Chsy1 (chondroitin sulfate synthase 1)

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Gene: Chsy1 (chondroitin sulfate synthase 1) Rattus norvegicus

Analyze

Symbol:

Chsy1

Name:

chondroitin sulfate synthase 1

RGD ID:

1311904

Description:

Predicted to have N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity and glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity. Involved in response to nutrient levels. Predicted to localize to extracellular region. Human ortholog(s) of this gene implicated in temtamy preaxial brachydactyly syndrome. Orthologous to human CHSY1 (chondroitin sulfate synthase 1); PARTICIPATES IN chondroitin sulfate biosynthetic pathway; INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

carbohydrate (chondroitin) synthase 1; LOC292999

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

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):	CHSY1 (chondroitin sulfate synthase 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Chsy1 (chondroitin sulfate synthase 1)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Chsy1 (chondroitin sulfate synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CHSY1 (chondroitin sulfate synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CHSY1 (chondroitin sulfate synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Chsy1 (chondroitin sulfate synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CHSY1 (chondroitin sulfate synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	CHSY1 (chondroitin sulfate synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Chsy1 (chondroitin sulfate synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CHSY1 (chondroitin sulfate synthase 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Chsy1 (chondroitin sulfate synthase 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	chsy1 (chondroitin sulfate synthase 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG9220	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	sqv-5	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Allele / Splice:

Chsy1^{Tn(sb-T2/Bart3)2.165Mcwi}

Genetic Models:

F344-Chsy1^{Tn(sb-T2/Bart3)2.165Mcwi}

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	119,689,626 - 119,750,711 (+)	NCBI
Rnor_6.0 Ensembl	1	127,010,588 - 127,071,570 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	127,010,587 - 127,071,570 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	128,095,353 - 128,156,041 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	120,539,002 - 120,600,102 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	120,616,912 - 120,677,080 (+)	NCBI
Celera	1	111,901,152 - 111,961,962 (+)	NCBI		Celera
Cytogenetic Map	1	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Experimental Liver Cirrhosis (ISO)

genetic disease (ISO)

Hearing Loss (ISO)

temtamy preaxial brachydactyly syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane (EXP)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (EXP,ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,3,7,8-Tetrachlorodibenzofuran (ISO)

3',5'-cyclic AMP (EXP)

3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine (ISO)

4,4'-diaminodiphenylmethane (EXP)

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

chloropicrin (ISO)

choline (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dioxygen (ISO)

disodium selenite (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

folic acid (ISO)

formaldehyde (ISO)

genistein (ISO)

gentamycin (EXP)

hydrogen peroxide (ISO)

L-methionine (ISO)

lipopolysaccharide (ISO)

N-nitrosodimethylamine (EXP)

nickel dichloride (EXP)

nickel subsulfide (EXP)

panobinostat (ISO)

paracetamol (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

poly(I:C) (EXP)

SB 431542 (ISO)

Soman (EXP)

sunitinib (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

trichostatin A (ISO)

triphenyl phosphate (EXP)

valproic acid (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

bone morphogenesis (ISO)

cartilage development (ISO)

chondrocyte development (ISO)

chondroitin sulfate biosynthetic process (IBA,ISO)

negative regulation of ossification (ISO)

positive regulation of smoothened signaling pathway (ISO)

proximal/distal pattern formation (ISO)

response to nutrient levels (IEP)

sulfation (ISO)

Cellular Component

cellular_component (ND)

extracellular region (ISO)

Golgi cisterna membrane (IEA)

integral component of membrane (IEA)

Molecular Function

acetylgalactosaminyltransferase activity (IBA)

glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (IBA,ISO)

molecular_function (ND)

N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (ISO)

transferase activity, transferring glycosyl groups (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

chondroitin sulfate biosynthetic pathway (IEA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	OMIM Disease Annotation Pipeline
3.	Pipeline to import KEGG annotations from KEGG into RGD
4.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	RGD automated import pipeline for gene-chemical interactions
6.	RGD comprehensive gene curation
7.	Titze J, etal., Am J Physiol Heart Circ Physiol. 2004 Jul;287(1):H203-8. Epub 2004 Feb 19.

