Sol Genomics Network

SGN Marker C2_At5g04910

SGN-M4643
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	310282 (SGN) 125515 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U198454	-	-	-
Lycopersicon Combined	Single	SGN-U242006	-	-	-
Solanum tuberosum	Single	SGN-U258707	-	-	-
Arabidopsis	Single	At5g04910 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38746)
Chromosome 10
Position 33.70 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39905

Forward primer (5'-3')

TCAACTTACCAACAGCTATGCAGTG

Accessions and product sizes

Solanum lycopersicum TA209

850

Solanum pennellii TA56

850

Approximate temperature

55°C

Reverse primer (5'-3')

TGTGGCGGTCAGTTGCAGCTTC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

500

Solanum lycopersicum TA209

200+300

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27031)
Chromosome 5
Position 1.44 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11627
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 850	Approximate temperature 55°C

PCR data Exp. ID 11628
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 850	Approximate temperature 55°C

PCR data Exp. ID 11629
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 850	Approximate temperature 55°C

PCR data Exp. ID 13627
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 850	Approximate temperature 55°C

PCR data Exp. ID 13628
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 450+800	Approximate temperature 55°C

PCR data Exp. ID 13629
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13630
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13631
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13632
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13633
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 200	Approximate temperature 55°C

PCR data Exp. ID 13634
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 150	Approximate temperature 55°C

PCR data Exp. ID 13635
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 150	Approximate temperature 55°C

PCR data Exp. ID 13636
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 200	Approximate temperature 55°C

PCR data Exp. ID 33167
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: Multiple	Approximate temperature 55°C

PCR data Exp. ID 33168
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 33169
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: Multiple	Approximate temperature 55°C

PCR data Exp. ID 33170
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: Multiple	Approximate temperature 55°C

PCR data Exp. ID 11630
Forward primer (5'-3') TCAACTTACCAACAGCTATGCAGTG	Digested band sizes (using AluI) Solanum pennellii LA716: 500 Solanum lycopersicum LA925: 200+300	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTGGCGGTCAGTTGCAGCTTC	Enzymes All possible enzymes for pennellii and and lycopersicum: AluI, MspI
Accessions and product sizes Solanum pennellii LA716: 850 Solanum lycopersicum LA925: 850	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U242006

Overgo hybridization and physical mapping

C2_At5g04910 was used as an overgo probe on plate 13 [well A11]

Plausible BAC Matches: P289P07, P043H14, P185D08, P310A08, P333J08, P235M14, P271C14, P163O16, P181D17, P089F02, P137F06, P328M14, P031D08

Overgo Sequences

A sequence

GCGTGCATATCCAGAAGATAACCG

B sequence

TCAGTGCCTGAAGCTTCGGTTATC

AB sequence

GCGTGCATATCCAGAAGATAACCGAAGCTT

Marker sequence

ATGAGGAAGTGGAGCATGGTTGAAGAATTGGAGAAGGTAGAAATTTCGGA
GGAAGGTAATCATGGAGAGAGGGATTCATTGAAAATTGTGGCAGTGCTTC
GAAGATTTGTGGGTGTGCAGCAACGCAGAGCCGAAGCTTATGCGAGGCTG
AAGCGNNNNNAGGATTTGAAGATTATATGGCTTCAGGAGTAGAATCAACT
TACCAACAGCTATGCAGTGAGATCACTGATGAATTTAATGATTGCTCAAA
GCAGNNNNNGTCCTTGAGATGGAGTCTCAGTTTCTAACTGCCCATTGCTT
CCGAGAAGATCTGTCTCTACTTTTGAGATCTGTTCAAAATCAAGAAAAGA
TGAAGCTGCAACTGNNNNNACCGCCACAATACAAGTCTTGAAAAGAGCTG
GCCGCCCCTCGGAGCGTCCAGTGAGTCATGAAAATTGTAGATTTAGTAAG
CCAACTGGACATGAATGCGTGCATATCCAGAAGATAACCGAAGCTTCAGG
CACTGAAGAAGCAGAAGCTGATGCTGAATTTGATAATGCTCTC

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