Sol Genomics Network

SGN Marker C2_At1g02140

SGN-M3864
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	299673 (SGN) 121932 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U204098	-	-	-
Lycopersicon Combined	Single	SGN-U237263	-	-	-
Solanum tuberosum	Multiple	SGN-U243161	-	-	-
Arabidopsis	Single	At1g02140 on TAIR	-	-	-

Mapped locations

Map: Pepper-COSII
Map version 58 (location: 41283)
Chromosome 2
Position 11.00 cM
Confidence I(LOD2)
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43259

Forward primer (5'-3')

TCCGTTATGCTAACAATTCCAAC

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

TGTGTTCATTTCCCATCACAATCTC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38048)
Chromosome 3
Position 71.00 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39353

Forward primer (5'-3')

TCCGTTATGCTAACAATTCCAAC

Accessions and product sizes

Solanum lycopersicum TA209

1500

Solanum pennellii TA56

1500

Approximate temperature

50°C

Reverse primer (5'-3')

TGTGTTCATTTCCCATCACAATCTC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

600

Solanum lycopersicum TA209

700

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 24869)
Chromosome 1
Position 0.40 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 9871
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1500	Approximate temperature 50°C

PCR data Exp. ID 9872
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1500	Approximate temperature 50°C

PCR data Exp. ID 9873
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1550	Approximate temperature 50°C

PCR data Exp. ID 12351
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1500	Approximate temperature 55°C

PCR data Exp. ID 12352
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1500+1900	Approximate temperature 55°C

PCR data Exp. ID 12353
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 320+1200	Approximate temperature 55°C

PCR data Exp. ID 12354
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 320+1200	Approximate temperature 55°C

PCR data Exp. ID 12355
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 320+1100	Approximate temperature 55°C

PCR data Exp. ID 12356
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 320+1100	Approximate temperature 55°C

PCR data Exp. ID 12357
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Physalis TA1367: Multiple	Approximate temperature 55°C

PCR data Exp. ID 12358
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 320	Approximate temperature 55°C

PCR data Exp. ID 32588
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1500	Approximate temperature 55°C

PCR data Exp. ID 32662
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1500	Approximate temperature 55°C

PCR data Exp. ID 32663
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1500	Approximate temperature 55°C

PCR data Exp. ID 32664
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 320+1200	Approximate temperature 55°C

PCR data Exp. ID 32665
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 320+1200	Approximate temperature 55°C

PCR data Exp. ID 32666
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 320+1100	Approximate temperature 55°C

PCR data Exp. ID 9874
Forward primer (5'-3') TCCGTTATGCTAACAATTCCAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGTTCATTTCCCATCACAATCTC	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference, AluI, MspI All possible enzymes for lycopersicum and pimpinellifolium: amplicon difference, AluI, HinfI
Accessions and product sizes Solanum lycopersicum LA925: 1500 Solanum pennellii LA716: 1500	Approximate temperature 50°C

Unigene blast matches for primers

SGN-U268176

Overgo hybridization and physical mapping

C2_At1g02140 was used as an overgo probe on plate 13 [well E2]

Plausible BAC Matches: None

Overgo Sequences

A sequence

GGTAAATTCGGGCATGAGTTCTTG

B sequence

GCCTAAACTCGAACTCCAAGAACT

AB sequence

GGTAAATTCGGGCATGAGTTCTTGGAGTTC

Marker sequence

ATGGCGGAGACAGGGGACGAAAATGCAGGGGAGTTTTACTTGAGGTACTA
TGTCGGCCACAAGGGTAAATTCGGGCATGAGTTCTTGGAGTTCGAGTTTA
GGCCCGACGGCAAGCTGCGGTATGCTAATAATTCCAACTATAAGAACGAC
ACCATGATCCGTAAAGAGGTCTTCGTCACCCCCGCCGTTCTAAAAGAATG
CCGTCGCATCGTCGTTGAAAGCGAGNNNNNATAATGAAGGAAGATGACAA
CAATTGGCCAGAACCAGATCGCGTTGGAAGGCAAGAGCTGGAGATTGTAA
TGGGGAACGAGCACATATCTTTTACCACTGCTAAGATTGGTTCTCTCGTG
GATGTTAATATCAGTAAAGATCCTGAAGGTCTTCGAATCTTCTATTATCT
TGTTCAGNNNNNGATTTGAAGTGTTTCGTGTTTTCTCTTATCTCACTCCA
CTTCAAGATCAAACCCATTTGA

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
Forward amplicon sequence for S. betaceum 6002061 plant #4, AB1 chromatogram - [View]
Forward amplicon sequence for S. betaceum 6002061 plant #4, plain text
Forward amplicon sequence for S. uniloba 6002078 plant #6, AB1 chromatogram - [View]
Forward amplicon sequence for S. uniloba 6002078 plant #6, plain text

BLASTX result of original unigene sequences against Arabidopsis protein database