-55381	BioCyc
Ensembl Genes	ENSRNOG00000014173	Ensembl, ENTREZGENE
Ensembl Transcript	ENSRNOT00000054686	ENTREZGENE
Gene3D-CATH	1.10.287.1490	UniProtKB/Swiss-Prot
	1.20.1060.20	UniProtKB/Swiss-Prot
	3.30.70.1620	UniProtKB/Swiss-Prot
	3.40.50.300	UniProtKB/Swiss-Prot
InterPro	P-loop_NTPase	UniProtKB/Swiss-Prot
	RecF/RecN/SMC_N	UniProtKB/Swiss-Prot
	SMC	UniProtKB/Swiss-Prot
	SMC3_ABC_euk	UniProtKB/Swiss-Prot
	SMC_hinge	UniProtKB/Swiss-Prot
	SMC_hinge_sf	UniProtKB/Swiss-Prot
NCBI Gene	29486	ENTREZGENE
PANTHER	STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3	UniProtKB/Swiss-Prot
Pfam	SMC_hinge	UniProtKB/Swiss-Prot
	SMC_N	UniProtKB/Swiss-Prot
PhenoGen	Smc3	PhenoGen
PIRSF	SMC	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000014173	RatGTEx
SMART	SMC_hinge	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF52540	UniProtKB/Swiss-Prot
	SSF75553	UniProtKB/Swiss-Prot
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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)