Sol Genomics Network

SGN Marker C2_At5g20890

SGN-M4692
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	301331 (SGN) 120522 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197719	-	-	-
Lycopersicon Combined	Single	SGN-U221520	-	-	-
Solanum tuberosum	Single	SGN-U248914	-	-	-
Arabidopsis	Single	At5g20890 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38810)
Chromosome 11
Position 76.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39942

Forward primer (5'-3')

AACTTATCGAGGAGATCATGATTGG

Accessions and product sizes

Solanum lycopersicum TA209

1400

Solanum pennellii TA56

1400

Approximate temperature

55°C

Reverse primer (5'-3')

AGCTGAGCAATCAGCTCAGCACTGTC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

1350

Solanum pennellii TA56

1400

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27247)
Chromosome 5
Position 7.09 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11778
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 350+750	Approximate temperature 55°C

PCR data Exp. ID 11779
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 750	Approximate temperature 55°C

PCR data Exp. ID 11780
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 750	Approximate temperature 55°C

PCR data Exp. ID 13774
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 800	Approximate temperature 55°C

PCR data Exp. ID 13775
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 800	Approximate temperature 55°C

PCR data Exp. ID 13776
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 800	Approximate temperature 55°C

PCR data Exp. ID 13777
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 700	Approximate temperature 55°C

PCR data Exp. ID 13778
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 700	Approximate temperature 55°C

PCR data Exp. ID 13779
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 700	Approximate temperature 55°C

PCR data Exp. ID 13780
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 800	Approximate temperature 55°C

PCR data Exp. ID 13781
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 800	Approximate temperature 55°C

PCR data Exp. ID 33228
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 800	Approximate temperature 55°C

PCR data Exp. ID 33229
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 700	Approximate temperature 55°C

PCR data Exp. ID 33230
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 700	Approximate temperature 55°C

PCR data Exp. ID 33231
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 700	Approximate temperature 55°C

PCR data Exp. ID 11781
Forward primer (5'-3') AACTTATCGAGGAGATCATGATTGG	Digested band sizes (using HinfI) Solanum pennellii LA716: 650 Solanum lycopersicum LA925: 350	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCTGAGCAATCAGCTCAGCACTGTC	Enzymes All possible enzymes for pennellii and and lycopersicum: DraI, TaqI, HinfI
Accessions and product sizes Solanum pennellii LA716: 350+750 Solanum lycopersicum LA925: 750	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U221520
SGN-U272615

Overgo hybridization and physical mapping

C2_At5g20890 was used as an overgo probe on plate 13 [well G10]

Plausible BAC Matches: None

Overgo Sequences

A sequence

TATGGTGCACGTGTTCGAGTTGAC

B sequence

CAACCTTGGCCATTGAGTCAACTC

AB sequence

TATGGTGCACGTGTTCGAGTTGACTCAATG

Marker sequence

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTAGATGAAGGNNNN
NGTTTATTTTGGACAAAAAGATTGGGGTTGGCCAACCAAAACGCATAGAA
AATGCTAAGATTTTGGTGGCAAATACTGCTATGGATACAGATAAAGTGAA
GATATATGGTGCACGTGTTCGAGTTGACTCAATGGCCAAGGTTGCTGATC
TAGAAGCAGCTGAAAAGGAAAAAATGAGAGAGAAGGTGCAAAAGATCATT
AGTCATGGAATAAATTGCTTTGTTAACCGACAGCTGATCTACAATTTCCC
AGAGGAACTATTTGCTGATGCTGGGATACTTGCAATAGAGCATGCTGACT
TTGATGGTATTGAGCGGTTGGGCTTAGTTACTGGGGGAGAAATTGCATCA
ACCTTTGATAACCCAGAGTCTGTCAAACTTGGCCACTGCAAACTTATCGA
GGAGATCATGATTGGCGAAGATAAGCTGATCCACTTCTCTGGGGTTGCAA
TGGGACAGGCATGTACAATTGTTCTGAGAGGTGCAAGNNNNNCCCTCATG
TACTGGATGAAGCTGAAAGATCTCTGCACGATGCATTGTGTGTACTATCT
CAGACGGTAAATGACAGCAGGGTTCTACTTGGAGGTGGATGGCCCGAGAT
GGTGATGGCTAAGGCGGTTGATGAACTAGCTAAGAAGACTCCAGGTAAAA
GGTCTCATGCAATTGAGGCTTTCACCCGTGCACTTCTGGCAATTCCAACC
ACCATTGCCGACAATGCTGGGTTAGACAGTGCTGAGCTGATTGCTCAGCT
TCGTGCTGAACACCACAAGGACGAAAGTAATGCAGGAATTGATGTCATCT
CTGGATCTNNNNNGTCGGAGATATGTCAGAGCTAGGAATATCCGAATCAT
TCAAAGTCAAACAGGCAGTATTGCTCTCTGCCACTGAGGCTGCTGAGATG
ATCCTAAGGGTTGACGAGATCATCACTTGCGCCCCACGGAGGAGGGAGGG
AATGTAA

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