SGN Marker C2_At5g23540

SGN-M8819
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
CoffeeSingle301793 (SGN)
120035 (CGN)
---
Capsicum annuumSingleSGN-U197074---
Lycopersicon CombinedMultipleSGN-U215454---
Solanum tuberosumSingleSGN-U244905---
ArabidopsisSingleAt5g23540 on TAIR---
Mapped locations  
Map: Arabidopsis COSII   
Map version
44 (location: 27280)
Chromosome
5
Position
7.94 MB
Confidence
uncalculated
Protocol
CAPS


Arabidopsis COSII

PCR data   Exp. ID 41758
Forward primer (5'-3')
TGGACTCTTCTGAGCAAGTCTACATCTC
Accessions and product sizes
Solanum pennellii TA56
1300
Solanum lycopersicum TA209
1300
Approximate temperature
55°C
Reverse primer (5'-3')
ATCCCCTAACATCAATCCCATCAC
Digested band sizes (using amplicon difference)
Solanum pennellii TA56
600
Solanum lycopersicum TA209
500
Mg+2 concentration
1.5mM
   Enzymes
  
Other PCR data 
PCR data   Exp. ID 11808
Forward primer (5'-3')
TGGACTCTTCTGAGCAAGTCTACATCTC
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCCCCTAACATCAATCCCATCAC
Enzymes
  
Accessions and product sizes
Solanum pennellii LA716: 350
Approximate temperature
55°C
  
PCR data   Exp. ID 11809
Forward primer (5'-3')
TGGACTCTTCTGAGCAAGTCTACATCTC
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCCCCTAACATCAATCCCATCAC
Enzymes
  
Accessions and product sizes
Solanum lycopersicum LA925: 350
Approximate temperature
55°C
  
PCR data   Exp. ID 11810
Forward primer (5'-3')
TGGACTCTTCTGAGCAAGTCTACATCTC
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCCCCTAACATCAATCCCATCAC
Enzymes
  
Accessions and product sizes
Solanum pimpinellifolium LA1589: 350
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_At5g23540  
%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D8819 marker 8819
User comments 
Please wait, checking for comments. (If comments do not show up, access them here)