Sol Genomics Network

SGN Marker C2_At3g24050

SGN-M4667
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	301821 (SGN) 125045 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197898	-	-	-
Lycopersicon Combined	Multiple	SGN-U220234	-	-	-
Solanum tuberosum	Single	SGN-U245332	-	-	-
Arabidopsis	Single	At3g24050 on TAIR	-	-	-

Mapped locations

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46680)
Chromosome 9
Position 29.00 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Pepper-COSII
Map version 58 (location: 41427)
Chromosome 3
Position 11.80 cM
Confidence F(LOD3)
Protocol dCAPS

Pepper-COSII

PCR data Exp. ID 43403

Forward primer (5'-3')

CAATACACTAGAGTTATATTTTTCTT

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

AGGGCCTGCCCGCCATTGTG

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38510)
Chromosome 9
Position 97.00 cM
Confidence CF(LOD3)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39735

Forward primer (5'-3')

ATGATGAAGATGACCTTCTCAACTTCTC

Accessions and product sizes

Solanum lycopersicum TA209

1700

Solanum pennellii TA56

1700

Approximate temperature

55°C

Reverse primer (5'-3')

AGGGCCTGCCCGCCATTGTG

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

1700

Solanum pennellii TA56

800+900

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26289)
Chromosome 3
Position 8.69 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11135
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1700	Approximate temperature 55°C

PCR data Exp. ID 11136
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1700	Approximate temperature 55°C

PCR data Exp. ID 11137
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1700	Approximate temperature 55°C

PCR data Exp. ID 13261
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1600	Approximate temperature 55°C

PCR data Exp. ID 13262
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 2000	Approximate temperature 55°C

PCR data Exp. ID 13263
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1800	Approximate temperature 55°C

PCR data Exp. ID 13264
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Physalis TA1367: 2200	Approximate temperature 55°C

PCR data Exp. ID 13265
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 1500	Approximate temperature 55°C

PCR data Exp. ID 13266
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 1500	Approximate temperature 55°C

PCR data Exp. ID 13267
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 1500	Approximate temperature 55°C

PCR data Exp. ID 32634
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1500	Approximate temperature 55°C

PCR data Exp. ID 33037
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1500	Approximate temperature 55°C

PCR data Exp. ID 33038
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 2000	Approximate temperature 55°C

PCR data Exp. ID 33039
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1800	Approximate temperature 55°C

PCR data Exp. ID 11138
Forward primer (5'-3') ATGATGAAGATGACCTTCTCAACTTCTC	Digested band sizes (using DraI) Solanum lycopersicum LA925: 1700 Solanum pennellii LA716: 900+800	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGCCTGCCCGCCATTGTG	Enzymes All possible enzymes for pennellii and and lycopersicum: AluI, RsaI, DraI, DpnII All possible enzymes for lycopersicum and pimpinellifolium: DraI
Accessions and product sizes Solanum lycopersicum LA925: 1700 Solanum pennellii LA716: 1700	Approximate temperature 55°C

Overgo hybridization and physical mapping

C2_At3g24050 was used as an overgo probe on plate 13 [well D9]

Plausible BAC Matches: P022M02

Overgo Sequences

A sequence

ACCCGGGTATGGTATTTGATCACC

B sequence

ACTGAAACCGGGCTATGGTGATCA

AB sequence

ACCCGGGTATGGTATTTGATCACCATAGCC

Marker sequence

ATGAAAATGGAGGATTTGGACCCAACTGCATGTTTCATGGTGGATGATGA
CCTTCTCAACTTCTCTTTGGAAGATGAAACTGTTGAAGAAGATGATGAAA
AATCAACTATTACTAGCAAAGACCCACTTTCTTATTCTTCTTCGTCTTCA
ACAAACCCTCTTGTTAGCCTTCTTCCCCACCCTGAGNNNNNTGTGTAGAG
GAAGAGTTGGAATGGCTGTCAAACAAAGATGCATTTCCAGCGATAGAGTT
TGGCATTCTTTCGGAGAACCCGGGTATGGTATTTGATCACCATAGCCCGG
TTTCAGTGCTGGAGAATAGTAGCAGCACTAGTCACAGCAGTGGCAATGGT
GTTGTTAGTGGAAATGCTTATACGAGCTGCTGCGTCAACTTAAAAGTTCC
GGTTAATTACCCTGTTCGTGCACGGAGCAAGAGAAGACGTAGAAGACGGA
GAGGTGGATTTGCTGACATGCCAAGCGAGCATTGTCTGCCGGTGACACAA
CCGAGTTTCAAGAACGTTAAGCAGCGTGAGCCATTGCTTTCTTTACCAAT
GAATTCAGCTAAGAGTGCTGCTAGCATTGGGAGGAGGTGCCAACACTGTG
GAGCCGATAAGACCCCACAATGGCGGGCAGGCCCTCTGGGGCCAAAAACA
CTGTGTAATGCTTGTGGTGTGCGCTATAAGTCAGGCAGGCTGTTACCAGA
GTATCGCCCGGCTAATAGCCCTACTTTCTCGGCTGCTGCGCATTCAAACT
CCCACCGGAAGGTTTTGGAGATGAGAAAGCATAAGATTGGTGTGGGAGGA
ATGTTGATTCATGAAGCTTGTGGATATAGGGTAGGACAGTAG

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