Sol Genomics Network

SGN Marker C2_At2g40760

SGN-M4678
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	302091 (SGN) 125183 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U205370	-	-	-
Solanum tuberosum	Single	SGN-U248976	-	-	-
Arabidopsis	Single	At2g40760 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38380)
Chromosome 3
Position 74.50 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39630

Forward primer (5'-3')

AGGAAGAGGCTCTTCATCATGGAC

Accessions and product sizes

Solanum lycopersicum TA209

250

Solanum pennellii TA56

250

Approximate temperature

55°C

Reverse primer (5'-3')

TCTCTCAATTGGTGAAACAGAAGG

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

200

Solanum pennellii TA56

220

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25899)
Chromosome 2
Position 17.02 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10837
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 250	Approximate temperature 55°C

PCR data Exp. ID 10838
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 250	Approximate temperature 55°C

PCR data Exp. ID 10839
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 250	Approximate temperature 55°C

PCR data Exp. ID 13079
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 300	Approximate temperature 55°C

PCR data Exp. ID 13080
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 300	Approximate temperature 55°C

PCR data Exp. ID 13081
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 300	Approximate temperature 55°C

PCR data Exp. ID 13082
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 300	Approximate temperature 55°C

PCR data Exp. ID 13083
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 300	Approximate temperature 55°C

PCR data Exp. ID 13084
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 300	Approximate temperature 55°C

PCR data Exp. ID 13085
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Physalis TA1367: 300	Approximate temperature 55°C

PCR data Exp. ID 13086
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 300	Approximate temperature 55°C

PCR data Exp. ID 13087
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 300	Approximate temperature 55°C

PCR data Exp. ID 13088
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 300	Approximate temperature 55°C

PCR data Exp. ID 32623
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 300	Approximate temperature 55°C

PCR data Exp. ID 32964
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 300	Approximate temperature 55°C

PCR data Exp. ID 32965
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 300	Approximate temperature 55°C

PCR data Exp. ID 32966
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 300	Approximate temperature 55°C

PCR data Exp. ID 32967
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 300	Approximate temperature 55°C

PCR data Exp. ID 32968
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 300	Approximate temperature 55°C

PCR data Exp. ID 10840
Forward primer (5'-3') AGGAAGAGGCTCTTCATCATGGAC	Digested band sizes (using RsaI) Solanum pennellii LA716: 220 Solanum lycopersicum LA925: 200	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTCTCAATTGGTGAAACAGAAGG	Enzymes All possible enzymes for pennellii and and lycopersicum: AluI,MspI,RsaI,DraI,TaqI,RV,HinfI,DpnII,KpnI
Accessions and product sizes Solanum pennellii LA716: 250 Solanum lycopersicum LA925: 250	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U229090

Overgo hybridization and physical mapping

C2_At2g40760 was used as an overgo probe on plate 13 [well F1]

Plausible BAC Matches: P019A16, P023A23, P054K19, P251N03, P050P05, P317D09

Overgo Sequences

A sequence

GAGGAGGTTGAAGGTAGCGTTTTG

B sequence

GTTGTGATTCGGAGCTCAAAACGC

AB sequence

GAGGAGGTTGAAGGTAGCGTTTTGAGCTCC

Marker sequence

ATGCTATCATCATCAACCGCCTTTTCACCAAACCCTAATCTTCCCATTAA
TTCACTCCATTGCACCATGAAAGCAACATCTGAACTACCTACAAAACCCC
CTAACTTTCCTTTCTTTTCTAATCCTAAGATTACTATAACCAATTTACCG
CAAAACCTTGCACCCTCTAACTGTTTCTCTGCAACAAATCCTGTTCCCAT
TCTGAAGGCTAATGCATCGAGGAACGAGGAGGTTGAAGGTAGCGTTTTGA
GCTCCGAATCACAACTTGTGGTGGTTTCTTTCTACAAATTTGCTGATTTT
CCTGACCATGCTGATTTGAGGAAACCATTGAAGGAACTTTGTGAAAAACT
NNNNNNGGTGGTATTATTCTTGCACCTGAAGGAATCAATGGCAGCATATG
CGGAAGACGGGATTCAGTGGAAACTGTTCTTGCATTCATTCAAAGTGATG
AGCGTCTGAAGGGGCTTAGATTGATCGAGTCACCAGTGAGCCCGGAGGAA
GAGGCTCTTCATCATGGACATATGAGCAGCTCTCCTCTTGCAGCGGGTGA
GGATGCTCCCTTTAGGTGGGATCACGTGAGGGTGAAGCTCAAAAAAGAGN
NNNNATAGTTACACTTGGAATGCCTTCTGTTTCACCAATTGAGAGAGTTG
GCAAGTACATTAAACCGACAGAGTGGAATGCATTGATTAGTGATCCAGAT
GTTNNNNNGTGNNNNN

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