Sol Genomics Network

SGN Marker C2_At5g19690

SGN-M4102
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	309468 (SGN) 127910 (CGN)	-	-	-
Lycopersicon Combined	Multiple	SGN-U222818	-	-	-
Solanum tuberosum	Single	SGN-U250368	-	-	-
Arabidopsis	Single	At5g19690 on TAIR	-	-	-

Mapped locations

Map: Pepper-COSII
Map version 58 (location: 41521)
Chromosome 9
Position 93.10 cM
Confidence F(LOD3)
Protocol PCR

Pepper-COSII

PCR data Exp. ID 43497

Forward primer (5'-3')

AGAGAGGCTTATGCATGGTTGAGC

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

TAGTTTGATAGCCATAGTCCCACC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38805)
Chromosome 12
Position 27.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39939

Forward primer (5'-3')

AGAGAGGCTTATGCATGGTTGAGC

Accessions and product sizes

Solanum pennellii TA56

1350

Solanum lycopersicum TA209

1350

Approximate temperature

55°C

Reverse primer (5'-3')

TAGTTTGATAGCCATAGTCCCACC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

1100

Solanum lycopersicum TA209

770

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27227)
Chromosome 5
Position 6.66 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11757
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1350	Approximate temperature 55°C

PCR data Exp. ID 11758
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1350	Approximate temperature 55°C

PCR data Exp. ID 11759
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1350	Approximate temperature 55°C

PCR data Exp. ID 13745
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1200	Approximate temperature 55°C

PCR data Exp. ID 13746
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 900	Approximate temperature 55°C

PCR data Exp. ID 13747
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1200	Approximate temperature 55°C

PCR data Exp. ID 13748
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Physalis TA1367: 1200	Approximate temperature 55°C

PCR data Exp. ID 32655
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1000	Approximate temperature 55°C

PCR data Exp. ID 33217
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1000	Approximate temperature 55°C

PCR data Exp. ID 33218
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1000	Approximate temperature 55°C

PCR data Exp. ID 33219
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1200	Approximate temperature 55°C

PCR data Exp. ID 11760
Forward primer (5'-3') AGAGAGGCTTATGCATGGTTGAGC	Digested band sizes (using HaeIII) Solanum lycopersicum LA925: 770 Solanum pennellii LA716: 1100	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGTTTGATAGCCATAGTCCCACC	Enzymes All possible enzymes for pennellii and and lycopersicum: DraI, HaeIII, DpnII
Accessions and product sizes Solanum lycopersicum LA925: 1350 Solanum pennellii LA716: 1350	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U222818

Overgo hybridization and physical mapping

C2_At5g19690 was used as an overgo probe on plate 13 [well H7]

Plausible BAC Matches: None

Overgo Sequences

A sequence

AACAGTTGGTACAGCCATGTCCTC

B sequence

GGCTGCTTTTTCAGGAGAGGACAT

AB sequence

AACAGTTGGTACAGCCATGTCCTCTCCTGA

Marker sequence

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNGGANNNNNAAACAGGCTGATGCAGGGGATA
ATGGTGATGGGGTTACACAGAATGATGTGGTGAAATCTGATAGAAATGAA
GAACTCCCAAAGGAAAAAGCTTCGAGAAAAAAGAAGAAAGAAAAGGAGAA
TGTTGAAAAAGTTCCCATTGCTAATAAAAAAAGTGAGAAGAGGCTTTTGA
TGTTACCCATGGAGGCTTCTTTTGTTGCTATTCTATTACTTGTGTTGCTG
GGTGCCTTTTATGTGNNNNNGTTCATTGTGTCTGGGCAGCTGCGGAAGCT
TACTCAGCTCCTTCTATTGTACTAACATCACAATCGCATGATGGACTTCA
TGTTTTTGATGACTTCAGAGAGGCTTATGCATGGTTGAGCCACAATACTG
ATGTAGATGATAAANNNNNGTGGCATCATGGTGGGACTATGGCTATCAAA
CTACTGCTATGGCCAATCGCACTGTTATAGTTGATAATAACACCTGGAAC
AATACACATATTGCAACAGTTGGTACAGCCATGTCCTCTCCTGAAAAAGC
AGCCTGGGAGATCTTCAACTCTTTGGATGTAAAATATGTTCTTGTTGTCT
TTGGAGNNNNNGTCTTGTTGGGTATCCCAGTGATGATATCAATAAGTTCC
TCTGGATGGTTAGAATCGGTGGGGGTGTCTTCCCTCATATCAAGGAACCT
GATTATCTGNNNNNAGAGATGGCCAGTACCGGATTGACTCTATGGCTACT
CCAACCATGCTGAACTCCCTCATGTACAAACTGTCTTATTACAGNNNNNG
TTTGTGGAGACAGATGGCAAGGGGTACGATAGAGTAAGGCGGACTGAAAT
TGGANNNNNNNNNN

Universal primers for Asterid species

No additional PCR data found.

Other COSII sequence data

BLASTX result of original unigene sequences against Arabidopsis protein database