Sol Genomics Network

SGN Marker C2_At5g51040

SGN-M4688
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	302371 (SGN) 119697 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U198037	-	-	-
Lycopersicon Combined	Multiple	SGN-U214915	-	-	-
Solanum tuberosum	Single	SGN-U246612	-	-	-
Arabidopsis	Single	At5g51040 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38884)
Chromosome 3
Position 134.00 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39986

Forward primer (5'-3')

TCGCCGATGAATATCGATCTTTCC

Accessions and product sizes

Solanum pennellii TA56

580+750

Solanum lycopersicum TA209

580+750

Approximate temperature

55°C

Reverse primer (5'-3')

TCCAAGAACAAGGTCTAGCTCCAGG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

510+640

Solanum lycopersicum TA209

410+510

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27501)
Chromosome 5
Position 20.77 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11986
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 250	Approximate temperature 55°C

PCR data Exp. ID 11987
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 250	Approximate temperature 55°C

PCR data Exp. ID 11988
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 250	Approximate temperature 55°C

PCR data Exp. ID 13900
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 250	Approximate temperature 55°C

PCR data Exp. ID 13901
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Solanum melongena TA2986: 250	Approximate temperature 55°C

PCR data Exp. ID 13902
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 250	Approximate temperature 55°C

PCR data Exp. ID 13903
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 250	Approximate temperature 55°C

PCR data Exp. ID 13904
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 250	Approximate temperature 55°C

PCR data Exp. ID 13905
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 250	Approximate temperature 55°C

PCR data Exp. ID 13906
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 250	Approximate temperature 55°C

PCR data Exp. ID 13907
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Physalis TA1367: 250	Approximate temperature 55°C

PCR data Exp. ID 13908
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 250	Approximate temperature 55°C

PCR data Exp. ID 13909
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 250	Approximate temperature 55°C

PCR data Exp. ID 13910
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Coffea canephora BP409: 200	Approximate temperature 55°C

PCR data Exp. ID 33283
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 250	Approximate temperature 55°C

PCR data Exp. ID 33284
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 250	Approximate temperature 55°C

PCR data Exp. ID 33285
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 250	Approximate temperature 55°C

PCR data Exp. ID 33286
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 250	Approximate temperature 55°C

PCR data Exp. ID 11989
Forward primer (5'-3') TCGCCGATGAATATCGATCTTTCC	Digested band sizes (using MspI) Solanum pennellii LA716: 100 Solanum lycopersicum LA925: 250	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCAAGAACAAGGTCTAGCTCCAGG	Enzymes All possible enzymes for pennellii and and lycopersicum: MspI
Accessions and product sizes Solanum lycopersicum LA925: 250 Solanum pennellii LA716: 250	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U214915

Overgo hybridization and physical mapping

C2_At5g51040 was used as an overgo probe on plate 13 [well G5]

Plausible BAC Matches: None

Overgo Sequences

A sequence

AGGGTGGGATGATATCAAGAGAGG

B sequence

TATAGGTGCATCACGGCCTCTCTT

AB sequence

AGGGTGGGATGATATCAAGAGAGGCCGTGA

Marker sequence

ATGGCGAATTTGCGAAGGGCACTTCTCTTCACCATTCCTCGAATCATCAA
TTCCTCTAAAACAGCATCTGTTGCAACCTCCACACTCCAGTCTCACAATC
TCTANNNNNCAGGCCTTTAGCTGGAACATTTTCGCGTTTTATTTCTTCTA
ATGAGACTTCATCGCCGATGAATATCGATCTTTCCGACGAAGAGAGCAAA
AGACGTTTGTTTAACAGNNNNNGCTTATTTATCGTAGTAAACAGAGAGGT
TACCTGGAGCTAGACCTTGTTCTTGGAAAATGGGTGGAGGAACATATACA
ATCCATGGATGAAAATGGAATTAAGTCCCTTGTTCATGTCCTTGACCTGN
NNNNGAGAATCCAGATTTGTGGAAGTGGCTGACTGGTCAGGAGCAACCCC
CAGATGCAATAAGCACAAATCCTNNNNNGTGTTTTCTGCTGTGCATGAAA
AGGTTATGAACAACCTTAACAATCATACTTCTCCCGAGACTCGTGCTGTT
CCAGGAAAACCTTGGGTGAGAGGGTGGGATGATATCAAGAGAGGCCGTGA
TGCACCTATAGCTGGGAACCAGTAG

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

Input file for PAUP, NEXUS format
Phylogenetic tree
Phylogenetic tree | [View]
Forward amplicon sequence for S. hirtum 120062 plant #28, AB1 chromatogram - [View]
Forward amplicon sequence for S. hirtum 120062 plant #28, plain text
Forward amplicon sequence for S. quitoense plant #3, AB1 chromatogram - [View]
Forward amplicon sequence for S. quitoense plant #3, plain text

BLASTX result of original unigene sequences against Arabidopsis protein database