SGN Marker C2_At5g60620

SGN-M9141
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
CoffeeSingle304516 (SGN)
122514 (CGN)
---
Capsicum annuumMultipleSGN-U196890---
Lycopersicon CombinedSingleSGN-U215074---
Solanum tuberosumSingleSGN-U245570---
ArabidopsisSingleAt5g60620 on TAIR---
Mapped locations  
Map: Tobacco N. tomentosiformis   
Map version
91 (location: 46784)
Chromosome
1
Position
56.00 cM
Confidence
F(LOD3)
Protocol
dCAPS


Tobacco N. tomentosiformis

Map: Tomato-EXPEN 2000   
Map version
52 (location: 38906)
Chromosome
8
Position
87.00 cM
Confidence
I
Protocol
CAPS


Tomato-EXPEN 2000

PCR data   Exp. ID 40008
Forward primer (5'-3')
AAATCCACCAGAACCTTGGAACTG
Accessions and product sizes
Solanum lycopersicum TA209
2000
Solanum pennellii TA56
2000
Approximate temperature
55°C
Reverse primer (5'-3')
TCCTGAATTTATCGTGCCCTTTC
Digested band sizes (using unknown enzyme)
Mg+2 concentration
1.5mM
   Enzymes
  

Map: Arabidopsis COSII   
Map version
44 (location: 27616)
Chromosome
5
Position
24.39 MB
Confidence
uncalculated
Protocol
CAPS


Arabidopsis COSII
Other PCR data 
PCR data   Exp. ID 12066
Forward primer (5'-3')
AAATCCACCAGAACCTTGGAACTG
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
TCCTGAATTTATCGTGCCCTTTC
Enzymes
  
Accessions and product sizes
Solanum pennellii LA716: 300
Approximate temperature
55°C
  
PCR data   Exp. ID 12067
Forward primer (5'-3')
AAATCCACCAGAACCTTGGAACTG
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
TCCTGAATTTATCGTGCCCTTTC
Enzymes
  
Accessions and product sizes
Solanum lycopersicum LA925: 300
Approximate temperature
55°C
  
PCR data   Exp. ID 12068
Forward primer (5'-3')
AAATCCACCAGAACCTTGGAACTG
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
TCCTGAATTTATCGTGCCCTTTC
Enzymes
  
Accessions and product sizes
Solanum pimpinellifolium LA1589: 300
Approximate temperature
55°C
  
PCR data   Exp. ID 12069
Forward primer (5'-3')
AAATCCACCAGAACCTTGGAACTG
Digested band sizes (using ApoI)
Solanum pennellii LA716: 250
Solanum lycopersicum LA925: 300
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
TCCTGAATTTATCGTGCCCTTTC
Enzymes
All possible enzymes for pennellii and and lycopersicum: ApoI,EcoRI,HaeIII,StuI
  
Accessions and product sizes
Solanum pennellii LA716: 300
Solanum lycopersicum LA925: 300
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]

Amplicon sequence alignment, FASTA
At5g60620F.cds.txt, plain text
Forward amplicon sequence for S. lycopersicum TA209, AB1 chromatogram - [View]
Forward amplicon sequence for S. lycopersicum TA209, plain text
Forward amplicon sequence for S. pennellii TA56, AB1 chromatogram - [View]
Forward amplicon sequence for S. pennellii TA56, plain text

Genomic location of C2_At5g60620  
%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D9141 marker 9141
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