Sol Genomics Network

SGN Marker C2_At2g15890

SGN-M4650
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	304671 (SGN) 121575 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197114	-	-	-
Lycopersicon Combined	Single	SGN-U217919	-	-	-
Solanum tuberosum	Single	SGN-U245682	-	-	-
Arabidopsis	Single	At2g15890 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49227)
Chromosome 1
Position 87.80 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47158)
Chromosome 1
Position 139.59 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tomato-EXPEN 2000
Map version 52 (location: 38303)
Chromosome 1
Position 150.00 cM
Confidence CF(LOD3)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39566

Forward primer (5'-3')

AGCCTATTTTGAACTCAAAGATCTTG

Accessions and product sizes

Solanum lycopersicum TA209

850

Solanum pennellii TA56

850

Approximate temperature

55°C

Reverse primer (5'-3')

TTCTCTCGACTTTGGCAATCCATC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

650

Solanum pennellii TA56

600

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25621)
Chromosome 2
Position 6.93 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10567
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 850	Approximate temperature 55°C

PCR data Exp. ID 10568
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 850	Approximate temperature 55°C

PCR data Exp. ID 10569
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 850	Approximate temperature 55°C

PCR data Exp. ID 12919
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 850	Approximate temperature 55°C

PCR data Exp. ID 12920
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 850	Approximate temperature 55°C

PCR data Exp. ID 12921
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 750	Approximate temperature 55°C

PCR data Exp. ID 12922
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 850	Approximate temperature 55°C

PCR data Exp. ID 12923
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 600	Approximate temperature 55°C

PCR data Exp. ID 12924
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 600	Approximate temperature 55°C

PCR data Exp. ID 12925
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 600	Approximate temperature 55°C

PCR data Exp. ID 12926
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 600	Approximate temperature 55°C

PCR data Exp. ID 12927
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Coffea canephora BP409: 580	Approximate temperature 55°C

PCR data Exp. ID 32900
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 850	Approximate temperature 55°C

PCR data Exp. ID 10570
Forward primer (5'-3') AGCCTATTTTGAACTCAAAGATCTTG	Digested band sizes (using TaqI) Solanum pennellii LA716: 600 Solanum lycopersicum LA925: 650	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTCTCGACTTTGGCAATCCATC	Enzymes All possible enzymes for pennellii and and lycopersicum: TaqI, HaeIII, DpnII
Accessions and product sizes Solanum pennellii LA716: 850 Solanum lycopersicum LA925: 850	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U217919
SGN-U271297

Overgo hybridization and physical mapping

C2_At2g15890 was used as an overgo probe on plate 13 [well B10]

Plausible BAC Matches: P244N11, P110L24, P322G03, P160P17, P116G17, P079G13, P003H02, P253N12, P248L05, P273G13, P214N18, P008L19

Overgo Sequences

A sequence

GAGGACTGTGTCCTATACCAGATG

B sequence

CTCGACTTTGGCAATCCATCTGGT

AB sequence

GAGGACTGTGTCCTATACCAGATGGATTGC

Marker sequence

ATGTTACAATCAATGGCTCTCAATTCCTTATCTTCTACTTCTCTCGTTGG
AGTTAATAATGAGCTTCATTCTTCAAGATTTCAAGTAAATTCGTCGACAA
TTCGTTGTTGTTCAAGAAGTCATGCTTACATACCAAAGCTCGAGCCTTTT
AGCAGAACCAAGTTTGATAGAGTTTTTAAAGATCCCCCTTTGATCGAAAA
ATCTGAAAATGAACTTGCCGNNNNNATTATTGTTCTGTTCTAGAAGGTGA
TGATTCTTATAGCTGCTGGCAAGCCTATTTTGAACTCAAAGATCTTGAAN
NNNNAAAGAAGCACCTAAGGAGGAGGTAGAGAGGCTAATACTTCAAGCAG
GGGGAGTGAAAACTCTCATTGGCTGCTTACATGGAGTTTCAGACATGCAC
AAAGCCAAAAAGGAAAGCAAAGAATCAGCCAAACCTGTCAATCTTGATGC
ACAACGGGCAGGAGGACTGTGTCCTATACCAGATGGATTGCCAAAGTCGA
GAGAAGAGCTCGAGGAAGAGGAGAAAGCTAGAATGCCAGATTCACCCTAT
ACTAAACTGCTCAGAGCCAAAGGAACACACCCTGTTTGGTACTGA

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