SGN Marker C2_At5g44200

SGN-M4645
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
CoffeeSingle309104 (SGN)
129995 (CGN)
---
Lycopersicon CombinedSingleSGN-U227678---
Solanum tuberosumSingleSGN-U253465---
ArabidopsisSingleAt5g44200 on TAIR---
Mapped locations  
Map: Tomato - Kazusa and SolCAP markers mapped to genome   
Map version
105 (location: 49301)
Chromosome
2
Position
28.93 MB
Confidence
uncalculated
Protocol
CAPS


Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map   
Map version
103 (location: 47241)
Chromosome
2
Position
13.00 cM
Confidence
uncalculated
Protocol
unknown


Kazusa F2-2000 genetic map

Map: Tobacco N. tomentosiformis   
Map version
91 (location: 46770)
Chromosome
5
Position
52.80 cM
Confidence
F(LOD3)
Protocol
CAPS


Tobacco N. tomentosiformis

Map: Pepper-COSII   
Map version
58 (location: 41536)
Chromosome
2
Position
0.00 cM
Confidence
F(LOD3)
Protocol
PCR


Pepper-COSII

PCR data   Exp. ID 43512
Forward primer (5'-3')
TTATGGAAAATTGGTCCAAAAGGA
Accessions and product sizes
Approximate temperature
55°C
Reverse primer (5'-3')
ATCTTCCCTGTGTCGCTTGCGATG
Digested band sizes (using unknown enzyme)
Mg+2 concentration
Unknown
   Enzymes
  

Map: Tomato-EXPEN 2000   
Map version
52 (location: 38865)
Chromosome
2
Position
9.00 cM
Confidence
I(LOD2)
Protocol
CAPS


Tomato-EXPEN 2000

PCR data   Exp. ID 39970
Forward primer (5'-3')
TCGTGGAGGCTCTTATCGACATGG
Accessions and product sizes
Solanum lycopersicum TA209
150
Solanum pennellii TA56
150
Approximate temperature
50°C
Reverse primer (5'-3')
ATCTTCCCTGTGTCGCTTGCGATG
Digested band sizes (using amplicon difference)
Solanum lycopersicum TA209
150
Solanum pennellii TA56
110
Mg+2 concentration
1.5mM
   Enzymes
  

Map: Arabidopsis COSII   
Map version
44 (location: 27422)
Chromosome
5
Position
17.82 MB
Confidence
uncalculated
Protocol
CAPS


Arabidopsis COSII
Other PCR data 
PCR data   Exp. ID 11912
Forward primer (5'-3')
TCGTGGAGGCTCTTATCGACATGG
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCTTCCCTGTGTCGCTTGCGATG
Enzymes
  
Accessions and product sizes
Solanum pennellii LA716: 150
Approximate temperature
50°C
  
PCR data   Exp. ID 11913
Forward primer (5'-3')
TCGTGGAGGCTCTTATCGACATGG
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCTTCCCTGTGTCGCTTGCGATG
Enzymes
  
Accessions and product sizes
Solanum lycopersicum LA925: 150
Approximate temperature
50°C
  
PCR data   Exp. ID 11914
Forward primer (5'-3')
TCGTGGAGGCTCTTATCGACATGG
 
 
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCTTCCCTGTGTCGCTTGCGATG
Enzymes
  
Accessions and product sizes
Solanum pimpinellifolium LA1589: 150
Approximate temperature
50°C
  
PCR data   Exp. ID 11915
Forward primer (5'-3')
TCGTGGAGGCTCTTATCGACATGG
Digested band sizes (using HinfI)
Solanum lycopersicum LA925: 150
Solanum pennellii LA716: 110
Mg+2 concentration
1.5mM
Reverse primer (5'-3')
ATCTTCCCTGTGTCGCTTGCGATG
Enzymes
All possible enzymes for pennellii and and lycopersicum: HinfI
  
Accessions and product sizes
Solanum lycopersicum LA925: 150
Solanum pennellii LA716: 150
Approximate temperature
50°C
  
Unigene blast matches for primers 
Overgo hybridization and physical mapping 
C2_At5g44200 was used as an overgo probe on plate 13 [well B4]

Plausible BAC Matches:   P038M12,   P082H04,   P023E12,   P120B14,   P117P22,   P073M09,   P019O07,   P076J16,   P242F12,   P216B16,   P177F21,   P051E01,   P191K05,   P074H18,   P210F16,   P165O24,   P285H08

 Overgo Sequences

A sequence
ATGGTGGAAACCATGGTCGTGGAG
B sequence
CCATGTCGATAAGAGCCTCCACGA
AB sequence
ATGGTGGAAACCATGGTCGTGGAGGCTCTT
Marker sequence
NNNNNNNNNNNNNNNNNNNNGTGGATTATGGTACAGGATCGTTGGGCGCG
TACCCACCAGTTATGCCGCCACCTCNNNNNACTATGGTAGACATAATGGT
GGAAACCATGGTCGTGGAGGCTCTTATCGACATGGTAGAGNNNNNACTAT
CATCGCAAGCGACACAGGGAAGATGACCACCATCGGCCAGATTATCCAAA
GAGGACTTATGAGCGTGAATCTAGGAGAAACTCTGATCATGAATCTAGAC
CGNNNNNGAAAAGAATCCGCGTTTCCGTGAGAGTGGTGATTCTGATGAAG
AGGATGATGATGATAGGAAGCGGCGTACCTAG
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_At5g44200  
%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D4645 marker 4645
User comments 
Please wait, checking for comments. (If comments do not show up, access them here)