D7Rat40 Marker Search Result - Rat Genome Database

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General

Marker: D7Rat40

Symbol:

D7Rat40

Previously known as:

oxsts7367; R048-C08; R0048-C08;

RGD ID:

37074

Expected Size:

240 (bp)

Position

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	17,777,285 - 17,777,527 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	23,783,311 - 23,783,552	NCBI	Rnor6.0
Rnor_5.0	7	23,933,259 - 23,933,500	UniSTS	Rnor5.0
RGSC_v3.4	7	19,915,731 - 19,916,213	RGD	RGSC3.4
RGSC_v3.4	7	19,915,925 - 19,916,166	UniSTS	RGSC3.4
RGSC_v3.1	7	19,928,649 - 19,929,131	RGD
Celera	7	15,011,032 - 15,011,271	UniSTS
RH 2.0 Map	7	78.0	RGD
SHRSP x BN Map	7	6.87	RGD
Cytogenetic Map	7	q13	UniSTS

Is Marker For:

Strains: AVN/Orl BBDP/Rhw BBDR/Rhw BC/CpbU BDIX/Han BDVII/Cub BN/SsNHsd BUF/Pit DA/PitN DON/Melb F344/Pit FHH/Eur LEW/Pit LH/Mav MHS/Gib MNRA/N WN/N WKY/OlaHsd WTC/Kyo LOU/CHan MNR/N MR/Pit ODU/N WF/Pit WIST/Nhg SR/Jr NP9 OKA/Wsl OM/Ztm P5C PVG/Pit SD/Rij SHR/OlaHsd SHRSP/Riv WAG/RijKyo GK/KyoSwe ACI/N BN-Lx/Cub LN/Mav GH/Omr NEDH/K SS/Jr COP/OlaHsd
Genes: Syn3

Annotation

References - curated

#	Reference Title	Reference Citation
1.	Data downloaded from Wellcome Trust, University of Oxford	Data downloaded from Wellcome Trust, University of Oxford
2.	Rat Genetic Map Data	Rat Genetic Map Data, Whitehead Institute for Biomedical Research/MIT Center for Genome Research Website, http://waldo.wi.mit.edu/rat/public/distribution/rat_sslp_releases/jan00/
3.	Electronic Transfer of SSLP Data	Rat Genetic Mapping Project, Whitehead Institute for Biomedical Research. APR. 2001.
4.	UniSTS Pipeline	RGD automated pipelines
5.	RH Map Project	RH Map Project, Laboratory of Genetic Research Website, 1-JUL-99, Laboratory of Genetic Research, Medical College of Wisconsin, http://www.lgr.mcw.edu/LGR/
6.	A high density integrated genetic linkage and radiation hybrid map of the laboratory rat	Steen RG, Kwitek-Black AE, etal., Genome Research, 1999, 6:1-8

Strains and Sequence

Sequence


Forward Primer	CTTCCTCCCCCACCTCACT
Reverse Primer	ATGTAAGTCAGCAGCCAGGG

Template	AGCTTCCATGCCTGCAGGTCGACTCTAGAGGATCCCCACAATGGAGACTAGATGGACAGCAGCA CTCACATCTCCTCCTTACCCCACAGATCAAAGTAGAAAACCAGCACGACTACCAGGACATCACC AGCGTGGTGGCCATGGCCAAAACCTATGCCACCACGGAGGCCTTTATTGACTCCAAGTATGACA TCCGCATACAGAAGATCGGATCCAACTACAAGGCATACATGTAAGTCAGCAGCCAGGGCTGGAA GGTGGGAGGAGTTAGTGGGCAGGGACAGGGATGTGGGAGGAGTCAGCAAGCTTGGACTGGAAGA TGGGAGGAGCTTGCTTTTGTTCTGTCCTCACCACTGGTTCTATTGCAACTTAGCTCAGGATAGA TCTCTCTACAAAAGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG TGTAGTGAGGTGGGGGAGGAAGAGAGAGAGGGAGAGGGAGGGGGAGAGAGAGAGAGAGAGAGAG AGAGA

Strain Variation

Strain, Expected Size(s)

