Sol Genomics Network

SGN Marker C2_At5g04590

SGN-M4693
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	302267 (SGN) 122231 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U205342	-	-	-
Lycopersicon Combined	Single	SGN-U214723	-	-	-
Solanum tuberosum	Multiple	SGN-U244211	-	-	-
Arabidopsis	Single	At5g04590 on TAIR	-	-	-

Mapped locations

Map: Pepper-COSII
Map version 58 (location: 41506)
Chromosome 11
Position 59.20 cM
Confidence I
Protocol dCAPS

Pepper-COSII

PCR data Exp. ID 43482

Forward primer (5'-3')

ATCACCACAGTCCTTGCACAGGG

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

AGCAACTTTCTGTTCTCTACATTTTGC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38745)
Chromosome 11
Position 56.00 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39904

Forward primer (5'-3')

ATCACCACAGTCCTTGCACAGGG

Accessions and product sizes

Solanum pennellii TA56

1100

Solanum lycopersicum TA209

1200

Approximate temperature

58°C

Reverse primer (5'-3')

AGGACAAAGTGGAAAAGCTGGG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

1100

Solanum lycopersicum TA209

1200

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27026)
Chromosome 5
Position 1.32 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11620
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1100	Approximate temperature 58°C

PCR data Exp. ID 11621
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1200	Approximate temperature 58°C

PCR data Exp. ID 11622
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1200	Approximate temperature 58°C

PCR data Exp. ID 13615
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13616
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Solanum melongena TA2986: 920	Approximate temperature 55°C

PCR data Exp. ID 13617
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1100	Approximate temperature 55°C

PCR data Exp. ID 13618
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 750	Approximate temperature 55°C

PCR data Exp. ID 13619
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 750	Approximate temperature 55°C

PCR data Exp. ID 13620
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 750	Approximate temperature 55°C

PCR data Exp. ID 13621
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13622
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13623
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Physalis TA1367: 800	Approximate temperature 55°C

PCR data Exp. ID 13624
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 1200	Approximate temperature 55°C

PCR data Exp. ID 13625
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 2000	Approximate temperature 55°C

PCR data Exp. ID 13626
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: Multiple	Approximate temperature 55°C

PCR data Exp. ID 32647
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1200	Approximate temperature 55°C

PCR data Exp. ID 33161
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1200	Approximate temperature 55°C

PCR data Exp. ID 33162
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1100	Approximate temperature 55°C

PCR data Exp. ID 33163
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 750	Approximate temperature 55°C

PCR data Exp. ID 33164
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 750	Approximate temperature 55°C

PCR data Exp. ID 33165
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 750	Approximate temperature 55°C

PCR data Exp. ID 33166
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: Multiple	Approximate temperature 55°C

PCR data Exp. ID 11623
Forward primer (5'-3') ATCACCACAGTCCTTGCACAGGG	Digested band sizes (using amplicon difference) Solanum pennellii LA716: 1100 Solanum lycopersicum LA925: 1200	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGACAAAGTGGAAAAGCTGGG	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference
Accessions and product sizes Solanum pennellii LA716: 1100 Solanum lycopersicum LA925: 1200	Approximate temperature 58°C

Unigene blast matches for primers

SGN-U214723
SGN-U269853

Overgo hybridization and physical mapping

C2_At5g04590 was used as an overgo probe on plate 13 [well G12]

