Sol Genomics Network

SGN Marker C2_At5g25760

SGN-M4651
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	301734 (SGN) 123753 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U198046	-	-	-
Lycopersicon Combined	Single	SGN-U216051	-	-	-
Solanum tuberosum	Single	SGN-U254400	-	-	-
Arabidopsis	Single	At5g25760 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49295)
Chromosome 11
Position 51.88 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47236)
Chromosome 11
Position 111.00 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46761)
Chromosome 1
Position 105.90 cM
Confidence I(LOD2)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Pepper Capsicum
Map version 65 (location: 42690)
Chromosome 11
Position 96.60 cM
Confidence uncalculated
Protocol PCR

Pepper Capsicum

Map: Tomato-EXPEN 2000
Map version 52 (location: 38828)
Chromosome 11
Position 89.50 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39949

Forward primer (5'-3')

TCCTTATGATGGTGGAGTTTTCCAG

Accessions and product sizes

Solanum pennellii TA56

350

Solanum lycopersicum TA209

350

Approximate temperature

55°C

Reverse primer (5'-3')

AAAGCAATTATAGCTCGACAAACAG

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27304)
Chromosome 5
Position 8.97 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11819
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1200	Approximate temperature 55°C

PCR data Exp. ID 11820
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1300	Approximate temperature 55°C

PCR data Exp. ID 11821
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1300	Approximate temperature 55°C

PCR data Exp. ID 13812
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1000	Approximate temperature 55°C

PCR data Exp. ID 13813
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Solanum melongena TA2986: 1400	Approximate temperature 55°C

PCR data Exp. ID 13814
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1650	Approximate temperature 55°C

PCR data Exp. ID 13815
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1200	Approximate temperature 55°C

PCR data Exp. ID 13816
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1200	Approximate temperature 55°C

PCR data Exp. ID 13817
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1150	Approximate temperature 55°C

PCR data Exp. ID 13818
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1150	Approximate temperature 55°C

PCR data Exp. ID 13819
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 1250	Approximate temperature 55°C

PCR data Exp. ID 13820
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Physalis TA1367: 1050	Approximate temperature 55°C

PCR data Exp. ID 13821
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 1250	Approximate temperature 55°C

PCR data Exp. ID 13822
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 450+1350	Approximate temperature 55°C

PCR data Exp. ID 13823
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 1250	Approximate temperature 55°C

PCR data Exp. ID 13824
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 1400	Approximate temperature 55°C

PCR data Exp. ID 13825
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Coffea canephora BP409: 850	Approximate temperature 55°C

PCR data Exp. ID 33245
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1200	Approximate temperature 55°C

PCR data Exp. ID 33246
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1200	Approximate temperature 55°C

PCR data Exp. ID 33247
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1150	Approximate temperature 55°C

PCR data Exp. ID 33248
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1150	Approximate temperature 55°C

PCR data Exp. ID 11822
Forward primer (5'-3') TCCTTATGATGGTGGAGTTTTCCAG	Digested band sizes (using amplicon difference) Solanum lycopersicum LA925: 1300 Solanum pennellii LA716: 1200	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AAAGCAATTATAGCTCGACAAACAG	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference All possible enzymes for lycopersicum and pimpinellifolium: AluI,DraI,TaqI,RV,HaeIII,HinfI,DpnII,KpnI
Accessions and product sizes Solanum lycopersicum LA925: 1300 Solanum pennellii LA716: 1200	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U198046
SGN-U206127
SGN-U216051
SGN-U275331

Overgo hybridization and physical mapping

C2_At5g25760 was used as an overgo probe on plate 13 [well B11]

Plausible BAC Matches: P176F18

Overgo Sequences

A sequence

CGCTAAACTGTGACTCAGGCAATC

B sequence

TCACCGGATCGAAGAAGATTGCCT

AB sequence

CGCTAAACTGTGACTCAGGCAATCTTCTTC

Marker sequence

ATGCAGGCTTCAAGGGCAAGACTTTTCAAGGAGTACAAAGAAGTACAGAG
AGAGAAAACAGCTGNNNNNATCCTGATATTCAATTAGTTTGTGATGACTC
TAATATNNNNNCTTTAAATGGACGGCTCTTGTTAAAGGGCCATCTGAAAC
TCCTTATGATGGTGGAGTTTTCCAGCTCGCTTTCTCAGTTCCAGAGCAGT
ATCCATTGCAACCTCCTCAAGTGCGGTTCCTGACCAAAATATTTCACCCA
AATGTTCATTTTAAGACCGGAGAGATTTGCCTTGATATTTTGAAAAATGC
ATGGAGCCCAGCATGGACACTCCAGTCTGTTTGTCGAGCTATAATTGCTT
TGATGGCTCANNNNNTCCTGAAGCTGATAGCCCGCTAAACTGTGACTCAG
GCAATCTTCTTCGATCCGGTGATATCAGAGGTTACCAGTCAATGGCAAGG
ATGTACACTAGGCTTGCTGCAATGCCCAAGAAGGGCTAANNNNN

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