Sds (serine dehydratase) - Rat Genome Database

Name: Sds
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Sds (serine dehydratase) Rattus norvegicus

Analyze

Symbol:

Sds

Name:

serine dehydratase

RGD ID:

67376

Description:

Predicted to have ammonia-lyase activity; protein homodimerization activity; and pyridoxal phosphate binding activity. Involved in protein-containing complex assembly; response to amino acid; and response to cobalamin. Predicted to localize to cytosol and mitochondrion. Orthologous to human SDS (serine dehydratase); PARTICIPATES IN dihydropyrimidine dehydrogenase deficiency pathway; dimethylglycine dehydrogenase deficiency pathway; nonketotic hyperglycinemia pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

L-serine deaminase; L-serine dehydratase/L-threonine deaminase; L-threonine dehydratase; MGC108581; RATSDHE1; Sdh; SDH2; Sdhe1; TDH

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):	SDS (serine dehydratase)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Sds (serine dehydratase)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Sds (serine dehydratase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SDS (serine dehydratase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SDS (serine dehydratase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Sds (serine dehydratase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SDS (serine dehydratase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	SDS (serine dehydratase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Sds (serine dehydratase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	SDSL (serine dehydratase like)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	SDS (serine dehydratase)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Sds (serine dehydratase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	sdsl (serine dehydratase-like)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoInspector\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	CHA1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

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
Rnor_6.0	12	41,620,429 - 41,627,741 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	41,620,393 - 41,627,741 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	43,473,323 - 43,480,635 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	37,281,091 - 37,288,403 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	37,144,510 - 37,151,603 (-)	NCBI
Celera	12	37,743,289 - 37,750,601 (-)	NCBI		Celera
Cytogenetic Map	12	q16	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)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (EXP)

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

2,6-dinitrotoluene (EXP)

2-nitrofluorene (EXP)

3,3',4,4',5-pentachlorobiphenyl (EXP,ISO)

4,4'-diaminodiphenylmethane (EXP)

4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one (EXP)

6-propyl-2-thiouracil (EXP)

acetylsalicylic acid (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

benzene (ISO)

benzo[a]pyrene (ISO)

beta-naphthoflavone (EXP)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

bromobenzene (EXP)

buspirone (EXP)

calcitriol (ISO)

ciguatoxin CTX1B (ISO)

copper atom (EXP)

copper(0) (EXP)

cyclosporin A (ISO)

decabromodiphenyl ether (EXP)

diethyl maleate (EXP)

endosulfan (ISO)

ethanol (EXP)

flutamide (EXP)

glafenine (EXP)

metformin (EXP)

methotrexate (ISO)

monosodium L-glutamate (ISO)

N-nitrosodiethylamine (EXP,ISO)

N-nitrosodimethylamine (EXP)

nefazodone (EXP)

nimesulide (EXP)

ozone (EXP)

paracetamol (EXP,ISO)

pentachlorophenol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (EXP,ISO)

phenethyl caffeate (EXP)

phenformin (EXP)

phenobarbital (EXP,ISO)

phlorizin (ISO)

piperonyl butoxide (EXP)

pirinixic acid (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

propiconazole (ISO)

resveratrol (EXP)

rotenone (EXP)

streptozocin (EXP)

tamoxifen (ISO)

tetrachloromethane (EXP,ISO)

theophylline (ISO)

thioacetamide (EXP)

triphenyl phosphate (EXP)

trovafloxacin (EXP)

valdecoxib (EXP)

valproic acid (ISO)

zinc atom (EXP)

zinc(0) (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

gluconeogenesis (IEA,TAS)

isoleucine biosynthetic process (IBA)

L-serine catabolic process (IEA,ISO)

protein-containing complex assembly (IDA)

pyruvate biosynthetic process (IEA,ISO)

response to amino acid (IEP)

response to cobalamin (IEP)

response to nutrient levels (IEP)

threonine catabolic process (IBA)

Cellular Component

cellular_component (ND)

cytoplasm (IEA)

cytosol (IEA,ISO)

mitochondrion (IEA,ISO)

Molecular Function

L-serine ammonia-lyase activity (IEA,ISO,TAS)

