D16Rat101 Marker Search Result - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources

Marker: D16Rat101

Symbol: D16Rat101
Previously known as: R0011-B07; oxsts9720; 
RGD ID: 35022
Expected Size: 160 (bp)
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21664,419,480 - 64,419,656 (+)MAPPERmRatBN7.2
mRatBN7.21664,464,262 - 64,464,425 (+)MAPPERmRatBN7.2
Rnor_6.01668,636,241 - 68,636,401NCBIRnor6.0
Rnor_6.01668,592,138 - 68,592,313NCBIRnor6.0
Rnor_5.01668,263,216 - 68,263,376UniSTSRnor5.0
Rnor_5.01668,218,646 - 68,218,821UniSTSRnor5.0
RGSC_v3.41668,770,845 - 68,771,223RGDRGSC3.4
RGSC_v3.11668,771,051 - 68,771,429RGD
Celera1662,404,762 - 62,404,924UniSTS
Celera1662,360,104 - 62,360,265UniSTS
RH 3.4 Map16594.2RGD
RH 3.4 Map16594.2UniSTS
RH 2.0 Map16712.1RGD
SHRSP x BN Map1630.54RGD
FHH x ACI Map1636.0599RGD
Cytogenetic Map16q12.3UniSTS
Is Marker For: Strains:   AVN/Orl   BBDP/Rhw   BBDR/Rhw   BC/CpbU   BDIX/Han   BDVII/Cub   BN/SsNHsd   BP/Cub   BUF/Pit   DA/PitN   DON/Melb   F344/Pit   FHH/Eur   IS/Kyo   LE/Mol   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   MNS/Gib   NP9   OKA/Wsl   OM/Ztm   P5C   PVG/Pit   SD/Rij   SHR/OlaHsd   SHRSP/Riv   WAG/RijKyo   GK/KyoSwe   M520/N   ACI/N   BN-Lx/Cub   LN/Mav   GH/Omr   NEDH/K   SS/Jr   COP/OlaHsd  
Genes:   Smok   RGD1564276   LOC100911229  


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. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
3. 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/
4. Electronic Transfer of SSLP Data Rat Genetic Mapping Project, Whitehead Institute for Biomedical Research. APR. 2001.
5. UniSTS Pipeline RGD automated pipelines
6. 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/
7. 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 CGCTGCTGCACATGATATCT
Reverse Primer AACAGGAAATCCATTACTTTGC
 
Template 
GCCAGTGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCTTGCATCTAACCCACCA
AGATTCAGAAACCTTCACAACTCAACCCATTTGGTGAGTTATTATTGGTGAGCGTGCCTGGTGC
GGTGCAGCCTGAGTCATCTGGGTGAACGCTGCTGCACATGATATCTGGACAGACAGGAACACAC
ACACACACACACAAACACACACACACACACACANAATTTCAAAAGTTCTNNGTCAGTGTTGCTT
CTNGTAGAATTTGTTTGNAATGGAGAGNATCTGCATTATNAGCAAAGTAATGGATTTCCTGTTA
CTATAGTNATCCCTCCAATATCAGTTCTCTTGTCTACACCCTCNTTCTGNGACNTTAACCTCTT
CAATTGCNNCATAGGNAAAGTGTGTTGTCGNAGGCACCACAGTGCATNCTNTGGNNGGGCTTCN
NNGNTCAGGCANNGTGGGAGNNCNCCATAGTGNNNNGGNGTGGNGGCAANGGGNGTGTGNNNNA
TTNGNTACATNNAAGNNTGAGNGGGGAGTGTGCTNNNNTNNGNNAAGCCC
Strain Variation
Strain, Expected Size(s)
ACI/N164
AVN/Orl164
BBDP/Rhw166
BBDR/Rhw156
BC/CpbU164
BDIX/Han164
BDVII/Cub164
BN-Lx/Cub164
BN/SsNHsd164
BP/Cub164
BUF/Pit162,156
COP/OlaHsd166
DA/PitN164
DON/Melb164
F344/Pit164
FHH/Eur164,156
GH/Omr166
GK/KyoSwe162,156
IS/Kyo162
LE/Mol160
LEW/Pit164
LH/Mav166
LN/Mav166
LOU/CHan164
M520/N162,156
MHS/Gib162,156
MNR/N168,156
MNRA/N168,156
MNS/Gib162,156
MR/Pit162,156
NEDH/K166
NP9166
ODU/N166
OKA/Wsl162,156
OM/Ztm166
P5C162,156
PVG/Pit166
SD/Rij166
SHR/OlaHsd166
SHRSP/Riv162,156
SR/Jr166
SS/Jr166
WAG/RijKyo162,156
WF/Pit164
WIST/Nhg164
WKY/OlaHsd166
WN/N162,156
WTC/Kyo166


Region

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
6494469LOC100911229sperm motility kinase-like166441253364424489Rat
1562638Smoksperm motility kinase166445734464469296Rat

Nucleotide Sequences
GenBank Nucleotide JH618807.1 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JH618808.1 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162173597566735975Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat


Additional Information

Database Acc Id Source(s)
NCBI Gene 100911229 UniSTS
  290818 UniSTS
  502093 UniSTS
UniSTS 121118 UniSTS