Sol Genomics Network

SGN Marker C2_At5g06430

SGN-M4669
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	312128 (SGN) 125884 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U201754	-	-	-
Lycopersicon Combined	Single	SGN-U225912	-	-	-
Arabidopsis	Single	At5g06430 on TAIR	-	-	-

Mapped locations

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46743)
Chromosome 11
Position 36.60 cM
Confidence F(LOD3)
Protocol PCR

Tobacco N. tomentosiformis

Map: Tobacco N. acuminata
Map version 89 (location: 46521)
Chromosome 11
Position 21.90 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. acuminata

Map: Tomato-EXPEN 2000
Map version 52 (location: 38755)
Chromosome 10
Position 3.20 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39910

Forward primer (5'-3')

ATTGTTATGGCTGATGCAGAGAATG

Accessions and product sizes

Solanum pennellii TA56

880

Solanum lycopersicum TA209

800

Approximate temperature

55°C

Reverse primer (5'-3')

ACGAAGCAAGGAACATACTTTATGTC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

800

Solanum pennellii TA56

880

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27053)
Chromosome 5
Position 1.96 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11649
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 880	Approximate temperature 55°C

PCR data Exp. ID 11650
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 800	Approximate temperature 55°C

PCR data Exp. ID 11651
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 880	Approximate temperature 55°C

PCR data Exp. ID 13649
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1200	Approximate temperature 55°C

PCR data Exp. ID 13650
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 1300	Approximate temperature 55°C

PCR data Exp. ID 13651
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 900	Approximate temperature 55°C

PCR data Exp. ID 13652
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1200	Approximate temperature 55°C

PCR data Exp. ID 13653
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1200	Approximate temperature 55°C

PCR data Exp. ID 13654
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 900	Approximate temperature 55°C

PCR data Exp. ID 13655
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 750	Approximate temperature 55°C

PCR data Exp. ID 13656
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 820	Approximate temperature 55°C

PCR data Exp. ID 13657
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Physalis TA1367: 650	Approximate temperature 55°C

PCR data Exp. ID 13658
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 900	Approximate temperature 55°C

PCR data Exp. ID 13659
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 750	Approximate temperature 55°C

PCR data Exp. ID 13660
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 750	Approximate temperature 55°C

PCR data Exp. ID 13661
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 900	Approximate temperature 55°C

PCR data Exp. ID 13662
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Coffea canephora BP409: 400	Approximate temperature 55°C

PCR data Exp. ID 33177
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1200	Approximate temperature 55°C

PCR data Exp. ID 33178
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1200	Approximate temperature 55°C

PCR data Exp. ID 33179
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 900	Approximate temperature 55°C

PCR data Exp. ID 33180
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 750	Approximate temperature 55°C

PCR data Exp. ID 11652
Forward primer (5'-3') ATTGTTATGGCTGATGCAGAGAATG	Digested band sizes (using amplicon difference) Solanum pennellii LA716: 880 Solanum lycopersicum LA925: 800	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGAAGCAAGGAACATACTTTATGTC	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference All possible enzymes for lycopersicum and pimpinellifolium: amplicon difference
Accessions and product sizes Solanum lycopersicum LA925: 800 Solanum pennellii LA716: 880	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U225912

Overgo hybridization and physical mapping

C2_At5g06430 was used as an overgo probe on plate 13 [well D12]

Plausible BAC Matches: P136O15, P293J06, P314F10, P124P08, P145N02, P017F14, P181O10, P229I22, P192C12, P206A18, P012D17, P317B16, P041P01, P155L18, P178H24, P181N09, P134O15, P181N10, P023N24, P254M12, P176J20, P322M11, P144K11, P096D08, P316L18, P145L02, P273M12, P209L08, P292A11, P116G06, P145L07, P096N06, P182E22, P025F04, P144M21, P052N10

Overgo Sequences

A sequence

ACTTGCAAAGACGGGTGTTCCTAG

B sequence

AACATGCAGTCGGCTACTAGGAAC

AB sequence

ACTTGCAAAGACGGGTGTTCCTAGTAGCCG

Marker sequence

ATGGATTCTACTTCCAAGAACTCTCCCTTTTGCTTAAAATGGCCTTGGGA
TGTTCATAACCAAAACCCAAAGAACCCTTTGCCTTGTACCTTTGAAACTC
CTTGGCTATTCAAACCATTCAAGAATCTTGGCTCTGGAGTGTTTAATTTC
ATCCAAAATATCTCAAAACCTGAACCTTTATCACCCAAATTTAATTTACA
GTCGAATGGTGGAGTTAACCAAAATAATACCTTGAAGTTGGTGAAGAAGA
AATTGACTCCTACAGAGCAAGCAGAGCTCGAGCAGAGTGCGTTAGCGTGT
GCCTTGGCCAGTGAAAAAGAGGCTACTGTAATTGAATTTTACTCCCCAAA
GTGCCGGCTCTGCAATTCGTTGGTTAATTTCGTTACTGAAGTTGAGAACA
GGAACTCTGACTGGCTCAATATTGTTATGGCTGATGCAGAGAATGACCAA
TGGTTGCCTGAGNNNNNCTTCTCCATTATGACATAAAGTATGTTCCTTGC
TTCGTTTTACTGGACAAAAACGGGAGGGCACTTGCAAAGACGGGTGTTCC
TAGTAGCCGACTGCATGTTTTGGCTGGTGTTTCTCATCTCCTCAAAATGA
GACATCCACAACACAAATAG

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