Additional References at PubMed

PMID:11514575	PMID:19946888	PMID:21129727	PMID:22280990	PMID:22952769	PMID:26356269

Genomics

Comparative Map Data

Chsy1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	119,689,626 - 119,750,711 (+)	NCBI
Rnor_6.0 Ensembl	1	127,010,588 - 127,071,570 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	127,010,587 - 127,071,570 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	128,095,353 - 128,156,041 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	120,539,002 - 120,600,102 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	120,616,912 - 120,677,080 (+)	NCBI
Celera	1	111,901,152 - 111,961,962 (+)	NCBI		Celera
Cytogenetic Map	1	q22	NCBI

CHSY1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	101,175,727 - 101,252,048 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	101,175,727 - 101,252,048 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	101,715,932 - 101,792,253 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	99,533,455 - 99,609,649 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	15	99,533,455 - 99,609,649	NCBI
Celera	15	78,129,035 - 78,204,977 (-)	NCBI
Cytogenetic Map	15	q26.3	NCBI
HuRef	15	77,838,413 - 77,914,374 (-)	NCBI		HuRef
CHM1_1	15	101,556,975 - 101,633,122 (-)	NCBI		CHM1_1

Chsy1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	65,759,240 - 65,823,546 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	7	65,759,263 - 65,823,546 (+)	Ensembl
GRCm38	7	66,109,492 - 66,173,798 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	66,109,515 - 66,173,798 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	73,254,401 - 73,318,684 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	7	65,988,465 - 66,052,748 (+)	NCBI			mm8
Celera	7	63,545,296 - 63,619,383 (+)	NCBI		Celera
Cytogenetic Map	7	C	NCBI

Chsy1
(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_004955416	28,070,710 - 28,135,590 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955416	28,070,981 - 28,136,848 (-)	NCBI	ChiLan1.0	ChiLan1.0

CHSY1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	15	99,186,705 - 99,259,882 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	99,186,705 - 99,260,591 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	15	79,901,340 - 79,976,067 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

CHSY1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	3	39,844,195 - 40,021,573 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	3	39,844,227 - 39,916,484 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Chsy1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936483	2,613,820 - 2,685,986 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CHSY1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	139,730,721 - 139,804,583 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	139,730,703 - 139,804,458 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	155,960,054 - 156,033,821 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CHSY1
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	29	19,633,335 - 19,707,547 (-)	NCBI
ChlSab1.1 Ensembl	29	19,632,026 - 19,707,425 (-)	Ensembl

Chsy1
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624768	3,567,770 - 3,628,360 (+)	NCBI

Position Markers

D1Rat185

Rat Assembly	Chr	Position (strand)	Source
Celera	1	111,906,278 - 111,906,428	UniSTS
RH 3.4 Map	1	1448.59	RGD
RH 3.4 Map	1	1448.59	UniSTS
SHRSP x BN Map	1	56.5	UniSTS
SHRSP x BN Map	1	56.5	RGD
FHH x ACI Map	1	57.02	RGD
Cytogenetic Map	1	q22	UniSTS

