Sol Genomics Network

SGN Marker C2_At4g34700

SGN-M4640
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	302552 (SGN) 122671 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U196971	-	-	-
Lycopersicon Combined	Single	SGN-U216646	-	-	-
Solanum tuberosum	Multiple	SGN-U245506	-	-	-
Arabidopsis	Single	At4g34700 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49284)
Chromosome 1
Position 88.87 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47224)
Chromosome 1
Position 148.95 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Pepper-COSII
Map version 58 (location: 41496)
Chromosome 1
Position 246.00 cM
Confidence I
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43472

Forward primer (5'-3')

TTCCATGGGCACCTGGTGG

Accessions and product sizes

Approximate temperature

60°C

Reverse primer (5'-3')

CAGCCTCTTCCTTGCCATAGTCATA

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38713)
Chromosome 1
Position 160.00 cM
Confidence CF(LOD3)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39883

Forward primer (5'-3')

TGAAGCATCCTACAATAAGTGGCG

Accessions and product sizes

Solanum lycopersicum TA209

1000

Solanum pennellii TA56

1100

Approximate temperature

55°C

Reverse primer (5'-3')

TCTGTTGAACTTGGAACCACCAGG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

1100

Solanum lycopersicum TA209

1000

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26919)
Chromosome 4
Position 16.56 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11575
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1100	Approximate temperature 55°C

PCR data Exp. ID 11576
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1000	Approximate temperature 55°C

PCR data Exp. ID 11577
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1100	Approximate temperature 55°C

PCR data Exp. ID 13554
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 250	Approximate temperature 55°C

PCR data Exp. ID 13555
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Solanum melongena TA2986: 250	Approximate temperature 55°C

PCR data Exp. ID 13556
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 900	Approximate temperature 55°C

PCR data Exp. ID 13557
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13558
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13559
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1000	Approximate temperature 55°C

PCR data Exp. ID 13560
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1000	Approximate temperature 55°C

PCR data Exp. ID 13561
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 900	Approximate temperature 55°C

PCR data Exp. ID 13562
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Physalis TA1367: 900	Approximate temperature 55°C

PCR data Exp. ID 13563
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 450	Approximate temperature 55°C

PCR data Exp. ID 13564
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 500	Approximate temperature 55°C

PCR data Exp. ID 13565
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 300	Approximate temperature 55°C

PCR data Exp. ID 13566
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 450	Approximate temperature 55°C

PCR data Exp. ID 13567
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Coffea canephora BP409: 580	Approximate temperature 55°C

PCR data Exp. ID 33141
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: Multiple	Approximate temperature 55°C

PCR data Exp. ID 33142
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 33143
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1000	Approximate temperature 55°C

PCR data Exp. ID 33144
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1000	Approximate temperature 55°C

PCR data Exp. ID 11578
Forward primer (5'-3') TGAAGCATCCTACAATAAGTGGCG	Digested band sizes (using amplicon difference) Solanum lycopersicum LA925: 1000 Solanum pennellii LA716: 1100	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCTGTTGAACTTGGAACCACCAGG	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: 1000 Solanum pennellii LA716: 1100	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U208184
SGN-U216646
SGN-U270528

Overgo hybridization and physical mapping

C2_At4g34700 was used as an overgo probe on plate 13 [well A5]

Plausible BAC Matches: P023C06

Overgo Sequences

A sequence

TGAGCGGAATAGCATCGGTATCGT

B sequence

GCTCTTCGAGCTAAGAACGATACC

AB sequence

TGAGCGGAATAGCATCGGTATCGTTCTTAG

Marker sequence

ATGAGCGGAATAGCATCGGTATCGTTCTTAGCTCGAAGAGCATCGCAGAG
GGAGAGGGTTCGGATCCTCTACAGGCGTGCTCTCAGAGACACTCTTAATT
GGGCCGTCCATCGTCATCTCTTCTATCCTGATNNNNNGCGGATGCCCTAA
GGGAGCGATTTGAGGTCAACAGAAAAGTGNNNNNGAAGATGTTGAAACTA
TTGATAGACTTATAGCTGATGGTGAAGCATCCTACAATAAGTGGCGGCAC
CCTGATCCTTACATTGNNNNNTTCCATGGGCACCTGGTGGTTCCAAGTTC
AACAGAAATCCAGTGCCGCCAGAAGGGNNNNNATTGAGATAGTGTATGAC
TATGGCAAGGAAGAGGCTGAACTAGTATGANNNNN

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