L-threonine ammonia-lyase activity (IBA)

protein binding (ISO)

protein homodimerization activity (IEA,ISO)

pyridoxal phosphate binding (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

cysteine and methionine metabolic pathway (IEA)

dihydropyrimidine dehydrogenase deficiency pathway (ISO)

dimethylglycine dehydrogenase deficiency pathway (ISO)

glycine, serine and threonine metabolic pathway (IEA)

nonketotic hyperglycinemia pathway (ISO)

sarcosinemia pathway (ISO)

References

References - curated


1.	Andoh Y, etal., Mamm Genome 1998 Apr;9(4):287-93.
2.	Ebara S, etal., Br J Nutr. 2008 Mar;99(3):503-10. Epub 2007 Aug 29.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	GOA data from the GO Consortium
5.	KEGG
6.	MGD data from the GO Consortium
7.	Nagao K, etal., Amino Acids. 2009 Mar;36(3):555-62. Epub 2008 Jun 27.
8.	Noda C, etal., J Biochem (Tokyo) 1990 Oct;108(4):622-8.
9.	Ogawa H, etal., Int J Biochem Cell Biol 2002 May;34(5):533-43.
10.	Ogawa H, etal., J Biol Chem 1990 Aug 25;265(24):14407-13.
11.	Ogawa H, etal., Nucleic Acids Res 1988 Nov 25;16(22):10921-3.
12.	Ogawa H, etal., Proc Natl Acad Sci U S A 1988 Aug;85(16):5809-13.
13.	OMIM Disease Annotation Pipeline
14.	Pipeline to import KEGG annotations from KEGG into RGD
15.	Pipeline to import SMPDB annotations from SMPDB into RGD
16.	Rees WD, etal., Reprod Nutr Dev. 2006 May-Jun;46(3):227-39. Epub 2006 May 30.
17.	RGD automated import pipeline for gene-chemical interactions
18.	RGD comprehensive gene curation
19.	Zhang B and Lin S, Biomed Environ Sci. 2009 Feb;22(1):40-3.

Additional References at PubMed

PMID:2228554	PMID:2228555	PMID:2660911	PMID:3391277	PMID:7581747	PMID:8311466	PMID:12477932	PMID:12882394	PMID:14596599	PMID:15689518	PMID:16793941	PMID:17928680
PMID:18342636	PMID:23087176

Genomics

Comparative Map Data

Sds
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	12	41,620,429 - 41,627,741 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	41,620,393 - 41,627,741 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	43,473,323 - 43,480,635 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	37,281,091 - 37,288,403 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	37,144,510 - 37,151,603 (-)	NCBI
Celera	12	37,743,289 - 37,750,601 (-)	NCBI		Celera
Cytogenetic Map	12	q16	NCBI

SDS
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	12	113,392,445 - 113,426,301 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	12	113,392,445 - 113,403,887 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	12	113,830,250 - 113,841,692 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	112,314,633 - 112,326,075 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	12	112,292,969 - 112,304,412	NCBI
Celera	12	113,457,510 - 113,468,952 (-)	NCBI
Cytogenetic Map	12	q24.13	NCBI
HuRef	12	110,841,538 - 110,852,991 (-)	NCBI		HuRef
CHM1_1	12	113,798,461 - 113,809,912 (-)	NCBI		CHM1_1

Sds
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	120,614,612 - 120,621,997 (+)	NCBI	GRCm39		mm39
GRCm38	5	120,476,547 - 120,483,932 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	120,476,526 - 120,483,932 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	120,926,556 - 120,933,914 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	5	120,737,164 - 120,744,522 (+)	NCBI			mm8
Celera	5	117,560,914 - 117,568,244 (+)	NCBI		Celera
Cytogenetic Map	5	F	NCBI

Sds
(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_004955482	9,643,919 - 9,653,375 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955482	9,646,523 - 9,653,471 (-)	NCBI	ChiLan1.0	ChiLan1.0

SDS
(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	12	114,377,643 - 114,388,839 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	114,377,650 - 114,388,839 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	12	110,995,164 - 111,006,668 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