AI598496

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	127,070,711 - 127,070,917	NCBI	Rnor6.0
Rnor_5.0	1	128,155,182 - 128,155,388	UniSTS	Rnor5.0
RGSC_v3.4	1	120,599,243 - 120,599,449	UniSTS	RGSC3.4
Celera	1	111,961,103 - 111,961,309	UniSTS
RH 3.4 Map	1	1447.0	UniSTS
Cytogenetic Map	1	q22	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	25951907	130917265	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34993530	173445086	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	49147799	156446783	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49578577	169852184	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	58354072	161711996	Rat
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	82788437	239853971	Rat
10054135	Gmadr2	Adrenal mass QTL 2	1.97	0.0129	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	83502376	128502376	Rat
61344	Bp29	Blood pressure QTL 29	7.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	85779320	130779320	Rat
1582234	Gluco18	Glucose level QTL 18	3.4	0.0003	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	85917265	130917265	Rat
4889494	Scort2	Serum corticosterone level QTL 2	4.2		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	86776571	131776571	Rat
724529	Cm16	Cardiac mass QTL 16	2.7		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	1	90804143	161321256	Rat
738022	Anxrr13	Anxiety related response QTL 13	4.6	0.00039	locomotor behavior trait (VT:0001392)	number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)	1	91093646	136093646	Rat
724521	Uae1	Urinary albumin excretion QTL 1	3.8	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	94201400	184846632	Rat
1358902	Bw47	Body weight QTL 47	1.67		body mass (VT:0001259)	body weight (CMO:0000012)	1	94201400	197187904	Rat
1302788	Scl19	Serum cholesterol QTL 19	4.6	0.001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	94225372	130917265	Rat
1300153	Bp171	Blood pressure QTL 171	3.37		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	94364073	153076991	Rat
724567	Tcas6	Tongue tumor susceptibility QTL 6	6.85		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	1	95304961	156446783	Rat
1331800	Scl25	Serum cholesterol level QTL 25	3.013		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	99983293	127203999	Rat
1331793	Bp200	Blood pressure QTL 200	3.71601		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	99983293	188289386	Rat
1331751	Bp199	Blood pressure QTL 199	3.60022		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	99983293	198656062	Rat
1331749	Hrtrt11	Heart rate QTL 11	2.973		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	99983293	216213510	Rat
70209	Niddm23	Non-insulin dependent diabetes mellitus QTL 23	2.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	99983293	216325819	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	100131562	236763528	Rat
2293142	Bp314	Blood pressure QTL 314			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	100354344	145354344	Rat
8655649	Arrd1	Age-related retinal degeneration QTL 1	4.89		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	106002252	202571904	Rat
61370	Mcs3	Mammary carcinoma susceptibility QTL 3	2.15		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	108057233	167517487	Rat
1641897	Alcrsp1	Alcohol response QTL 1			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	1	108417193	153417193	Rat
2317833	Alcrsp19	Alcohol response QTL 19	12.4	0.001	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	1	108417193	153417193	Rat
1354623	Rf46	Renal function QTL 46	3.8		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	1	108986301	161784422	Rat
1354591	Cm36	Cardiac mass QTL 36	4.1		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	108986301	219232156	Rat
1354615	Cm32	Cardiac mass QTL 32	5.2		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	108986301	219232156	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	108986301	238830534	Rat
2303591	Gluco41	Glucose level QTL 41	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	109634374	154634374	Rat
9590300	Scort16	Serum corticosterone level QTL 16	4.39	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	110620749	155620749	Rat
8694370	Bw154	Body weight QTL 154	8.91	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	1	110620749	155620749	Rat
61399	Tcat1	Tongue tumor resistance QTL 1	3.3		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 5 mm (CMO:0001879)	1	111446783	156446783	Rat
61346	Rf2	Renal disease susceptibility QTL 2	3.7		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	1	111446783	156446783	Rat
631569	Bp93	Blood pressure QTL 93		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	113593576	129209407	Rat
631496	Bp97	Blood pressure QTL 97	3.08		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	113593576	158593576	Rat
1300158	Bp173	Blood pressure QTL 173	3.48		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	1	122614824	201146953	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	122614824	262664716	Rat
2313060	Bss71	Bone structure and strength QTL 71	2.6	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	1	124090312	169090312	Rat
631199	Cm23	Cardiac mass QTL 23	4.6	0.0004	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	124603592	188289386	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	125875758	262433692	Rat
631205	Bp196	Blood pressure QTL 196	4	0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	126240667	217054291	Rat

Genetic Models

This gene Chsy1 is modified in the following models/strains

F344-Chsy1^{Tn(sb-T2/Bart3)2.165Mcwi}

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	809
Count of miRNA genes:	303
Interacting mature miRNAs:	378
Transcripts:	ENSRNOT00000016939
Prediction methods:	Microtar, 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	2	32	25	16	18	16	1	1	74	22	34	11	1
Low	1	11	32	25	1	25	7	10		13	7		7
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106268	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039105374	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473980	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000039	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000016939 ⟹ ENSRNOP00000016939

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	127,010,588 - 127,071,570 (+)	Ensembl

RefSeq Acc Id:

