Sol Genomics Network

SGN Marker C2_At5g13450

SGN-M4702
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	302239 (SGN) 120502 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U196778	-	-	-
Lycopersicon Combined	Multiple	SGN-U214615	-	-	-
Solanum tuberosum	Single	SGN-U254610	-	-	-
Arabidopsis	Single	At5g13450 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49292)
Chromosome 1
Position 73.80 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47233)
Chromosome 1
Position 48.70 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Pepper-COSII
Map version 58 (location: 41514)
Chromosome 1
Position 129.70 cM
Confidence F(LOD3)
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43490

Forward primer (5'-3')

AGGTTTGCTGAGTTAACCATGGC

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

TCTGTTCAATGTTCACCTTCTTCCC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38787)
Chromosome 1
Position 46.90 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39927

Forward primer (5'-3')

AGGTTTGCTGAGTTAACCATGGC

Accessions and product sizes

Solanum lycopersicum TA209

500

Solanum pennellii TA56

550

Approximate temperature

55°C

Reverse primer (5'-3')

TCTGTTCAATGTTCACCTTCTTCCC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

500

Solanum pennellii TA56

550

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27140)
Chromosome 5
Position 4.31 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11717
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 550	Approximate temperature 55°C

PCR data Exp. ID 11718
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 500	Approximate temperature 55°C

PCR data Exp. ID 11719
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 500	Approximate temperature 55°C

PCR data Exp. ID 13712
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 650	Approximate temperature 55°C

PCR data Exp. ID 13713
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 700	Approximate temperature 55°C

PCR data Exp. ID 13714
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 750	Approximate temperature 55°C

PCR data Exp. ID 13715
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 750	Approximate temperature 55°C

PCR data Exp. ID 13716
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 750	Approximate temperature 55°C

PCR data Exp. ID 13717
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 750	Approximate temperature 55°C

PCR data Exp. ID 13718
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 650	Approximate temperature 55°C

PCR data Exp. ID 13719
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Physalis TA1367: 650	Approximate temperature 55°C

PCR data Exp. ID 13720
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 800	Approximate temperature 55°C

PCR data Exp. ID 13721
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 750	Approximate temperature 55°C

PCR data Exp. ID 13722
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 750	Approximate temperature 55°C

PCR data Exp. ID 13723
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 800	Approximate temperature 55°C

PCR data Exp. ID 33207
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 750	Approximate temperature 55°C

PCR data Exp. ID 33208
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 750	Approximate temperature 55°C

PCR data Exp. ID 33209
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 750	Approximate temperature 55°C

PCR data Exp. ID 33210
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 750	Approximate temperature 55°C

PCR data Exp. ID 11720
Forward primer (5'-3') AGGTTTGCTGAGTTAACCATGGC	Digested band sizes (using amplicon difference) Solanum lycopersicum LA925: 500 Solanum pennellii LA716: 550	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTCAATGTTCACCTTCTTCCC	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference
Accessions and product sizes Solanum pennellii LA716: 550 Solanum lycopersicum LA925: 500	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U214615

Overgo hybridization and physical mapping

C2_At5g13450 was used as an overgo probe on plate 13 [well H12]

Plausible BAC Matches: None

Overgo Sequences

A sequence

GGATCTCTCTGTACCTACAGAGAC

B sequence

CATGGCCTTCACTCTTGTCTCTGT

AB sequence

GGATCTCTCTGTACCTACAGAGACAAGAGT

Marker sequence

ATGGCAGGGCGTATTAGATCTACACTTCCTCACCTACGCAAAGCCCTTTC
ATCTGATTCGAGATCCGCTCTTTATCCGGCCATTATCTCCAATCCCGAGT
TGNNNNNTCAAGAAATTATGCTACTGCCCCAGCTGCCAAAGAGAAAAAAG
TAAAGNNNNNGTTCCAGTGACTATGTATGGGGTTTCTGGAAATTATGCCT
CAGCTTTGTACATCTCAGCTGTAAAAGCTAATACATTGGAGAAGGTCGAG
TCCGAGCTTTTGGACCTTATTGCGGCTTCAAAGAAAAGTCCTAAATTTTC
TCAGTTTATGAAGGATCTCTCTGTACCTACAGAGACAAGAGTGAAGGCCA
TGACTGACATCTCTTCAGAGGCTAAATTTGGAGATCTCACAAAGAACTTC
TTGGNNNNNTTGTTTTGGCTGAAAATGGGAGGCTGAAACATATTGATGCG
ATAGCAAAAAGGTTTGCTGAGTTAACCATGGCACACAAGGGGGAACTTAA
AGCCATTGTAACAACTGTTATTNNNNNCCTATTCCTCCAGAGGAGGAGAA
AGAATTGAAGGAGACATTGCAAGAGGTGATGGGAAAAGGGAAGAAGGTGA
ACATTGAACAGAAGNNNNNATTGATCCTAGCATTCTCGGTGGGCTTGTGA
TAGAATTTGGCCAGAAGGTCTTTGACATGTCAATTAGGACTAGGGCACGC
CAGATGGAGAGACTCTTGAGGGAACCTATCAACTTCTGA

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