Sol Genomics Network

SGN Marker C2_At3g58470

SGN-M4697
COSII markers are Conserved Ortholog Set II - orthologs between many asterid species

Synonyms

None

Locus associations

None

Orthologs in this COSII group

Species	Copies	Sequence ID	CDS/Edited sequence	Peptide sequence	Predicted introns
Coffee	Single	299616 (SGN) 121357 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197077	-	-	-
Lycopersicon Combined	Single	SGN-U222473	-	-	-
Solanum tuberosum	Multiple	SGN-U249675	-	-	-
Arabidopsis	Single	At3g58470 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38583)
Chromosome 10
Position 61.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39778

Forward primer (5'-3')

ATTGCTTGTCCCACACTTTATGC

Accessions and product sizes

Solanum pennellii TA56

1000

Solanum lycopersicum TA209

1000

Approximate temperature

50°C

Reverse primer (5'-3')

TACTGTTCAAACCGTTTGTCATACTC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

950

Solanum pennellii TA56

1000

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26520)
Chromosome 3
Position 21.64 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11281
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1000	Approximate temperature 50°C

PCR data Exp. ID 11282
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1000	Approximate temperature 50°C

PCR data Exp. ID 11283
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1000	Approximate temperature 50°C

PCR data Exp. ID 13338
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1200	Approximate temperature 55°C

PCR data Exp. ID 13339
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 1100	Approximate temperature 55°C

PCR data Exp. ID 13340
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1150	Approximate temperature 55°C

PCR data Exp. ID 13341
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1100	Approximate temperature 55°C

PCR data Exp. ID 13342
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1200	Approximate temperature 55°C

PCR data Exp. ID 13343
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1650	Approximate temperature 55°C

PCR data Exp. ID 13344
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1150	Approximate temperature 55°C

PCR data Exp. ID 13345
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Physalis TA1367: 1150	Approximate temperature 55°C

PCR data Exp. ID 13346
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 1200	Approximate temperature 55°C

PCR data Exp. ID 13347
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 1200	Approximate temperature 55°C

PCR data Exp. ID 13348
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 1200	Approximate temperature 55°C

PCR data Exp. ID 13349
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 1200	Approximate temperature 55°C

PCR data Exp. ID 13350
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Coffea canephora BP409: 300	Approximate temperature 55°C

PCR data Exp. ID 32638
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1000	Approximate temperature 55°C

PCR data Exp. ID 33068
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1000	Approximate temperature 55°C

PCR data Exp. ID 33069
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1000	Approximate temperature 55°C

PCR data Exp. ID 33070
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1100	Approximate temperature 55°C

PCR data Exp. ID 33071
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1200	Approximate temperature 55°C

PCR data Exp. ID 33072
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1650	Approximate temperature 55°C

PCR data Exp. ID 33073
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1150	Approximate temperature 55°C

PCR data Exp. ID 11284
Forward primer (5'-3') ATTGCTTGTCCCACACTTTATGC	Digested band sizes (using HinfI) Solanum pennellii LA716: 1000 Solanum lycopersicum LA925: 950	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TACTGTTCAAACCGTTTGTCATACTC	Enzymes All possible enzymes for pennellii and and lycopersicum: RsaI, DraI, HinfI
Accessions and product sizes Solanum lycopersicum LA925: 1000 Solanum pennellii LA716: 1000	Approximate temperature 50°C

Unigene blast matches for primers

SGN-U222473

Overgo hybridization and physical mapping

C2_At3g58470 was used as an overgo probe on plate 13 [well H5]

Plausible BAC Matches: P268K08, P021O12

Overgo Sequences

A sequence

GACGATGATACTCCGACGTTAAGC

B sequence

CTTCTAGAGCGTGAGAGCTTAACG

AB sequence

GACGATGATACTCCGACGTTAAGCTCTCAC

Marker sequence

ATGGAGACAGCGAGAGACACCGTACAGCACGACGCCGTTCTGCCGGCCGG
CGACGATGATACTCCGACGTTAAGCTCTCACGCTCTAGAAGCACTGAAGG
AGTTCCTTGCTGAGCAGAGCCGAGCAGTTGAGGAAGCTTCGTCAGCTGCG
GCGGAGGATGACGTGGCGCTGGTATCGGAGGATTGGCGGCTAAGCCAGTT
CTGGTATAACCGTGAAACAGCTGAAACTGTCGCTAATGAAGTCCTTAATC
TCTGTCGATCGATTGATTCGCCGGCGATTGCCTGCATTGCTTGTCCCACA
CTTTATGCTTATCTCAAGNNNNNAAAATTGACCCTAATGCACCTGCACAA
ATTCTCGAGTATGACAAACGGTTTGAACAGTATGGAAGTGAGTTCACATT
CTACGACTACAACCTACCAGAAGATCTTCCTTCTTCAATGAAACACTCAT
ATCCAATAATTGTTGCAGATCCTCCTTACCTGNNNNNAGTCAGGAATGCT
TAGAGAAAGTTGCTAAAACAATTTCTTTTCTCACGAGACCAGGACAAGCC
TACTTGCTTTTACTCACAGNNNNNGTNACATACTGAATTTTATGCAGTGT
TTTACGACTTGGTCTCCCGTTGGCTGTCGTTCATCATGTTAATGGTCATT
GAATCTAGTTATTGTTTTTTAAGGATCCTTAAACAATGAATCCAGTTATN
NNNN

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