Sol Genomics Network

SGN Marker C2_At4g03280

SGN-M4652
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	300390 (SGN) 125275 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U196559	-	-	-
Lycopersicon Combined	Multiple	SGN-U212832	-	-	-
Solanum tuberosum	Single	SGN-U245707	-	-	-
Arabidopsis	Single	At4g03280 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49268)
Chromosome 12
Position 0.33 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47205)
Chromosome 12
Position 10.00 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Eggplant-COSII
Map version 63 (location: 42235)
Chromosome 10
Position 46.20 cM
Confidence I(LOD2)
Protocol dCAPS

Eggplant-COSII

PCR data Exp. ID 43801

Forward primer (5'-3')

TGACTCGTTGAAATCAATCATTCTCG

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

ATCTTTGGCAGGGGTACCACCAC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Pepper-COSII
Map version 58 (location: 41463)
Chromosome 9
Position 52.40 cM
Confidence F(LOD3)
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43439

Forward primer (5'-3')

CATACCTGAATTATCAGGTGTGAGA

Accessions and product sizes

Approximate temperature

60°C

Reverse primer (5'-3')

ATCTTTGGCAGGGGTACCACCAC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38616)
Chromosome 12
Position 12.50 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39805

Forward primer (5'-3')

TATGAATTTGCTTTTATTGGGTGC

Accessions and product sizes

Solanum pennellii TA56

650

Solanum lycopersicum TA209

650

Approximate temperature

55°C

Reverse primer (5'-3')

ATCTTTGGCAGGGGTACCACCAC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

550

Solanum lycopersicum TA209

420

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26620)
Chromosome 4
Position 1.44 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11351
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 650	Approximate temperature 55°C

PCR data Exp. ID 11352
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 650	Approximate temperature 55°C

PCR data Exp. ID 11353
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 650	Approximate temperature 55°C

PCR data Exp. ID 13363
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 780	Approximate temperature 55°C

PCR data Exp. ID 13364
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 1200	Approximate temperature 55°C

PCR data Exp. ID 13365
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 2200	Approximate temperature 55°C

PCR data Exp. ID 13366
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1650	Approximate temperature 55°C

PCR data Exp. ID 13367
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Physalis TA1367: 900	Approximate temperature 55°C

PCR data Exp. ID 13368
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 700+800	Approximate temperature 55°C

PCR data Exp. ID 13369
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 750	Approximate temperature 55°C

PCR data Exp. ID 13370
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 800	Approximate temperature 55°C

PCR data Exp. ID 13371
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 1200	Approximate temperature 55°C

PCR data Exp. ID 33079
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1650	Approximate temperature 55°C

PCR data Exp. ID 11354
Forward primer (5'-3') TATGAATTTGCTTTTATTGGGTGC	Digested band sizes (using RsaI) Solanum lycopersicum LA925: 420 Solanum pennellii LA716: 550	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTTGGCAGGGGTACCACCAC	Enzymes All possible enzymes for pennellii and and lycopersicum: RsaI, TaqI, DpnII
Accessions and product sizes Solanum lycopersicum LA925: 650 Solanum pennellii LA716: 650	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U212832

Overgo hybridization and physical mapping

C2_At4g03280 was used as an overgo probe on plate 13 [well B12]

Plausible BAC Matches: P140M01

Overgo Sequences

A sequence

TGGGTGCACTTGCTTTACCAACTG

B sequence

GGTACAAGCATTCCACCAGTTGGT

AB sequence

TGGGTGCACTTGCTTTACCAACTGGTGGAA

Marker sequence

ATGGCTTCTTCCACTCTTTCTCATGTAACTCCTTCTCAGCTATGCTCAAG
CAAAAGTGGTATTTCATCGGTTTCACAAGCCTTGCTTGTGAAGCCGATGA
AGATTAATGGTCATGGAATGGGAAAGGATAATAAGAGGATGAAAGTGAAA
TGTATGGCAGCTAGTATTCCAGCAGATGATAGAGTGCCTGATATGGAGAA
AAGGAATCTTATGAATTTGCTTTTATTGGGTGCACTTGCTTTACCAACTG
GTGGAATGCTTGTACCTTATGCTACTTTCTTTGCACCTCCTGNNNNNGCT
CAGGAGGTGGTAGTGGTGGTACCCCTGCCAAAGATGCTAATGGCAATGAT
GTTGTTGTGACTGAATGGCTCAAAACTCATGCACCTGGAACTCGAACCCT
CACACAAGGACTAANNNNNAGGGAGATCCTACTTACCTTGTTGTGGAGAA
CGATGGAACACTCGCGACCTATGGTATCAATGCTGTGTGCACTCACCTTG
GTTGTGTCGTGCCGTGGAATACTGCTGAGAACAAGTTCATTTGCCCTTGC
CATGGATCTCAATACAACAATCAAGGAAAAGTTGTTAGAGGACCTGCTCC
TTTNNNNNATCCTTGGCATTGGCTCATGCAGACGTTGATGATGGGAAAGT
GGTGTTTGTTCCATGGGTTGAAACAGACTTCAGAACTGGTGATGCTCCAT
GGTGGGCTTA

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_At4g03280

%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D4652 marker 4652