Sol Genomics Network

SGN Marker C2_At5g27620

SGN-M4642
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	311770 (SGN) 127841 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U198357	-	-	-
Lycopersicon Combined	Single	SGN-U228276	-	-	-
Solanum tuberosum	Single	SGN-U245969	-	-	-
Arabidopsis	Single	At5g27620 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38838)
Chromosome 1
Position 115.00 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39955

Forward primer (5'-3')

ATCTACAATGGTCCGTGATGGAAC

Accessions and product sizes

Solanum lycopersicum TA209

350

Solanum pennellii TA56

300

Approximate temperature

55°C

Reverse primer (5'-3')

TTCCTCTGCCTTGCAAGCTGC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

350

Solanum pennellii TA56

300

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27322)
Chromosome 5
Position 9.77 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11843
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 300	Approximate temperature 55°C

PCR data Exp. ID 11844
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 350	Approximate temperature 55°C

PCR data Exp. ID 11845
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 350	Approximate temperature 55°C

PCR data Exp. ID 13826
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 250	Approximate temperature 55°C

PCR data Exp. ID 13827
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 350	Approximate temperature 55°C

PCR data Exp. ID 13828
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 250	Approximate temperature 55°C

PCR data Exp. ID 13829
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 250	Approximate temperature 55°C

PCR data Exp. ID 13830
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 250	Approximate temperature 55°C

PCR data Exp. ID 13831
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 250	Approximate temperature 55°C

PCR data Exp. ID 13832
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 300	Approximate temperature 55°C

PCR data Exp. ID 13833
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Physalis TA1367: 350	Approximate temperature 55°C

PCR data Exp. ID 13834
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 350	Approximate temperature 55°C

PCR data Exp. ID 13835
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 250	Approximate temperature 55°C

PCR data Exp. ID 13836
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 250	Approximate temperature 55°C

PCR data Exp. ID 13837
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Coffea canephora BP409: 300	Approximate temperature 55°C

PCR data Exp. ID 33249
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 250	Approximate temperature 55°C

PCR data Exp. ID 33250
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 250	Approximate temperature 55°C

PCR data Exp. ID 33251
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 250	Approximate temperature 55°C

PCR data Exp. ID 33252
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 250	Approximate temperature 55°C

PCR data Exp. ID 11846
Forward primer (5'-3') ATCTACAATGGTCCGTGATGGAAC	Digested band sizes (using amplicon difference) Solanum lycopersicum LA925: 350 Solanum pennellii LA716: 300	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCCTCTGCCTTGCAAGCTGC	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference
Accessions and product sizes Solanum pennellii LA716: 300 Solanum lycopersicum LA925: 350	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U272198

Overgo hybridization and physical mapping

C2_At5g27620 was used as an overgo probe on plate 13 [well A9]

Plausible BAC Matches: None

Overgo Sequences

A sequence

GGGTCGTTCTCATATGCTGAAAGC

B sequence

CTTTGGCGTCATTTTGGCTTTCAG

AB sequence

GGGTCGTTCTCATATGCTGAAAGCCAAAAT

Marker sequence

ATGGCTGATTTTGTGACATCTACTCATAGAACCAAGTGGATTTTTACTCC
CCAAGATATTNNNNNAAACATAAGTATAAAGTTGCTAATCACAGAGCGAA
ACAAGCACTGGAGAAGNNNNNTATGGAACAACGCGAATGGAAGTTGATAT
TGATGGGTCGTTCTCATATGCTGAAAGCCAAAATGACGCCAAAGATAATG
NNNNNCTGAAAAGCGTCCTAAACCACTCAAGGTTGAAGAAGAACAACTTC
TAAAGGCTTTCTACGAGTTCAAAATTCAAGACGTCTGTGATGCCTTTAAG
TTCCCACGTAAGATTCAGNNNNNGCGACAGCTCTCATTTATTTTAAGAGG
GTTTATCTACATGGTCCGTGATGGAACATCACCCCAAAGACATTATGNNN
NNTTAACCTGCATATATGCAGCTTGCAAGGCAGAGGAAAACCATGTATCA
GCTGAGGGACTTGGGNAAGGGGATTGGACAGGATCATCATGTAATCCTNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

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]