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SGN Marker C2_At3g44890

SGN-M4657
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	310069 (SGN) 126194 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U202325	-	-	-
Lycopersicon Combined	Single	SGN-U222824	-	-	-
Arabidopsis	Single	At3g44890 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49251)
Chromosome 11
Position 49.27 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47187)
Chromosome 11
Position 78.80 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Pepper-COSII
Map version 58 (location: 41434)
Chromosome 11
Position 102.70 cM
Confidence I(LOD2)
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43410

Forward primer (5'-3')

ATTGGGCAAAGCTCAAATTGTGAC

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

AGCCTCAATTTTCTCGTCTTCCATC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38530)
Chromosome 11
Position 62.00 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39749

Forward primer (5'-3')

ATTGGGCAAAGCTCAAATTGTGAC

Accessions and product sizes

Solanum pennellii TA56

1650

Solanum lycopersicum TA209

1650

Approximate temperature

55°C

Reverse primer (5'-3')

AGCCTCAATTTTCTCGTCTTCCATC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

400+450+800

Solanum pennellii TA56

750

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26358)
Chromosome 3
Position 16.40 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11183
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1650	Approximate temperature 55°C

PCR data Exp. ID 11184
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1650	Approximate temperature 55°C

PCR data Exp. ID 11185
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1650	Approximate temperature 55°C

PCR data Exp. ID 13282
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1200	Approximate temperature 55°C

PCR data Exp. ID 13283
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1500	Approximate temperature 55°C

PCR data Exp. ID 13284
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1400	Approximate temperature 55°C

PCR data Exp. ID 13285
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1400	Approximate temperature 55°C

PCR data Exp. ID 13286
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Physalis TA1367: 1450	Approximate temperature 55°C

PCR data Exp. ID 13287
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13288
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Coffea canephora BP409: 1300	Approximate temperature 55°C

PCR data Exp. ID 33046
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1500	Approximate temperature 55°C

PCR data Exp. ID 33047
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1400	Approximate temperature 55°C

PCR data Exp. ID 33048
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1400	Approximate temperature 55°C

PCR data Exp. ID 11186
Forward primer (5'-3') ATTGGGCAAAGCTCAAATTGTGAC	Digested band sizes (using HinfI) Solanum pennellii LA716: 750 Solanum lycopersicum LA925: 800+450+400	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCAATTTTCTCGTCTTCCATC	Enzymes All possible enzymes for pennellii and and lycopersicum: RsaI, DraI, HinfI All possible enzymes for lycopersicum and pimpinellifolium: HinfI
Accessions and product sizes Solanum lycopersicum LA925: 1650 Solanum pennellii LA716: 1650	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U222824

Overgo hybridization and physical mapping

C2_At3g44890 was used as an overgo probe on plate 13 [well C9]

Plausible BAC Matches: P176A22, P335E08, P103A03, P163F21

Overgo Sequences

A sequence

ATTGGAGCCTTCAAGGTGAAGCGT

B sequence

TTCCTTTCCCACCCTTACGCTTCA

AB sequence

ATTGGAGCCTTCAAGGTGAAGCGTAAGGGT

Marker sequence

ATGGCGTCATGGGGTTCATCTTCTTGTCTCCAAAATTACAGCTTAACCAA
AAACCCATTTTCCGAAACAGTGAAATTTTCAGAAAGAACTTCAATTTTAA
CAATTGTTGCTCAGAAAAAAGCCAAGAAAGTTCGAAAGNNNNNATAATAC
TGAAAGAGGATATTTCACAGTTGGGTAAAAAGGGAGACCTTTTGGATGTT
AAAGCTGGATTCTTTAGGAATTATTTGCTACCATTGGGCAAAGCTCAAAT
TGTGACAGCTGCACTTATCAANNNNNGGAAATGAAGATGGAAGACGAGAA
AATTGAGGCTGAAAAACAACGGNNNNNGTGAAAGATGAGGCACAACAGCT
TGCTCGAATTTTTGAAACTATTGGAGCCTTCAAGGTGAAGCGTAAGGGTG
GGAAAGGAAAGCAAATATTTGGAAGNNNNNTGTCACTGCTCAGGATCTCG
TTGATATTATAAAAGCACAGATACAGAGNNNNNGGACGTGGACAAGAAAA
TTGTCAATCTGCCTGAGATTCGAGAAACCGGAGAATATGTTGCCGAATTG
AAGCTGCATCCAGAAGTTACAGCTAGAGTAAGGTTGACAGTGTATGCCAA
TTGANNNNN

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