Sol Genomics Network

SGN Marker C2_At3g06580

SGN-M4654
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	309509 (SGN) 125989 (CGN)	-	-	-
Lycopersicon Combined	Single	SGN-U226619	-	-	-
Arabidopsis	Single	At3g06580 on TAIR	-	-	-

Mapped locations

Map: Eggplant-COSII
Map version 63 (location: 42210)
Chromosome 1
Position 54.30 cM
Confidence F(LOD3)
Protocol CAPS

Eggplant-COSII

PCR data Exp. ID 43776

Forward primer (5'-3')

GCCAAGTTGAAAGGGATAGATGT

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

AGCAAACCCAGATTTTGCCATAAC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38433)
Chromosome 1
Position 30.20 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39677

Forward primer (5'-3')

TGCTCAACTCACATGTGAGTGTGAAAG

Accessions and product sizes

Solanum lycopersicum TA209

300

Solanum pennellii TA56

300

Approximate temperature

55°C

Reverse primer (5'-3')

AGCAAACCCAGATTTTGCCATAAC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

270

Solanum lycopersicum TA209

170

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26064)
Chromosome 3
Position 2.05 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10976
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 300	Approximate temperature 55°C

PCR data Exp. ID 10977
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 300	Approximate temperature 55°C

PCR data Exp. ID 10978
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 300	Approximate temperature 55°C

PCR data Exp. ID 13154
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 320	Approximate temperature 55°C

PCR data Exp. ID 13155
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 300	Approximate temperature 55°C

PCR data Exp. ID 13156
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 300	Approximate temperature 55°C

PCR data Exp. ID 13157
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 300	Approximate temperature 55°C

PCR data Exp. ID 13158
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 300	Approximate temperature 55°C

PCR data Exp. ID 13159
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 300	Approximate temperature 55°C

PCR data Exp. ID 13160
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 300	Approximate temperature 55°C

PCR data Exp. ID 13161
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 320	Approximate temperature 55°C

PCR data Exp. ID 13162
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Physalis TA1367: 300	Approximate temperature 55°C

PCR data Exp. ID 13163
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 300	Approximate temperature 55°C

PCR data Exp. ID 13164
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 250	Approximate temperature 55°C

PCR data Exp. ID 13165
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 250	Approximate temperature 55°C

PCR data Exp. ID 13166
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 300	Approximate temperature 55°C

PCR data Exp. ID 13167
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Coffea canephora BP409: 850	Approximate temperature 55°C

PCR data Exp. ID 32998
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 300	Approximate temperature 55°C

PCR data Exp. ID 32999
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 300	Approximate temperature 55°C

PCR data Exp. ID 33000
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 300	Approximate temperature 55°C

PCR data Exp. ID 33001
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 300	Approximate temperature 55°C

PCR data Exp. ID 10979
Forward primer (5'-3') TGCTCAACTCACATGTGAGTGTGAAAG	Digested band sizes (using DpnII) Solanum pennellii LA716: 270 Solanum lycopersicum LA925: 170	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCAAACCCAGATTTTGCCATAAC	Enzymes All possible enzymes for pennellii and and lycopersicum: DpnII
Accessions and product sizes Solanum pennellii LA716: 300 Solanum lycopersicum LA925: 300	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U226619

Overgo hybridization and physical mapping

C2_At3g06580 was used as an overgo probe on plate 13 [well C4]

Plausible BAC Matches: P057E13, P286L06, P252C11, P096C10, P218J06, P115H10, P113G22, P235G07, P032K04, P137E03, P163P10, P050N22

Overgo Sequences

A sequence

CTCACATGTGAGTGTGAAAGGCAC

B sequence

CAGACTGAGTCCCAATGTGCCTTT

AB sequence

CTCACATGTGAGTGTGAAAGGCACATTGGG

Marker sequence

ATGGCTAGACACGAGGAATTACCAATTCCAATTTTCTCTGATCTTGAACC
TGTTTATGGTAGTGGATCACAGCTTGAAGAGGCTCAACTTCGATTCAAGA
ATTTGAAAGCCAAGTTTATAGACTTATTTGGCCAATCCCCTCATGTCTAC
GCTCGATCCCCAGNNNNNGGAGAGTGAATCTGATTGGAGAACACATAGAC
TATGAGGGTTACTCTGTTTTGCCTATGGCAATTCGGCAAGATACAATTGT
GGCTATACGAAAACACGACTCTAGTGAACCTCAGAAACTTCTTAGAATTG
CCAATGTGAATAGTGATAAGTACTCCTTGTGTACTTACCCTGCTGATCCT
CTACAGNNNNNGAGGTTGATCTGAAGAATCACAGATGGGGTCATTATTTC
ATTTGTGGNNNNNGTACAAGGGTTTCTATGAATATGCCAAGTTGAAAGGG
ATAGATGTTGGTAAACCTGTTGGACTTGATGTTATTGTTGATGGTACAGT
TCCTACAGNNNNNGGTCTGGACTTTCGAGCTCTGCAGCATTTGTTTGCTC
TTCCTTTATTGCTATAATGGCTTCAATTGGTGTTAACATGCCCAAGNNNN
NAAAGAAATTGCTCAACTCACATGTGAGTGTGAAAGGCACATTGGGACTC
AGTCTGGTGGAATGGATCAGNNNNNGCCATCTCTGTTATGGCAAAATCTG
GGTTTGCTGAGCTGATTGACTTCAATCCTATACGTGCAACTGATGTACAA
CTGCCTGATGGTGGCACTTTTGTGATAGCCCATTCATTAGCTGAATCACA
AAAAGCAGTTACTGCTGCAGTTAACTATAATAATCGGGTTGTTGAATGCC
GACTAGCTGCTNNNNNATTGTACTGGGCATTAAGCTGGGGATGGAACCTA
AGGAGGCGATATCTAGTGTAAAAACTCTTTCTGATGTTGAAGGGTTGTGC
GTATCATTTGCTGGTACACACAGTTCTTCTGATCCTGTCCTTGCTGTCAA
GNNNNNGAGCTATTGCATGAGGAACCATATACCAGCGAAGATGTTGAGAA
TATCACCAAGGAAAAGGTGGAAACAATCTTTGCGGCCTCACCAACTTCTT
TGGATGTGCTTNNNNNNNNNNNNNNNNNNNN

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