SDS
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	26	10,725,123 - 10,728,087 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Sds
(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_004936668	3,208,810 - 3,213,465 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SDS
(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	38,503,930 - 38,513,880 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	38,503,922 - 38,513,908 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	40,856,187 - 40,866,181 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SDS
(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	11	108,643,198 - 108,654,927 (-)	NCBI
ChlSab1.1 Ensembl	11	108,642,694 - 108,654,620 (-)	Ensembl

Sds
(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_004624747	19,124,706 - 19,131,757 (+)	NCBI

Position Markers

D12Wox15

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	41,628,734 - 41,628,890	NCBI	Rnor6.0
Rnor_5.0	12	43,481,628 - 43,481,784	UniSTS	Rnor5.0
RGSC_v3.4	12	37,289,396 - 37,289,552	UniSTS	RGSC3.4
Celera	12	37,751,594 - 37,751,750	UniSTS
Cytogenetic Map	12	q16	UniSTS

D12Arb7

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	41,628,580 - 41,628,927	NCBI	Rnor6.0
Rnor_5.0	12	43,481,474 - 43,481,821	UniSTS	Rnor5.0
RGSC_v3.4	12	37,289,242 - 37,289,589	UniSTS	RGSC3.4
RGSC_v3.4	12	37,289,241 - 37,289,589	RGD	RGSC3.4
RGSC_v3.1	12	37,152,629 - 37,152,977	RGD
Celera	12	37,751,440 - 37,751,787	UniSTS
Cytogenetic Map	12	q16	UniSTS
SHRSP x BN Map	12	44.3599	UniSTS
SHRSP x BN Map	12	44.3599	RGD

D12Arb16

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	41,625,632 - 41,626,027	NCBI	Rnor6.0
Rnor_5.0	12	43,478,526 - 43,478,921	UniSTS	Rnor5.0
RGSC_v3.4	12	37,286,294 - 37,286,689	UniSTS	RGSC3.4
Celera	12	37,748,492 - 37,748,887	UniSTS
Cytogenetic Map	12	q16	UniSTS

D12Wox17

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	41,628,715 - 41,628,891	NCBI	Rnor6.0
Rnor_5.0	12	43,481,609 - 43,481,785	UniSTS	Rnor5.0
RGSC_v3.4	12	37,289,377 - 37,289,553	UniSTS	RGSC3.4
Celera	12	37,751,575 - 37,751,751	UniSTS
Cytogenetic Map	12	q16	UniSTS

RH141130

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	41,620,119 - 41,620,378	NCBI	Rnor6.0
Rnor_5.0	12	43,473,013 - 43,473,272	UniSTS	Rnor5.0
RGSC_v3.4	12	37,280,781 - 37,281,040	UniSTS	RGSC3.4
Celera	12	37,742,979 - 37,743,238	UniSTS
Cytogenetic Map	12	q16	UniSTS
RH 3.4 Map	12	647.4	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
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	150810	45150810	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	150810	45150810	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	492578	45492578	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	2475687	47475687	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	2513442	47513442	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	2513442	47513442	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	4210051	49210051	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	9223626	52716770	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223630	52716770	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	9789834	52716770	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13127211	50320041	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	14419775	52716770	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	15021986	52716770	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	15908900	52716770	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	15908900	52716770	Rat
631543	Bp83	Blood pressure QTL 83	5.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	17185580	44098244	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	18342477	52716770	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	18342477	52716770	Rat
2302060	Pia37	Pristane induced arthritis QTL 37	6.1	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	18729043	52716770	Rat
1549902	Bp269	Blood pressure QTL 269			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	18752593	52716770	Rat
1549912	Bp268	Blood pressure QTL 268			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	18752593	52716770	Rat
737822	Alc10	Alcohol consumption QTL 10	2.2		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	12	22650702	45946937	Rat
5684888	Pia42	Pristane induced arthritis QTL 42			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	22650702	48598906	Rat
61324	Eae5	Experimental allergic encephalomyelitis QTL 5	14		nervous system integrity trait (VT:0010566)	percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)	12	22650702	52716770	Rat
70213	Niddm27	Non-insulin dependent diabetes mellitus QTL 27	3.72		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	22876297	43799153	Rat
631560	Apr1	Acute phase response QTL 1	6.1		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	24906590	52716770	Rat
7411643	Foco20	Food consumption QTL 20		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	26098845	52716770	Rat
70169	Eae13	Experimental allergic encephalomyelitis QTL 13		0.032	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	12	27190240	42196641	Rat
8693658	Alc33	Alcohol consumption QTL 33	2.1	0.68	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	12	29113609	49560679	Rat
8693635	Alc28	Alcohol consumption QTL 28	2.7	0.439	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	12	29113609	50757185	Rat
1556747	Calcic1	Intracellular calcium level QTL 1		3.6	platelet calcium amount (VT:0010500)	platelet intracellular calcium level (CMO:0000922)	12	31723565	47433663	Rat
1300175	Cm5	Cardiac mass QTL 5	3.78		heart mass (VT:0007028)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	31723565	51955754	Rat
1600386	Calcic2	Intracellular calcium level QTL 2		0.001	platelet physiology trait (VT:0005464)	platelet intracellular calcium level (CMO:0000922)	12	31723565	52716770	Rat
1331787	Rf41	Renal function QTL 41	2.998		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	12	31723688	45946802	Rat
631829	Alc6	Alcohol consumption QTL 6	4.7		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	12	32289782	43305579	Rat
1300162	Bp188	Blood pressure QTL 188	3.19		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	37521884	51955754	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	183
Count of miRNA genes:	109
Interacting mature miRNAs:	113
Transcripts:	ENSRNOT00000001875, ENSRNOT00000001876
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			16	16		16				4
Low	3		10	7	7	7	1	1	10	11	12	6	1
Below cutoff		8	17	4	12	4	6	9	15		4	5	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053962	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07036391	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01072588	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC088110	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473973	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D00746	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	J03863	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	Y00752	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000001875 ⟹ ENSRNOP00000001875