NM_001106268 ⟹ NP_001099738

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	119,689,626 - 119,750,601 (+)	NCBI
Rnor_6.0	1	127,010,587 - 127,071,570 (+)	NCBI
Rnor_5.0	1	128,095,353 - 128,156,041 (+)	NCBI
RGSC_v3.4	1	120,539,002 - 120,600,102 (+)	RGD
Celera	1	111,901,152 - 111,961,962 (+)	RGD

Sequence:

show sequence

CGCGCGGCCGGCGCGCCTGGCTCAGCATGCTGCTCGGGCTCGTGCTGGGCTTCGTGCTGGCCTC
GCGACTCGTCCTGCCCCGCGCCTCGGAGCTGAAGCGAGTGGGCCCGCGGCGGCGCCCCAATCCC
GAGGGATGCCGGCCAGGACAGGCAGCGTCGCAGCCCGGCGGTGCTCCGGGGGATGCGCGCGGGG
CGCAGCTCTGGCCGCAGGGCTCGGCCGCGGAGGGCGTCCCGCGCGACAGGAACTTTCTCTTCGT
GGGAGTCATGACCGCCCAGAAATACCTGCAGACTCGCGCCGTGGCCGCTTACAGAACATGGTCC
AAGACAATTCCCGGGAAGGTTGAGTTCTTCTCTAGTGAGGGTTCAGACACATCTATACCCATTC
CAGTAGTGCCACTGAGGGGTGTGGACGACTCCTATCCCCCCCAGAAGAAGTCTTTCATGATGCT
CAAGTACATGCACGATCACTACTTGGACAAGTACGAATGGTTTATGAGAGCAGATGATGATGTC
TACATCAAGGGAGATCGTCTGGAGAGCTTTCTGAGGAGTTTGAATAGCAGCGAGCCCCTCTTTC
TCGGGCAGACAGGACTGGGCACCACTGAAGAAATGGGGAAACTGGCTCTTGAGCCTGGAGAGAA
CTTCTGCATGGGGGGACCTGGTGTGATTCTGAGCCGGGAAGTGCTTCGGAGAATGGCACCACAC
ATTGGCAAGTGTCTCCGGGAAATGTACACCACCCACGAGGATGTAGAGGTGGGGAGGTGCGTCC
GGAGATTCGCAGGCGTGCAGTGCGTCTGGTCATATGAGATGCAGCAGCTTTTTTACGAGAATTA
TGAACAGAACAAGAAAGGGTACATTAGAGATCTCCATAGCAGTAAAATCCACCGAGCGATCACT
TTACACCCCAACAAAAACCCGCCCTACCAGTACAGGCTACACAGTTACATGCTCAGCCGCAAGA
TCGCTGAGCTGCGCCATCGCACAATCCAGCTGCACCGGGAGATCGTCCTGATGAGCAAGTACAG
CAGCACGGAAATCCAGAAGGAAGACCTCCAGCTGGGCATCCCTCCCTCCTTCATGCGCTTTCAG
GCCCGCCAGCGAGAGGAGATCCTGGAGTGGGAGTTTCTGACTGGGAAATACTTATATTCAGCCA
CGGAAGGCCAGCCTCCCCGGAGAGGGATGGACTCAGCGCAGAGGGAGGCCTTGGATGACATTGT
CCTGCAAGTGATGGAGATGATCAATGCCAATGCCAAGACCCGGGGCCGCATCATCGACTTCAAG
GAGATCCAGTATGGCTACAGACGCGTGAATCCCATGTACGGGGCAGAGTACATCCTGGATCTGC
TGCTCCTGTATAAGAAGCACAAAGGGAAGAAGATGACGGTCCCTGTGAGGAGGCACGCGTACCT
GCAGCAGACCTTCAGCAAGATCCAGTTTGTGGAGCATGAGGGCCTGGATGCACAAGAGCTCGCT
GACAGAATCAACCAGGACTCTGGGTCCCTGTCATTCCTCTCCAATTCCTTGAAGAAGCTCGTTC
CCTTCCAGCTTCCTGGATCCAAGATGGAGCACAAAGAGCCCAAAGAAAAGAAGATAAACATTCT
GATCCCTTTGTCTGGACGCTTCGACATGTTTGTGAGGTTCATGGGAAACTTTGAGAAGACGTGT
CTCATTCCAAATCTGAACGTGAAGCTGGTCATTCTGCTTTTCAATTCTGACTCTAACCCCGACA
