Sol Genomics Network

SGN Marker C2_At3g52220

SGN-M4648
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	312142 (SGN) 126998 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U202666	-	-	-
Lycopersicon Combined	Multiple	SGN-U218204	-	-	-
Solanum tuberosum	Single	SGN-U245879	-	-	-
Arabidopsis	Single	At3g52220 on TAIR	-	-	-

Mapped locations

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46693)
Chromosome 5
Position 72.70 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Tomato-EXPEN 2000
Map version 52 (location: 38554)
Chromosome 11
Position 10.00 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39762

Forward primer (5'-3')

TGCTCGGGTGGATGGTCTTGG

Accessions and product sizes

Solanum lycopersicum TA209

250

Solanum pennellii TA56

400

Approximate temperature

55°C

Reverse primer (5'-3')

TGATGGTGAACTTGGTTCTTCCC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

400

Solanum lycopersicum TA209

250

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26428)
Chromosome 3
Position 19.38 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11219
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 400	Approximate temperature 55°C

PCR data Exp. ID 11220
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 250	Approximate temperature 55°C

PCR data Exp. ID 11221
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 250	Approximate temperature 55°C

PCR data Exp. ID 13289
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 300+500	Approximate temperature 55°C

PCR data Exp. ID 13290
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 250	Approximate temperature 55°C

PCR data Exp. ID 13291
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 350	Approximate temperature 55°C

PCR data Exp. ID 13292
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 350	Approximate temperature 55°C

PCR data Exp. ID 13293
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 350	Approximate temperature 55°C

PCR data Exp. ID 13294
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 350	Approximate temperature 55°C

PCR data Exp. ID 13295
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 400	Approximate temperature 55°C

PCR data Exp. ID 13296
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Physalis TA1367: 400	Approximate temperature 55°C

PCR data Exp. ID 13297
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 420	Approximate temperature 55°C

PCR data Exp. ID 13298
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 400	Approximate temperature 55°C

PCR data Exp. ID 13299
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 400	Approximate temperature 55°C

PCR data Exp. ID 13300
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 420	Approximate temperature 55°C

PCR data Exp. ID 33049
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 350	Approximate temperature 55°C

PCR data Exp. ID 33050
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 350	Approximate temperature 55°C

PCR data Exp. ID 33051
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 350	Approximate temperature 55°C

PCR data Exp. ID 11222
Forward primer (5'-3') TGCTCGGGTGGATGGTCTTGG	Digested band sizes (using amplicon difference) Solanum pennellii LA716: 400 Solanum lycopersicum LA925: 250	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATGGTGAACTTGGTTCTTCCC	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference
Accessions and product sizes Solanum pennellii LA716: 400 Solanum lycopersicum LA925: 250	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U218204

Overgo hybridization and physical mapping

C2_At3g52220 was used as an overgo probe on plate 13 [well B8]

Plausible BAC Matches: None

Overgo Sequences

A sequence

GAAGAGACGAGAAGAGAAGAGACG

B sequence

CCTCTCATCCTTTTCCCGTCTCTT

AB sequence

GAAGAGACGAGAAGAGAAGAGACGGGAAAA

Marker sequence

GTCATTCTGTGTTCTCCGTTTTCAACACCTCAATTTTGAGTTCATTTGTG
AAATTCAAAATCTGAGTTTAGAGAGGAGAAGAAGGGGCAAACGATGTATC
ATCCTACTAGAGGCGGCGTTCGTGGCGGCCGAGATCNNNNNAATTTAGTT
GGGATGATGTGAAGGTTGATAAACATCGAGAAAATTATATTGGCCATAGT
ATCAAAGCAGCAGTTGGGAGATGGCAGAAAGNNNNNGGAAAGATCTTCAT
TGGTACACCCGTGATAAGAAATCCCAGGATAAGGATATGGAGGCAGCAAA
AGAAGAAATACGTAGGATTAAAGAAGAGGAGGAGCAGTCAATGAGGGAGG
CTCTGGGCTTAGCTCCTAAGCGTGCCACACGTCCTCAAGGTACTCGGCTA
GACAAACATGAGTTGTCTGAACTTGTGAAGAGAGGTTCAACTGCAGAAGA
CTTGGGAGCAGGGCATTCTGAAGCTGCTCGGGTGGATGGTCTTGGTTTCT
CAAANNNNNATTGCCCAAGCCTTGGGAAGAACCAAGTTCACCATCAGCTT
TTCCATCTAATCCGATCGATGAGCCTGTAGAAAAGATTAATGCAAGTCTC
CCTGTTGCACCCCTACAGAATGAAGAAGAGTCTGAGGACGAAAGGAGCCA
AAAGAAGAAGAGACGAGAAGAGAAGAGACGGGAAAAGGATGAGAGGAGAG
ATAAGCGACATTTGCATGATACAAATGATAGAAGGAAGCATTCCCGCGAT
TCAGATGACAGGAGGAAACGTTCCCGTGATTCTGACGATAAGAGGAAGCA
CACCCGCGATTCAGATGACAGGAAGAAACACAAGAAAGACAAGGAGAAGA
GAAGAAGACATGATTCTGATTCAGATTAAACTTCAATAAATCCTTTTAGT
TATTGTGTGCTTGCTATCATTTACCTTAACGATTTCATTCTGAATATTTG
TGTTGAATTCAGTTTGTTCTGTTGTATTTAGATGGAAAAAGGTCAGATAT
ACTCTTCAGCTTGTATTTATTAAAAAAAAAA

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_At3g52220

%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D4648 marker 4648