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	41,620,393 - 41,627,741 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000001876 ⟹ ENSRNOP00000001876

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	41,620,591 - 41,625,403 (-)	Ensembl

RefSeq Acc Id:

NM_053962 ⟹ NP_446414

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	12	41,620,429 - 41,627,741 (-)	NCBI
Rnor_5.0	12	43,473,323 - 43,480,635 (-)	NCBI
RGSC_v3.4	12	37,281,091 - 37,288,403 (-)	RGD
Celera	12	37,743,289 - 37,750,601 (-)	RGD

Sequence:

show sequence

GACACAGACAAAATCTACCCTTCTCGCTCGCTCTGTCCAGCTCCTCCTGTGCCGGGTGCGGCGG
GGCATACCTGTGATCCCAGCAATTGGGAGACTGAGACAGGAGGATCCAACCTTCAAAGCTACAT
GCCATGGCTGCCCAGGAGTCCCTGCACGTGAAGACCCCACTACGTGACAGCATGGCATTGTCCA
AAGTGGCCGGCACTAGTGTGTTCCTTAAGATGGACAGCTCTCAGCCCTCTGGCTCCTTCAAGAT
CCGAGGCATTGGGCATCTCTGCAAGATGAAGGCAAAACAAGGCTGTAAACATTTCGTCTGCTCT
TCAGCGGGCAACGCGGGCATGGCGACTGCCTATGCTGCCAGGAGGCTGGGCCTCCCAGCCACTA
TTGTTGTGCCAAGCACCACACCTGCCCTCACCATTGAGCGGCTGAAGAACGAAGGGGCCACAGT
TGAAGTGGTGGGAGAGATGCTGGATGAGGCCATCCAACTGGCCAAGGCTCTGGAAAAGAACAAC
CCAGGTTGGGTGTACATCTCCCCCTTCGATGACCCTCTCATCTGGGAAGGCCACACTTCCCTTG
TGAAGGAGCTGAAGGAGACACTGAGCGCCAAGCCCGGGGCCATTGTGCTGTCTGTGGGCGGTGG
AGGCCTGCTGTGCGGAGTGGTCCAGGGGCTGCGGGAGGTGGGCTGGGAGGATGTGCCCATCATC
GCCATGGAGACCTTCGGCGCCCACAGCTTCCACGCTGCCGTCAAGGAAGGAAAGCTGGTCACCC
TGCCCAAGATCACCAGTGTTGCCAAGGCCTTGGGTGTGAACACTGTGGGGGCACAGACCCTGAA
GCTGTTTTACGAACACCCCATTTTCTCTGAGGTCATCTCAGACCAGGAGGCTGTGACTGCTATC
GAGAAGTTCGTAGACGATGAGAAGATCCTGGTGGAGCCCGCGTGTGGCGCTGCCCTGGCTGCAG
TGTACAGCGGTGTGGTGTGCAGGCTGCAGGCTGAGGGCCGACTGCAAACCCCACTGGCCTCGCT
GGTTGTCATTGTGTGTGGTGGCAGCAACATCAGCCTGGCACAGCTGCAGGCACTCAAGGCACAG
CTGGGCCTGAATGAGCTACTCAAGTGATATCTGCTGCTGCCCTGGCCACCCTGAGGGGTCACCA
GCACCCCTGAGTAGGCTGGGTGGGCGTCCGCCTGACAGTGGCCCACCCTCCTTTATCCATGTTT
ATAATATGCACTTTTTCATTGTAAATAAAAATTAATATATATATGTTTATAAAGCAAAAAAAAA
AAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_446414	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA42123	(Get FASTA)	NCBI Sequence Viewer
	AAH88110	(Get FASTA)	NCBI Sequence Viewer
	CAA68721	(Get FASTA)	NCBI Sequence Viewer
	EDM13781	(Get FASTA)	NCBI Sequence Viewer
	EDM13782	(Get FASTA)	NCBI Sequence Viewer
	EDM13783	(Get FASTA)	NCBI Sequence Viewer
	P09367	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_446414 ⟸ NM_053962

