Sol Genomics Network

SGN Marker C2_At4g09010

SGN-M4663
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	300205 (SGN) 122397 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U204785	-	-	-
Lycopersicon Combined	Single	SGN-U218672	-	-	-
Solanum tuberosum	Single	SGN-U258329	-	-	-
Arabidopsis	Single	At4g09010 on TAIR	-	-	-

Mapped locations

Map: Pepper-COSII
Map version 58 (location: 41466)
Chromosome 4
Position 106.30 cM
Confidence F(LOD3)
Protocol dCAPS

Pepper-COSII

PCR data Exp. ID 43442

Forward primer (5'-3')

TAAGGGGCTTGATGCTGCTTTG

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

GTGTATTCTTTATTAATGAAGCTTGCT

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38623)
Chromosome 4
Position 82.50 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39809

Forward primer (5'-3')

TAAGGGGCTTGATGCTGCTTTG

Accessions and product sizes

Solanum pennellii TA56

570

Solanum lycopersicum TA209

570

Approximate temperature

55°C

Reverse primer (5'-3')

TAAAGGTCGATTTGACTGCACTTTG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

300+340

Solanum lycopersicum TA209

570

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26637)
Chromosome 4
Position 5.78 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11358
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 570	Approximate temperature 55°C

PCR data Exp. ID 11359
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 570	Approximate temperature 55°C

PCR data Exp. ID 11360
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 570	Approximate temperature 55°C

PCR data Exp. ID 13372
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 580	Approximate temperature 55°C

PCR data Exp. ID 13373
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Solanum melongena TA2986: 580	Approximate temperature 55°C

PCR data Exp. ID 13374
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 580	Approximate temperature 55°C

PCR data Exp. ID 13375
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 580	Approximate temperature 55°C

PCR data Exp. ID 13376
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 750	Approximate temperature 55°C

PCR data Exp. ID 13377
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 750	Approximate temperature 55°C

PCR data Exp. ID 13378
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Physalis TA1367: 600	Approximate temperature 55°C

PCR data Exp. ID 13379
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 700	Approximate temperature 55°C

PCR data Exp. ID 13380
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 750	Approximate temperature 55°C

PCR data Exp. ID 13381
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 750	Approximate temperature 55°C

PCR data Exp. ID 13382
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 700	Approximate temperature 55°C

PCR data Exp. ID 33080
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 580	Approximate temperature 55°C

PCR data Exp. ID 33081
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 750	Approximate temperature 55°C

PCR data Exp. ID 33082
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 750	Approximate temperature 55°C

PCR data Exp. ID 11361
Forward primer (5'-3') TAAGGGGCTTGATGCTGCTTTG	Digested band sizes (using RsaI) Solanum lycopersicum LA925: 570 Solanum pennellii LA716: 300+340	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAAAGGTCGATTTGACTGCACTTTG	Enzymes All possible enzymes for pennellii and and lycopersicum: AluI, MspI,RsaI,DraI,TaqI,RV,HinfI,DpnII,KpnI
Accessions and product sizes Solanum lycopersicum LA925: 570 Solanum pennellii LA716: 570	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U218672

Overgo hybridization and physical mapping

C2_At4g09010 was used as an overgo probe on plate 13 [well D5]

Plausible BAC Matches: None

Overgo Sequences

A sequence

CATTCTTGGGTCCTGATCAAGCTG

B sequence

AGTAGGGCCTCTGTTGCAGCTTGA

AB sequence

CATTCTTGGGTCCTGATCAAGCTGCAACAG

Marker sequence

ATGGTCTCTTTTGCTTCAACACTTCCCTCTTTGGTTTCATTCATTCCTTC
ACCATCTTCCATTACCAATGCCTCAAGAAACCCTCCTCAACCTNNNNNGG
TATGATTTGTTGTAAGTTTAGATCAGAGCTTAATAATGAAGATCGCTTTC
ATAGACGTGATATTCTTCAATCTGTTGGAGCAGCAGTAGGCNNNNNATGG
ACTTGATAGCAAGATCGAGTGCATTCATCGAAGTAGCTAATGCTGCTGAT
TTAATACAACGCAGACAGCGGTCAGATTTTCAATNNNNNCAAAGATCAAA
CTGACTCTTTATGATGCTATAAAGGCAAATCCGGATATAATTCCATCCTT
ACTAACTTTAGCACTTAACGATGCCATAACATATGATAAGNNNNNGCAAC
AAAAACCGGGGGTCCCAATGGATCCATACGTTTCAGNNNNNCTCAGAGAT
CAGCAGACCAGAAAATAAGGGGCTTGATGCTGCTTTGAATTTGTTGGAGG
AATCAAAGAAGGTTATTGATTTAGATTCCAAAGGTGGACCAATCTCATAT
GCAGATCTCATCCAATTTGCTGNNNNNCACAAAGTGCAGTCAAATCGACC
TTTATCGCTTCTGCAATTAGCAAATGTGGTGGTAATGTAGAGAAGGGGAC
TTTGTTGTACTCTGCATATGGTTCTAATGGACAGNNNNNTGGGGCCAATT
TGATAGGATATTCGGGAGGTCAGATGCCCAGGAGCCTGATCCAGAGGGAA
GGGTGCCTCAGTGGGATAAAGCAAGTGTGCAGGAAATGAAAGACAAGTTC
AAAGCTGTTGGCTTGGGCCCTCGTCAGNNNNNTTAGCAGTAATGTCTTCA
TTCTTGGGTCCTGATCAAGCTGCAACAGAGGCCCTACTCGCCAGTGATCC
AGAAGTTCTTCCTTGGATTCAGAAGTACCAAAGGAGCAGGGAAACAGTGT
CTCGAACTGATTATGAGNNNNNGTTGACTTGATTACTACTGTTACAAAAT
TAAGCAGTTTGGGACAAGTAATAAACTATGAGGCATATACTTATCCTCCC
AGGAAAATTGATGTTACCAAACTCAAGTTGTAG

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