Plausible BAC Matches: None

Overgo Sequences

A sequence

TGGGTTCAACTCTTGGTGCATGTG

B sequence

TTCCTGTTGAGGTCACCACATGCA

AB sequence

TGGGTTCAACTCTTGGTGCATGTGGTGACC

Marker sequence

ATGACGACGTCGTTTGGAGCAGCGATCAATATCGCCGCCGTCGATGACCC
CAACCCGAAGCTACAAATTCAGAGGTTCAATGGATTGAAAAGCACCTCTA
ATTCGATTTTGCTTAGCAGACGTATCCATCGCTCATTTTCTCATTCCAAT
TCTACTTCTATTGTCCGTGCTGTATCTACGCCANNNNNGCGAAGCCAGCT
GCGGTGGAGCCCAAGCGTAGTAAGGTTGAAATCTTCAAAGAACAGAGTAA
CTTCATAAGATATCCTCTAAATGAGGAGATTCTTAATGATGCCCCAAACA
TCAATGAGGCTGCAACACAATTGATTAAGTTTCATGGAAGCTATATGCAA
TACAACAGAGACGAGCGTGGATCAAGATCATACTCATTTATGCTTCGGAC
AAAGAACCCTGGTGGTGAAGTACCGAACAAACTCTACTTAGTCATGGATG
ATCTTGCTGACCAATTTGGGATTGGGACACTCCGTTTGACAACAAGACAG
ACCTTTCAGCTGCATGGGGTCTTGAAGAAAGACCTAAAGACAGTAATGAG
TACAATCATCCACAACATGGGTTCAACTCTTGGTGCATGTGGTGACCTCA
ACAGGAACGTTCTGGCTCCAGCTGCCCCATTTGCAAAAAAAGATTATGTT
TTTGCTAAACAAACAGCTGACAACATTGCAGCACTTTTAACTCCCCAGTC
TGGATTTTACTATGACGTTTGGGTGGATGGGGAGAAATTTATGTCAGTAG
AACCTCCTGAAGTTGTGAAAGCTCGGAATGATAACTCCCATGGAACGAAC
TTTCCTGACTCACCTGAACCCATTTATGGAACTCAGTTCTTGCCAAGAAA
GTTCAAAATCGCAGTTACTGTGCCAAGTGATAACTCGGTGGACATTTTCA
CGAATGACATAGGTGTTGTTGTTGTATCTGATGAGGATGGAGAACCTCAG
GGATTCAATATATATNNNNNGTAGGTGGTGGTATGGGACGAACTCATAGG
ATGGAAACTACTTTTCCTCGTCTGGCTGAGCCATTAGGTTATGTTCCTAA
AGCGGATATACTTTATGCAGTTAAAGCTATTGTTGTTACTCAGAGAGAGA
ATGGGAGAAGAGATGATCGCAGATATAGCAGATTGAAATATTTACTCAGT
TCATGGGGGATTGAGAAGTTCCGATCTGTCACTGAACAATATTACGGAAA
GAAGTTTGAACCCTGCCGTGAATTGCCTCAATGGGAATTTAAAAGTTACT
TGGGATGGCATGAACAGNNNNNGGAGACGGTAGTTTGTTTTGTGGTCTAC
ATGTTGACAATGGTCGTGTAAAAGGAGAGATGAAGAAGGCACTCAGGGAA
GTTATTGAGAAGTATAATCTGAATGTGCGTCTCACACCCAACCAAAATAT
TATCTTGAGCAATATTCGGCAATCTTGGAAGCGCTCCATCACCACAGTCC
TTGCACAGGGTGGTTTGCTGNNNNNCAACCTAGGTTTGTCGATCCTCTCA
ATCTAACAGCAATGGCGTGCCCAGCTTTTCCACTTTGTCCTCTAGCAATC
ACTGAAGCTGAGCGTGGAATACCTGACATCCTCAAGCGTGTTAGAGCTAT
GTTTGACAAGNNNNNGTTGGTCTGAGGTTCTATGAATCCGTTGTTATAAG
GGTAACAGGTTGTCCCAATGGATGTGCTCGACCATACATGGCTGAACTTG
GATTGGTTGGAGATGGTCCAAACAGCTATCAGNNNNNATCTGGCTCGGTG
GAACTCCCAATCAAACTGTATTGGCAAGAACTTTCAAGGATAAGGTTAAG
GTTCAGGATCTTGAAAAAGTTCTGGAGCCTTTATTTTTCCATTGGAAAAG
AAAGCGACAATCTAAAGAATCGTTTGGGGAGTTCTCAAACCGCTTGNNNN
NGGATTTGAGAAACTAGGGGACTTGGTTGAGAAATGGGATGGCATCCCTG
AGTCATCATCTCGTTATAACTTAAAGCTATTTGCTGATAAAGAGACGTAT
CAAGCCATGGATGCACTTGCAAGAATACAAAATAAGAATGCCCATCAATT
GGCGATTGATGTAATTCGCAATTATGTTGCTTCCCAGCAAAATGGGAAAA
GCATGGACTGA

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