Sol Genomics Network

SGN Marker C2_At1g19140

SGN-M4682
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	303267 (SGN) 120328 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U205310	-	-	-
Lycopersicon Combined	Single	SGN-U218348	-	-	-
Solanum tuberosum	Single	SGN-U250893	-	-	-
Arabidopsis	Single	At1g19140 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38119)
Chromosome 7
Position 23.50 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39407

Forward primer (5'-3')

AGGCCCTTGTACTCAGTGCCTCTC

Accessions and product sizes

Solanum lycopersicum TA209

850

Solanum pennellii TA56

850

Approximate temperature

55°C

Reverse primer (5'-3')

TCATGGCGGTTTCAGTCCATCC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

850

Solanum pennellii TA56

750

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25062)
Chromosome 1
Position 6.61 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10057
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 850	Approximate temperature 55°C

PCR data Exp. ID 10058
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 850	Approximate temperature 55°C

PCR data Exp. ID 10059
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1000	Approximate temperature 55°C

PCR data Exp. ID 12468
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 900	Approximate temperature 55°C

PCR data Exp. ID 12469
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 750	Approximate temperature 55°C

PCR data Exp. ID 12470
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1000	Approximate temperature 55°C

PCR data Exp. ID 12471
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 900	Approximate temperature 55°C

PCR data Exp. ID 12472
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 12473
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 900	Approximate temperature 55°C

PCR data Exp. ID 12474
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 850	Approximate temperature 55°C

PCR data Exp. ID 12475
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Physalis TA1367: 900	Approximate temperature 55°C

PCR data Exp. ID 12476
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 850	Approximate temperature 55°C

PCR data Exp. ID 12477
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: Multiple	Approximate temperature 55°C

PCR data Exp. ID 12478
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 850	Approximate temperature 55°C

PCR data Exp. ID 12479
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 500	Approximate temperature 55°C

PCR data Exp. ID 32711
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 900	Approximate temperature 55°C

PCR data Exp. ID 32712
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 32713
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 900	Approximate temperature 55°C

PCR data Exp. ID 32714
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 850	Approximate temperature 55°C

PCR data Exp. ID 10060
Forward primer (5'-3') AGGCCCTTGTACTCAGTGCCTCTC	Digested band sizes (using DraI) Solanum lycopersicum LA925: 850 Solanum pennellii LA716: 750	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCATGGCGGTTTCAGTCCATCC	Enzymes All possible enzymes for pennellii and and lycopersicum: AluI, DraI All possible enzymes for lycopersicum and pimpinellifolium: amplicon difference
Accessions and product sizes Solanum lycopersicum LA925: 850 Solanum pennellii LA716: 850	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U218348

Overgo hybridization and physical mapping

C2_At1g19140 was used as an overgo probe on plate 13 [well F8]

Plausible BAC Matches: P002M15, P312N21, P201H14, P110D23, P110P10, P008J07, P333K04, P247L14, P292K09, P060E05

Overgo Sequences

A sequence

CTGCCACCGGAAATATTCCTGATC

B sequence

ACCGGAATAGGGTTCTGATCAGGA

AB sequence

CTGCCACCGGAAATATTCCTGATCAGAACC

Marker sequence

ATGTATCGATCGGCGGCAAAGAGGTTACTACCGGCGTTTTACCGGCGACG
CCAGGATGCAGTATCATGCATTCGAACCCTAGCAGCAGACTACCCCACTC
GATTCATGACTTCAGCTGCCACCGGAAATATTCCTGATCAGAACCCTATT
CCGGTTAACCCTATTCTTCCTAGCTCTAATCCGACCGACTCTACCGCATC
ATCATCTTGGAAGGAAGAAGAAAGGACACGTTTTCAGGATACTGATGCAA
AATCTAGCTCGAGAACAAAGCGGCCTAAAGCGCATTACAAGGACGAAGAG
GCCCTTGTACTCAGTGCCTCTCTTTCTCATGTGNNNNNATTCGGCTAGGA
TGGACTGAAACCGCCATGATTGCAGGTGCAAGGGATGTCGGAGTGTCACC
TTCCATTGTTGGATCATTTCCTCGGAAAGAAGCTGCACTAGTGGAGNNNN
NTATTTTATGGACGAGTGTCTGGAAAGACTCATTGATATCATTGAATCAA
GGAACGATCTGAATAACTTAATACCTAGTGAGCGGATAGCAAAGCTTGTA
CGAATTCGCTTGGAAATGCAAACCCCTTACATATCAAAATGGCCACAAGC
TCTCAGTATACAGNNNNNGCTCAANNNNNNNNNN

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 130005 plant #3, AB1 chromatogram - [View]
Forward amplicon sequence for S. hirtum 130005 plant #3, plain text
Forward amplicon sequence for S. quitoense SE plant #1, AB1 chromatogram - [View]
Forward amplicon sequence for S. quitoense SE plant #1, plain text

BLASTX result of original unigene sequences against Arabidopsis protein database