SGN Marker C2_At5g63380

SGN-M9175
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
CoffeeSingle304806 (SGN)
124999 (CGN)
---
Capsicum annuumSingleSGN-U204250---
Solanum tuberosumSingleSGN-U252775---
ArabidopsisSingleAt5g63380 on TAIR---
Mapped locations  
Map: Tobacco N. tomentosiformis   
Map version
91 (location: 46787)
Chromosome
3
Position
52.20 cM
Confidence
CF(LOD3)
Protocol
CAPS


Tobacco N. tomentosiformis

Map: Tomato-EXPEN 2000   
Map version
52 (location: 38914)
Chromosome
3
Position
83.30 cM
Confidence
I
Protocol
CAPS


Tomato-EXPEN 2000

PCR data   Exp. ID 40016
Forward primer (5'-3')
AGCAGGGGAGATTCCTATGGC
Accessions and product sizes
Solanum lycopersicum TA209
850
Solanum pennellii TA56
850
Approximate temperature
55°C
Reverse primer (5'-3')
ATCTTTCCAGCAGGAGATTTTGG
Digested band sizes (using amplicon difference)
Solanum lycopersicum TA209
850
Solanum pennellii TA56
450
Mg+2 concentration
1.5mM
   Enzymes
  

Map: Arabidopsis COSII   
Map version
44 (location: 27651)
Chromosome
5
Position
25.41 MB
Confidence
uncalculated
Protocol
CAPS


Arabidopsis COSII
Other PCR data 
PCR data   Exp. ID 12097
Forward primer (5'-3')
AGCAGGGGAGATTCCTATGGC
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCTTTCCAGCAGGAGATTTTGG
Enzymes
  
Accessions and product sizes
Solanum pennellii LA716: 350
Approximate temperature
55°C
  
PCR data   Exp. ID 12098
Forward primer (5'-3')
AGCAGGGGAGATTCCTATGGC
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCTTTCCAGCAGGAGATTTTGG
Enzymes
  
Accessions and product sizes
Solanum lycopersicum LA925: 350
Approximate temperature
55°C
  
PCR data   Exp. ID 12099
Forward primer (5'-3')
AGCAGGGGAGATTCCTATGGC
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCTTTCCAGCAGGAGATTTTGG
Enzymes
  
Accessions and product sizes
Solanum pimpinellifolium LA1589: 350
Approximate temperature
55°C
  
PCR data   Exp. ID 12100
Forward primer (5'-3')
AGCAGGGGAGATTCCTATGGC
Digested band sizes (using DpnII)
Solanum pennellii LA716: 180
Solanum lycopersicum LA925: 200
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCTTTCCAGCAGGAGATTTTGG
Enzymes
All possible enzymes for pennellii and and lycopersicum: DpnII
  
Accessions and product sizes
Solanum lycopersicum LA925: 350
Solanum pennellii LA716: 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]
Forward amplicon sequence for S. hirtum 130005 plant #3, AB1 chromatogram - [View]
Forward amplicon sequence for S. hirtum 130005 plant #3, plain text
Forward amplicon sequence for S. hirtum 120062 plant #28, AB1 chromatogram - [View]
Forward amplicon sequence for S. hirtum 120062 plant #28, plain text
Forward amplicon sequence for S. quitoense plant #3, AB1 chromatogram - [View]
Forward amplicon sequence for S. quitoense plant #3, plain text
Forward amplicon sequence for S. betaceum 6002061 plant #4, AB1 chromatogram - [View]
Forward amplicon sequence for S. betaceum 6002061 plant #4, plain text
Forward amplicon sequence for S. uniloba 6002078 plant #6, AB1 chromatogram - [View]
Forward amplicon sequence for S. uniloba 6002078 plant #6, plain text
Forward amplicon sequence for S. quitoense SE plant #1, AB1 chromatogram - [View]
Forward amplicon sequence for S. quitoense SE plant #1, plain text

Genomic location of C2_At5g63380  
%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D9175 marker 9175
User comments 
Please wait, checking for comments. (If comments do not show up, access them here)