Sol Genomics Network

SGN Marker C2_At3g15290

SGN-M4674
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	309818 (SGN) 131802 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197340	-	-	-
Lycopersicon Combined	Single	SGN-U219933	-	-	-
Solanum tuberosum	Multiple	SGN-U244533	-	-	-
Arabidopsis	Single	At3g15290 on TAIR	-	-	-

Mapped locations

Map: Solanum michoacanum 2011
Map version 155 (location: 109233)
Chromosome 7S
Position 51.53 cM
Confidence uncalculated
Protocol CAPS

Solanum michoacanum 2011

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46666)
Chromosome 7
Position 19.90 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Tobacco N. acuminata
Map version 89 (location: 46484)
Chromosome 7
Position 32.60 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. acuminata

Map: Pepper-COSII
Map version 58 (location: 41416)
Chromosome 7
Position 107.90 cM
Confidence F(LOD3)
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43392

Forward primer (5'-3')

TCTGCTATTTTGGCTTCTAATACAAG

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

ACAATATGTGTCTTCTGATGTATCTGC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38468)
Chromosome 7
Position 63.50 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39708

Forward primer (5'-3')

TCTGCTATTTTGGCTTCTAATACAAG

Accessions and product sizes

Solanum pennellii TA56

1200

Solanum lycopersicum TA209

1100

Approximate temperature

55°C

Reverse primer (5'-3')

ACAATATGTGTCTTCTGATGTATCTGC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

1200

Solanum lycopersicum TA209

1100

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26175)
Chromosome 3
Position 5.15 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11055
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1200	Approximate temperature 55°C

PCR data Exp. ID 11056
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1100	Approximate temperature 55°C

PCR data Exp. ID 11057
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1100	Approximate temperature 55°C

PCR data Exp. ID 13216
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1000	Approximate temperature 55°C

PCR data Exp. ID 13217
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 1200	Approximate temperature 55°C

PCR data Exp. ID 13218
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1350	Approximate temperature 55°C

PCR data Exp. ID 13219
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1300	Approximate temperature 55°C

PCR data Exp. ID 13220
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1300	Approximate temperature 55°C

PCR data Exp. ID 13221
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1300	Approximate temperature 55°C

PCR data Exp. ID 13222
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1300	Approximate temperature 55°C

PCR data Exp. ID 13223
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Physalis TA1367: 580	Approximate temperature 55°C

PCR data Exp. ID 13224
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 1300	Approximate temperature 55°C

PCR data Exp. ID 13225
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 1000	Approximate temperature 55°C

PCR data Exp. ID 13226
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 1350	Approximate temperature 55°C

PCR data Exp. ID 13227
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 1300	Approximate temperature 55°C

PCR data Exp. ID 33024
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1300	Approximate temperature 55°C

PCR data Exp. ID 33025
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1300	Approximate temperature 55°C

PCR data Exp. ID 33026
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1300	Approximate temperature 55°C

PCR data Exp. ID 33027
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1300	Approximate temperature 55°C

PCR data Exp. ID 11058
Forward primer (5'-3') TCTGCTATTTTGGCTTCTAATACAAG	Digested band sizes (using amplicon difference) Solanum pennellii LA716: 1200 Solanum lycopersicum LA925: 1100	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAATATGTGTCTTCTGATGTATCTGC	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference
Accessions and product sizes Solanum pennellii LA716: 1200 Solanum lycopersicum LA925: 1100	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U197340
SGN-U219933
SGN-U269010

Overgo hybridization and physical mapping

C2_At3g15290 was used as an overgo probe on plate 13 [well E8]

Plausible BAC Matches: P032P02, P046G04

Non-Plausible BAC matches

P156J17, P154M19

Overgo Sequences

A sequence

TGATGCTGTGAAGCGTCTTCGTTG

B sequence

ATCCAAGCGCGAAGAACAACGAAG

AB sequence

TGATGCTGTGAAGCGTCTTCGTTGTTCTTC

Marker sequence

ATGGCCGATATAACAAGGATCGGAGTTGTTGGCGCCGGCCAAATGGGTGC
CGGAATCGCCCAACTCGCCGCCGTCAACGGCGTCGACGTTTGGCTTTACG
ATTTGGATTCTGAAGCTCTTACTAAAGCTCAAAAATCTATTTCCAATAAT
ATTCAACGCCTCCTCACCAAAGGACAAATCTCTCAGNNNNNGCAACGAGT
GTTGATGCTGTGAAGCGTCTTCGTTGTTCTTCGCGCTTGGATGATTTACA
GTCAGTTGATATTGTTGTTGAGGCTATTGTGGAGTCTGAACAAGTGAAGA
AATCTTTATTTGCTAACTTGGATAAGATTGTAAAGAGTTCTGCTATTTTG
GCTTCTAATACAAGCTCTATTTCCATTACTCGTCTAGCATCTGCAACGAG
CCGACCCTCTCAGNNNNNGTGATCGGCATGCACTTTATGAATCCTCCGCC
GATTATGAAGCTGGTTGAAATTATTCGGGGTGCAGATACATCAGAAGACA
CATATTGTGCCACTAAATGCCTGGCAGAGAGNNNNNGTTTGGTAAGACAG
TTATCTGCTCTCAGGATTACTCTGGTTTCATAGTAAACCGAATTTTGATG
CCAATGATAAACGAAGCCTTTCATACACTGTACACCGGAGTTGCAACAAA
AGAAGATATCGATACAGGAATGAAACTAGGAACCAACCATCCTATGGGTC
CTTTTGAACTTGCAGATTTTATCGGACTGGATGTTTGTTTGTCAATCATG
AAAGTTTTTCAAGCCGGTTTAGGGGACGATAAATATGCCCCATGCCCTCT
CCTTGTGCAGTATGTTGATGCTGGTAGACTTGGTAAAAAACGAGGGGTTG
GGGTATATGATTACCGTAATGCTGGTAAAAAAACAGGAGGATCGCCTCGA
CTTTGA

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]

BLASTX result of original unigene sequences against Arabidopsis protein database

Input file for PAUP, NEXUS format
Phylogenetic tree
Phylogenetic tree | [View]

Related Markers

Related Genotyped Markers: These markers have been genotyped and share a name with this marker

Genomic location of C2_At3g15290

%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D4674 marker 4674