AGGCCAAGCAGGTCGAGCTGATGCGAGATTACCGAGTCAAGTACCCGAAGGCTGACATGCAAGT
TTTGCCTGTGTCTGGAGGGTTTTCGAGAGCACTGGCCCTAGAAGTAGGCTCTTCGCAGTTTAGT
AATGAGTCTCTGCTCTTCTTCTGTGATGTGGACCTGGTGTTTACAGCGGAGTTCCTGCAGAGGT
GCCGAGCCAACACTGTGCTGGGCCAGCAGATCTACTTCCCAATCATCTTTAGCCAGTACGATCC
AAAGATTGTCTATAGTGGGAAGGTTCCCAGTGACAACCATTTTGCCTTTACTCAAAAAACCGGC
TTCTGGAGAAACTATGGGTTTGGCATTACTTGTATCTATAAGGGAGATCTTGTCAGAGTGGGAG
GCTTCGATGTCTCCATCCAGGGCTGGGGGCTGGAGGATGTGGACCTCTTTAACAAGGTCGTCCA
GGCAGGATTGAAGACATTCCGGAGCCAGGAGGTCGGGGTTGTTCACGTCCACCACCCTGTCTTC
TGTGACCCGAATCTGGACCCCAAGCAGTATAAAATGTGCCTGGGGTCGAAGGCGTCAACATTCG
GGTCCACACAGCAGTTGGCTGAAATGTGGCTGGAGAAGAATGACCCCAGTTACAGCAGAGGCGG
CAACGGCTCGGCCAGGACAGTCTGATTCCGGCCCGCTGCGAAGGACAGTTTTAATTGCCTAATT
TATTTTTAAAAAATTTTTGTATAATCAGTTTTTGAAGTCCGTACAAGGATATATTTTCCAAGTG
GTTTTCTTACACAGGACTCCTTTAAGATTGAGCTTTTTGAACAAAAATGTGATCAATGTTTGCC
TTTGAACACACCTTGCTGAACACTATGTAGCACCGGCTTAGTCCTGACTTGAAGCCCACCCAAT
GAGCAAAACTTTTCTATAAGAATTTTTTGGTCTTTGGTTTTTACATTTCTTTTCCAGACAACTC
CCCTTTTTCTCTCTAGTCCTAAGGCAGAAAAAACGTGAACATTCCTAAGAAGTATTATCGTGAT
AAGAACACTGTAACCCTGGTGGATGTCCTGTTGAGACTGTTGACCTGTCTCTGGTAAATGTCCT
GTTGTGACTGTTAACCTGTTGCCTTTGCACAAATTCTACCTTTTTCCTGTTTTTTTTTTTAAAC
AGTTTGGTTTTTTTTTTTAAAGCCATCCTGAGTTCCAGTCACAAAGTAAAGAGATGTGATAGTG
GTTGTATTGTCATTCTCTCCAGGAGAGCCTTCCAAATCAGATTACTTCCCCGCTGTGCTCCACC
CCCCACTGTCACAGGTTTTTCCCACCCAGCCCGTGGTGGGTGGGGGATGGAGGAAGGCACGCAT
GTGCTGACCCCTCTCTAATCCTGCGACCCAGACGGACCTGGCACTGAAGTCCAAGAAGGACTCG
GCATTTTCTCTGCCCCGCCCTTCTCTGTAGAGGGTACAGTATTATTAGGGTGACAAAGAACGGC
TGGTAGCAGTGGAATGAATGCAAGCTTACAGACAAACCCCTGATGGACGTGTGAGGGAAGTTGG
CGCTTTGTTCTCTGTCCTGTGTTGTGGATGGAGATGACTGCTCCATTTTTTAATTACTGGTTTT
TCTATCTTGTTATCTGCAATACCTTTAATTTATTTAATACCATTGTTTAGATCTCTGCCATTTT
GAGTACTTGTCAGTCACTAGTATTTATGTGTACCATGAGTGTGGTTAGAACGTTTTATTTGCAG
TAAACTGATCTCCAAAGATTTCCTTTTGAAAACACTTTTCCCTCATCCTTAATTTTTACATTCC
CGTCTTACTAAAGATTAAGTGTTCTTTGATAATTTTGGTGCTCATGTGTTTTGGGGACAAAGGT
GAAATGAGTCTGTTGTTATACCAGAGTGTTTGTTTTCAACTTACAGATCCAATGTGCCTTAATA
ATTTGTTTTCATTTAGAGTTCAGACAGTTGATAGAGTTGCCATTTTTAATATACATCATTGGAG
ATCTGCTTATCTGTAAATAGCCTGTTGCACATCCGAACAAATAAAC

hide sequence

RefSeq Acc Id:

XM_039105374 ⟹ XP_038961302

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	119,731,589 - 119,750,711 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001099738	(Get FASTA)	NCBI Sequence Viewer
	XP_038961302	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM08427	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001099738 ⟸ NM_001106268
- Peptide Label:	precursor
- UniProtKB:	D3ZRM3 (UniProtKB/TrEMBL)
- Sequence:	show sequence MLLGLVLGFVLASRLVLPRASELKRVGPRRRPNPEGCRPGQAASQPGGAPGDARGAQLWPQGSA AEGVPRDRNFLFVGVMTAQKYLQTRAVAAYRTWSKTIPGKVEFFSSEGSDTSIPIPVVPLRGVD DSYPPQKKSFMMLKYMHDHYLDKYEWFMRADDDVYIKGDRLESFLRSLNSSEPLFLGQTGLGTT EEMGKLALEPGENFCMGGPGVILSREVLRRMAPHIGKCLREMYTTHEDVEVGRCVRRFAGVQCV WSYEMQQLFYENYEQNKKGYIRDLHSSKIHRAITLHPNKNPPYQYRLHSYMLSRKIAELRHRTI QLHREIVLMSKYSSTEIQKEDLQLGIPPSFMRFQARQREEILEWEFLTGKYLYSATEGQPPRRG MDSAQREALDDIVLQVMEMINANAKTRGRIIDFKEIQYGYRRVNPMYGAEYILDLLLLYKKHKG KKMTVPVRRHAYLQQTFSKIQFVEHEGLDAQELADRINQDSGSLSFLSNSLKKLVPFQLPGSKM EHKEPKEKKINILIPLSGRFDMFVRFMGNFEKTCLIPNLNVKLVILLFNSDSNPDKAKQVELMR DYRVKYPKADMQVLPVSGGFSRALALEVGSSQFSNESLLFFCDVDLVFTAEFLQRCRANTVLGQ QIYFPIIFSQYDPKIVYSGKVPSDNHFAFTQKTGFWRNYGFGITCIYKGDLVRVGGFDVSIQGW GLEDVDLFNKVVQAGLKTFRSQEVGVVHVHHPVFCDPNLDPKQYKMCLGSKASTFGSTQQLAEM WLEKNDPSYSRGGNGSARTV hide sequence

RefSeq Acc Id:

ENSRNOP00000016939 ⟸ ENSRNOT00000016939

RefSeq Acc Id:	XP_038961302 ⟸ XM_039105374
- Peptide Label:	isoform X1

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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

ACI/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

BBDP/Wor (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

BN/SsN (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

Buf/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

COP/CrCrl (MCW & UW)

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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)

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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

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311904	AgrOrtholog
Ensembl Genes	ENSRNOG00000012698	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000016939	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016939	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.90.550.10	UniProtKB/TrEMBL
InterPro	Chond_GalNAc	UniProtKB/TrEMBL
	Nucleotide-diphossugar_trans	UniProtKB/TrEMBL
KEGG Report	rno:292999	UniProtKB/TrEMBL
NCBI Gene	292999	ENTREZGENE
Pfam	CHGN	UniProtKB/TrEMBL
PhenoGen	Chsy1	PhenoGen
Superfamily-SCOP	SSF53448	UniProtKB/TrEMBL
Transposagen	Chsy1_predicted	Transposagen
UniProt	D3ZRM3	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-18	Chsy1	chondroitin sulfate synthase 1	Chsy1_predicted	carbohydrate (chondroitin) synthase 1 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-12	Chsy1_predicted	carbohydrate (chondroitin) synthase 1 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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 - OMIM

Imported Annotations - KEGG (archival)