Sol Genomics Network

SGN Marker C2_At4g30930

SGN-M4670
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
Capsicum annuum	Single	SGN-U203042	-	-	-
Lycopersicon Combined	Single	SGN-U217708	-	-	-
Solanum tuberosum	Single	SGN-U245365	-	-	-
Arabidopsis	Single	At4g30930 on TAIR	-	-	-

Mapped locations

Map: Eggplant-RAD 2012
Map version 174 (location: 132191)
Chromosome 2
Position 48.63 cM
Confidence uncalculated
Protocol CAPS

Eggplant-RAD 2012

Map: Tomato-EXPEN 2000
Map version 52 (location: 38690)
Chromosome 2
Position 63.10 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39866

Forward primer (5'-3')

ATCATACCTTCTCTCTCCAAACCC

Accessions and product sizes

Solanum pennellii TA56

700

Solanum lycopersicum TA209

700

Approximate temperature

55°C

Reverse primer (5'-3')

TCGCCATTGCTCACTTTAAACTG

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

220+340

Solanum pennellii TA56

220+380

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26855)
Chromosome 4
Position 15.05 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11525
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 700	Approximate temperature 55°C

PCR data Exp. ID 11526
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 700	Approximate temperature 55°C

PCR data Exp. ID 11527
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 700	Approximate temperature 55°C

PCR data Exp. ID 13486
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 750	Approximate temperature 55°C

PCR data Exp. ID 13487
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Solanum melongena TA2986: 700	Approximate temperature 55°C

PCR data Exp. ID 13488
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 680+850	Approximate temperature 55°C

PCR data Exp. ID 13489
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 580	Approximate temperature 55°C

PCR data Exp. ID 13490
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 750+580	Approximate temperature 55°C

PCR data Exp. ID 13491
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 580	Approximate temperature 55°C

PCR data Exp. ID 13492
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 650	Approximate temperature 55°C

PCR data Exp. ID 13493
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Physalis TA1367: 650	Approximate temperature 55°C

PCR data Exp. ID 13494
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 420+750	Approximate temperature 55°C

PCR data Exp. ID 13495
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 750	Approximate temperature 55°C

PCR data Exp. ID 13496
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 750	Approximate temperature 55°C

PCR data Exp. ID 13497
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Coffea canephora BP409: 1100	Approximate temperature 55°C

PCR data Exp. ID 33118
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 580	Approximate temperature 55°C

PCR data Exp. ID 33119
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 750+580	Approximate temperature 55°C

PCR data Exp. ID 33120
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 580	Approximate temperature 55°C

PCR data Exp. ID 33121
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 650	Approximate temperature 55°C

PCR data Exp. ID 11528
Forward primer (5'-3') ATCATACCTTCTCTCTCCAAACCC	Digested band sizes (using DpnII) Solanum pennellii LA716: 380+220 Solanum lycopersicum LA925: 340+220	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCGCCATTGCTCACTTTAAACTG	Enzymes All possible enzymes for pennellii and and lycopersicum: RsaI, DpnII
Accessions and product sizes Solanum lycopersicum LA925: 700 Solanum pennellii LA716: 700	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U217708
SGN-U271552

Overgo hybridization and physical mapping

C2_At4g30930 was used as an overgo probe on plate 13 [well E1]

Plausible BAC Matches: None

Overgo Sequences

A sequence

TATAAGGTGATCGGCCCACTTCAG

B sequence

AAACCCGGTCCGATTTCTGAAGTG

AB sequence

TATAAGGTGATCGGCCCACTTCAGAAATCG

Marker sequence

ATGGCAAATCGGCGATGCCTTCAAACCCTAACCCGTCATTTATCATACCT
TCTCTCTCCAAACCCGTCTCTTTGTTCCCCTCAAACCCTAACCCCACCAC
TGCTCAATTCCATCAACACACTAACTTCGTCTCCCAAATGCCCCCAAGTT
ACCACTCAACTTTCATCTTTCCACCGGCATTTCTCTTCGAATCGACCGAG
CAATAGCGACGAGGAGGAAGAGGATGAAAGTGAAGATGAAACAGATTATG
ATGATGACGATGATGATGACGTTGAGGGCTTCAAATCGAATAGTGAGCCC
GGTAGAGTATACACTCCGGAGGAGAAAGAGTACGAGGCGGCAGAAATTGG
ATATAAGGTGATCGGCCCACTTCAGAAATCGGACCGGGTTTTCAAACCAT
ATGAACCCGTTTATGCTGTTATTCAGNNNNNATTGGTTCCCACCAGTTTA
AAGTGAGCAATGGCGATTCCATTTTTGTGGAGAAACTGAAGTTCTGTGAA
GTCAATGACAAGNNNNNTTGATTCTAAACAAGGTTCTGCTGCTGGGCTCA
AAGACACAGACAATCATTGGCAGGCCTGTATTGCCTGATGCAGCTGTTCA
TGCTGTTGTTGAGGAGCATNNNNNGCATTAGATGCTAAAGTACTGATATT
CAAGAAGAAGAGACGAAAGAATTATCGACGAACACGAGGGCATCGACAGN
NNNNGAATTAACAAAGTTGAGGATTACGGATATTCAAGGAGTTGAAAAGC
CTGAAGTGGTACCAATTCTCAAGACAGAGAAGAAAGATGCTAAGAAGGTA
GCAGTAGCAGCTTAAAAATGGTGA

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