Sol Genomics Network

SGN Marker C2_At1g74970

SGN-M4675
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	310719 (SGN) 126534 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U203855	-	-	-
Lycopersicon Combined	Single	SGN-U219328	-	-	-
Solanum tuberosum	Single	SGN-U245738	-	-	-
Arabidopsis	Single	At1g74970 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38262)
Chromosome 4
Position 109.70 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39532

Forward primer (5'-3')

TCATCATCAACTATCGTGATGCTAAG

Accessions and product sizes

Solanum pennellii TA56

1000

Solanum lycopersicum TA209

1000

Approximate temperature

55°C

Reverse primer (5'-3')

ACGCTTGCGAGCCTTCTTGAGAC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

550

Solanum lycopersicum TA209

850

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25467)
Chromosome 1
Position 28.16 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10422
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1000	Approximate temperature 55°C

PCR data Exp. ID 10423
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1000	Approximate temperature 55°C

PCR data Exp. ID 10424
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1000	Approximate temperature 55°C

PCR data Exp. ID 12813
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1700	Approximate temperature 55°C

PCR data Exp. ID 12814
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 1500	Approximate temperature 55°C

PCR data Exp. ID 12815
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1500+2500	Approximate temperature 55°C

PCR data Exp. ID 12816
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1500	Approximate temperature 55°C

PCR data Exp. ID 12817
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1500	Approximate temperature 55°C

PCR data Exp. ID 12818
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 2500	Approximate temperature 55°C

PCR data Exp. ID 12819
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 2500	Approximate temperature 55°C

PCR data Exp. ID 12820
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 1500	Approximate temperature 55°C

PCR data Exp. ID 12821
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Physalis TA1367: 1500	Approximate temperature 55°C

PCR data Exp. ID 12822
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 1500	Approximate temperature 55°C

PCR data Exp. ID 12823
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 1600	Approximate temperature 55°C

PCR data Exp. ID 12824
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 1600	Approximate temperature 55°C

PCR data Exp. ID 12825
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 1500	Approximate temperature 55°C

PCR data Exp. ID 12826
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Coffea canephora BP409: 650	Approximate temperature 55°C

PCR data Exp. ID 32849
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1500	Approximate temperature 55°C

PCR data Exp. ID 32850
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1500	Approximate temperature 55°C

PCR data Exp. ID 32851
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 2500	Approximate temperature 55°C

PCR data Exp. ID 32852
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 2500	Approximate temperature 55°C

PCR data Exp. ID 10425
Forward primer (5'-3') TCATCATCAACTATCGTGATGCTAAG	Digested band sizes (using AluI) Solanum pennellii LA716: 550 Solanum lycopersicum LA925: 850	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACGCTTGCGAGCCTTCTTGAGAC	Enzymes All possible enzymes for pennellii and and lycopersicum: AluI, DraI, HaeIII, HinfI; DpnII
Accessions and product sizes Solanum pennellii LA716: 1000 Solanum lycopersicum LA925: 1000	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U219328

Overgo hybridization and physical mapping

C2_At1g74970 was used as an overgo probe on plate 13 [well E9]

Plausible BAC Matches: None

Overgo Sequences

A sequence

CCTTGCTCATTCGAAGCAATTCTC

B sequence

GGAAGCGAGAGAGAAAGAGAATTG

AB sequence

CCTTGCTCATTCGAAGCAATTCTCTTTCTC

Marker sequence

ATGGCGATTTCCGTGGCTTCTCTTGCTTCATCTTTTGCTTCCCTTTCATT
TTCTTCTCAGATTTCTCAAAAACCCTATGCTGTATCCCTTGCTCATTCGA
AGCAATTCTCTTTCTCTCTCGCTTCCAAAATCTCTACGCTTGTAGTGTCA
GCTTCTGTTGCTGAAGCACCGGAGACGGAGGAATTGGAAACCAGAGAGAA
TCTTTTGAAGCTTGTGAAAAGTAGACTTCCTGGAGGTTTCGCTGCACAGC
CTATTTTTGGAACTGGTAGACGTAAAAGTGCTAGTGCTCGTGTTGTTCTT
CAGGAAGGTTCTGGAAAAATCATCATCAACTATCGTGATGCTAAGNNNNN
GAATATCTTCAAGGAAATCCATTATGGATTCAATATGTCAAAACTCCACT
GGCCACTTTAGGATATGAGGCTAGTTATGACATTTTTGTCAAGGTGGAAG
GCGGTGGTCTTTCTGGGCAGGCTCAAGCAATTTCCCTTGGCATTGCTCGT
GCACTCCTAAAGGTTAGTGAGAGCCATAGAAAACCATTGAGGGAGGAGGG
TCTGTTAACTAGAGATGCCAGAGTTGTTGAGCGGAAGAAAGTTGGTCTCA
AGAAGGCTCGCAAGCGTCCACAATTTTCCAAGCGTTGA

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]
Forward amplicon sequence for S. betaceum 6002061 plant #4, AB1 chromatogram - [View]
Forward amplicon sequence for S. betaceum 6002061 plant #4, plain text
Forward amplicon sequence for S. uniloba 6002078 plant #6, AB1 chromatogram - [View]
Forward amplicon sequence for S. uniloba 6002078 plant #6, plain text

BLASTX result of original unigene sequences against Arabidopsis protein database