SGN Marker C2_At5g63890

SGN-M9185
COSII markers are Conserved Ortholog Set II - orthologs between many asterid species

SynonymsNone
Locus associationsNone
Orthologs in this COSII group 
SpeciesCopiesSequence IDCDS/Edited sequencePeptide sequencePredicted introns
Capsicum annuumSingleSGN-U201519---
Solanum tuberosumSingleSGN-U258062---
ArabidopsisSingleAt5g63890 on TAIR---
Mapped locations  
Map: Tomato-EXPEN 2000   
Map version
52 (location: 38917)
Chromosome
2
Position
47.70 cM
Confidence
I(LOD2)
Protocol
CAPS


Tomato-EXPEN 2000

PCR data   Exp. ID 40019
Forward primer (5'-3')
TGAAGATGTCAATGAGCTTCCAGATCC
Accessions and product sizes
Solanum lycopersicum TA209
300
Solanum pennellii TA56
300
Approximate temperature
55°C
Reverse primer (5'-3')
AGGCTTTTGAGCAGCATGAAAGG
Digested band sizes (using amplicon difference)
Solanum lycopersicum TA209
300
Solanum pennellii TA56
250
Mg+2 concentration
1.5mM
   Enzymes
  

Map: Arabidopsis COSII   
Map version
44 (location: 27661)
Chromosome
5
Position
25.58 MB
Confidence
uncalculated
Protocol
CAPS


Arabidopsis COSII
Other PCR data 
PCR data   Exp. ID 12108
Forward primer (5'-3')
TGAAGATGTCAATGAGCTTCCAGATCC
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
AGGCTTTTGAGCAGCATGAAAGG
Enzymes
  
Accessions and product sizes
Solanum pennellii LA716: 250
Approximate temperature
55°C
  
PCR data   Exp. ID 12109
Forward primer (5'-3')
TGAAGATGTCAATGAGCTTCCAGATCC
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
AGGCTTTTGAGCAGCATGAAAGG
Enzymes
  
Accessions and product sizes
Solanum lycopersicum LA925: 250
Approximate temperature
55°C
  
PCR data   Exp. ID 12110
Forward primer (5'-3')
TGAAGATGTCAATGAGCTTCCAGATCC
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
AGGCTTTTGAGCAGCATGAAAGG
Enzymes
  
Accessions and product sizes
Solanum pimpinellifolium LA1589: 250
Approximate temperature
55°C
  
PCR data   Exp. ID 12111
Forward primer (5'-3')
TGAAGATGTCAATGAGCTTCCAGATCC
Digested band sizes (using DraI)
Solanum pennellii LA716: 200
Solanum lycopersicum LA925: 100
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
AGGCTTTTGAGCAGCATGAAAGG
Enzymes
All possible enzymes for pennellii and and lycopersicum: DraI
  
Accessions and product sizes
Solanum lycopersicum LA925: 250
Solanum pennellii LA716: 250
Approximate temperature
55°C
  
Unigene blast matches for primers 
Universal primers for Asterid species 
No additional PCR data found.
Other COSII sequence data 

BLASTX result of original unigene sequences against Arabidopsis protein database

Alignment of Arabidopsis CDS and edited Asterid unigenes, FASTA
Alignment of DNA and translated peptides from Arabidopsis CDS and edited Asterid unigenes, plain text
Alignment of translated peptides from Arabidopsis CDS and edited Asterid unigenes, ClustalW
Alignment of translated peptides from Arabidopsis CDS and edited Asterid unigenes, FASTA

Input file for PAUP, NEXUS format
Phylogenetic tree
Phylogenetic tree   |   [View]

Genomic location of C2_At5g63890  
%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D9185 marker 9185
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