ACI/N	240
AVN/Orl	240
BBDP/Rhw	240
BBDR/Rhw	240
BC/CpbU	240
BDIX/Han	236
BDVII/Cub	236
BN-Lx/Cub	244
BN/SsNHsd	244
BUF/Pit	242
COP/OlaHsd	242

DA/PitN	242
DON/Melb	242
F344/Pit	242
FHH/Eur	240
GH/Omr	240
GK/KyoSwe	242
LEW/Pit	240
LH/Mav	242
LN/Mav	242
LOU/CHan	240
MHS/Gib	242

MNR/N	240
MNRA/N	240
MR/Pit	240
NEDH/K	240
NP9	238
ODU/N	242
OKA/Wsl	236
OM/Ztm	242
P5C	240
PVG/Pit	242
SD/Rij	242

SHR/OlaHsd	236
SHRSP/Riv	236
SR/Jr	240
SS/Jr	242
WAG/RijKyo	236
WF/Pit	246
WIST/Nhg	240
WKY/OlaHsd	242
WN/N	242
WTC/Kyo	242

Region

Genes in Region

The following Genes overlap with this region.

RGD ID	Symbol	Name	Chr	Start	Stop	Species
3799	Syn3	synapsin III	7	16216055	17808790	Rat

Nucleotide Sequences


GenBank Nucleotide	CH473960	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CM000237	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2317059	Aia15	Adjuvant induced arthritis QTL 15	2.46		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	7	17004598	62004598	Rat
61410	Bw19	Body weight QTL 19	6.2	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	7	1	44782185	Rat
1300176	Hrtrt10	Heart rate QTL 10	3.19		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	7	664270	26029351	Rat
9590102	Sffal5	Serum free fatty acids level QTL 5	8.62	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	7	5329019	50329019	Rat
1578652	Bmd15	Bone mineral density QTL 15	5.2		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	7	9866467	60460686	Rat
1643004	Pain2	Pain QTL 2	1		mechanical nociception trait (VT:0002734)	self mutilation severity score (CMO:0002145)	7	9462246	98011544	Rat
631503	Bp102	Blood pressure QTL 102	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	1	44822433	Rat
634336	Anxrr17	Anxiety related response QTL 17	3.66		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	7	924703	115097879	Rat
10755438	Coatc9	Coat color QTL 9		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	3529280	48529280	Rat
9590142	Scort5	Serum corticosterone level QTL 5	24.4	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	7	1	31962314	Rat
1582260	Bw72	Body weight QTL 72	3.2	0.0043	body mass (VT:0001259)	body weight (CMO:0000012)	7	15795565	38073970	Rat
1582261	Bw69	Body weight QTL 69	3.2	0.0048	body mass (VT:0001259)	body weight (CMO:0000012)	7	15795565	38073970	Rat
1582262	Bw75	Body weight QTL 75	3	0.0038	body mass (VT:0001259)	body weight (CMO:0000012)	7	15795565	38073970	Rat
2298547	Neuinf5	Neuroinflammation QTL 5	3.7		nervous system integrity trait (VT:0010566)	spinal cord Cd74 protein level (CMO:0002131)	7	9462246	58265113	Rat
10059592	Kidm45	Kidney mass QTL 45	3.95	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	7	7573985	52573985	Rat
2317047	Wbc4	White blood cell count QTL 4		0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	7	1	35342956	Rat
10755440	Coatc10	Coat color QTL 10		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	7496499	52496499	Rat
2298550	Neuinf6	Neuroinflammation QTL 6	3.3		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	7	1	27829089	Rat
738033	Anxrr6	Anxiety related response QTL 6	4.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	7	15573889	60573889	Rat
724560	Plsm3	Polydactyly-luxate syndrome (PLS) morphotypes QTL 3		0.0003	tibia length (VT:0004357)	tibia length (CMO:0000450)	7	1	34000259	Rat
7411566	Bw136	Body weight QTL 136	10.4	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	7	1	31962314	Rat

Additional Information

External Database Links

Database	Acc Id	Source(s)
NCBI Gene	29130	UniSTS

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)

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Marker: D7Rat40