- UniProtKB:

P09367 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MAAQESLHVKTPLRDSMALSKVAGTSVFLKMDSSQPSGSFKIRGIGHLCKMKAKQGCKHFVCSS
AGNAGMATAYAARRLGLPATIVVPSTTPALTIERLKNEGATVEVVGEMLDEAIQLAKALEKNNP
GWVYISPFDDPLIWEGHTSLVKELKETLSAKPGAIVLSVGGGGLLCGVVQGLREVGWEDVPIIA
METFGAHSFHAAVKEGKLVTLPKITSVAKALGVNTVGAQTLKLFYEHPIFSEVISDQEAVTAIE
KFVDDEKILVEPACGAALAAVYSGVVCRLQAEGRLQTPLASLVVIVCGGSNISLAQLQALKAQL
GLNELLK

hide sequence

RefSeq Acc Id:

ENSRNOP00000001875 ⟸ ENSRNOT00000001875

RefSeq Acc Id:

ENSRNOP00000001876 ⟸ ENSRNOT00000001876

Protein Domains

PALP

Transcriptome

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

Promoters

RGD ID:

13698667

Promoter ID:

EPDNEW_R9192

Type:

single initiation site

Name:

Sds_1

Description:

serine dehydratase

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	12	41,627,751 - 41,627,811	EPDNEW

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

Damaging Variants

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
12	37281278	37281279	T	G	snv	SS/JrHsdMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:67376	AgrOrtholog
Ensembl Genes	ENSRNOG00000001388	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000001875	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000001876	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000001875	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOT00000001876	UniProtKB/TrEMBL
Gene3D-CATH	3.40.50.1100	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	PLP-dep	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ser/Thr_deHydtase_PyrdxlP-BS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Trypto_synt_PLP_dependent	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:25044	UniProtKB/Swiss-Prot
NCBI Gene	25044	ENTREZGENE
Pfam	PALP	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Sds	PhenoGen
PROSITE	DEHYDRATASE_SER_THR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF53686	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene	Rn.9918	ENTREZGENE
UniProt	F1LMK6_RAT	UniProtKB/TrEMBL
	P09367	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q5M8C4	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2003-04-09	Sds	serine dehydratase			Symbol and Name updated	629477	APPROVED
2003-03-06	Sds	serine dehydratase	Sdh	Serine dehydratase	Data Merged	628472	PROVISIONAL
2002-06-10	Sds	serine dehydratase			Symbol and Name status set to approved	70586	APPROVED
2002-06-10	Sdh	Serine dehydratase			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_product	dimer with a M(r) of 66,800	633956
gene_transcript	consists of two species of mRNA, due to alternative splicing and transcription initiation but only one transcript is translated into the mature enzyme	633958

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 - CTD

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)