Sol Genomics Network

SGN Marker C2_At1g60200

SGN-M3919
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	309095 (SGN) 130754 (CGN)	-	-	-
Lycopersicon Combined	Single	SGN-U228043	-	-	-
Arabidopsis	Single	At1g60200 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38216)
Chromosome 5
Position 7.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39489

Forward primer (5'-3')

TTCTCTTATGAGATAAACTGGGC

Accessions and product sizes

Solanum pennellii TA56

850

Solanum lycopersicum TA209

850

Approximate temperature

55°C

Reverse primer (5'-3')

AGCCTCTCCAGCATCTCAGTTG

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

300

Solanum pennellii TA56

450

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25318)
Chromosome 1
Position 22.21 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10305
Forward primer (5'-3') TTCTCTTATGAGATAAACTGGGC		Mg⁺² concentration 3mM
Reverse primer (5'-3') AGCCTCTCCAGCATCTCAGTTG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 850	Approximate temperature 55°C

PCR data Exp. ID 10306
Forward primer (5'-3') TTCTCTTATGAGATAAACTGGGC		Mg⁺² concentration 3mM
Reverse primer (5'-3') AGCCTCTCCAGCATCTCAGTTG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 850	Approximate temperature 55°C

PCR data Exp. ID 12209
Forward primer (5'-3') TCATGACAGATCCAGCCAGAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCAGAACAAACATTTCAGCTTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 850	Approximate temperature 55°C

PCR data Exp. ID 12210
Forward primer (5'-3') TCATGACAGATCCAGCCAGAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCAGAACAAACATTTCAGCTTC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 850	Approximate temperature 55°C

PCR data Exp. ID 12211
Forward primer (5'-3') TCATGACAGATCCAGCCAGAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCAGAACAAACATTTCAGCTTC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 850	Approximate temperature 55°C

PCR data Exp. ID 12212
Forward primer (5'-3') TCATGACAGATCCAGCCAGAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCAGAACAAACATTTCAGCTTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: Multiple	Approximate temperature 55°C

PCR data Exp. ID 12213
Forward primer (5'-3') TCATGACAGATCCAGCCAGAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCAGAACAAACATTTCAGCTTC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 1800	Approximate temperature 55°C

PCR data Exp. ID 12214
Forward primer (5'-3') TCATGACAGATCCAGCCAGAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCAGAACAAACATTTCAGCTTC	Enzymes
Accessions and product sizes Coffea canephora BP409: 850	Approximate temperature 55°C

PCR data Exp. ID 12728
Forward primer (5'-3') TTCTCTTATGAGATAAACTGGGC		Mg⁺² concentration 3mM
Reverse primer (5'-3') AGCCTCTCCAGCATCTCAGTTG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 900	Approximate temperature 55°C

PCR data Exp. ID 12729
Forward primer (5'-3') TTCTCTTATGAGATAAACTGGGC		Mg⁺² concentration 3mM
Reverse primer (5'-3') AGCCTCTCCAGCATCTCAGTTG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 750	Approximate temperature 55°C

PCR data Exp. ID 12730
Forward primer (5'-3') TTCTCTTATGAGATAAACTGGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCTCCAGCATCTCAGTTG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 700	Approximate temperature 55°C

PCR data Exp. ID 32602
Forward primer (5'-3') TTCTCTTATGAGATAAACTGGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCTCCAGCATCTCAGTTG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 850	Approximate temperature 55°C

PCR data Exp. ID 32807
Forward primer (5'-3') TTCTCTTATGAGATAAACTGGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCTCCAGCATCTCAGTTG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: Multiple	Approximate temperature 55°C

PCR data Exp. ID 32808
Forward primer (5'-3') TTCTCTTATGAGATAAACTGGGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCTCTCCAGCATCTCAGTTG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 850	Approximate temperature 55°C

PCR data Exp. ID 33324
Forward primer (5'-3') TCATGACAGATCCAGCCAGAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCAGAACAAACATTTCAGCTTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: Multiple	Approximate temperature 55°C

PCR data Exp. ID 10307
Forward primer (5'-3') TTCTCTTATGAGATAAACTGGGC	Digested band sizes (using HaeIII) Solanum lycopersicum LA925: 300 Solanum pennellii LA716: 450	Mg⁺² concentration 3mM
Reverse primer (5'-3') AGCCTCTCCAGCATCTCAGTTG	Enzymes All possible enzymes for pennellii and and lycopersicum: HaeIII
Accessions and product sizes Solanum pennellii LA716: 850 Solanum lycopersicum LA925: 850	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U228043
SGN-U272249

Overgo hybridization and physical mapping

C2_At1g60200 was used as an overgo probe on plate 12 [well E12]

Plausible BAC Matches: P156O15, P224M24, P215K16, P261K11

Non-Plausible BAC matches

P018E12, P017C23, P316H03

Overgo Sequences

A sequence

GACGAACATATGGTCCAACCTTCC

B sequence

GCGATGCTACAGAGATGGAAGGTT

AB sequence

GACGAACATATGGTCCAACCTTCCATCTCT

Marker sequence

NNNNNNNNNNNNNNNNNNNNGCCCCTACAAAAAGGTTAGAATTTGGCCTC
TCAGGGTCAGGAAAAAGAGCTGCTGTCCCTTCTTTCTTCAATGCGGATGA
GGATGAGGATACTCAAAAAGAAAAGAAAATGAGGCCATTGGTTCCAATTG
ACTACTCAGCTGACGAACATATGGTCCAACCTTCCATCTCTGTAGCATCG
CCGACTATGGCTGCAGAATTTGCAAAGCGAATTTCAAATGTCAATGCTAA
AGAAGAGAGGCCTGATATAGAGAAGGAGAGACACAGAAGAACTCATGACA
GATCCAGCCAGAGGGATCGGGACAGGCATGACGAGGAGACTAACCGAACC
AGGGATGACGGTAGAAACCTTGATCATGGCAGAGTTCGGGAAACTAGACC
TGATAAGGTTAAGACACCTGATAATCAGAAGCTTTTAGATGCAAAGCAAT
TGATTGACATGATTCCAAAGACCAAAGATGAGTTGTTCTCTTATGAGATA
AACTGGGCTACTTATGACAAGNNNNNAATGCATTACATGAAAGGATGAGA
CCGTGGATCAGTAAGAAGATCACTGATTTCCTTGGTGAGGAGGAGCCGAC
GCTGGTAGACTACATCGTCTCCAGCACTCAAGAACATGTCAAGGCAACTG
AGATGCTGGAGAGGCTCCAAAGTATATTAGATGAAGAAGCTGAAATGTTT
GTTCTGAAGATGTGGAGGATGCTTATATTTGAAATCAAGAAAGTTGAGAC
AGGTCTGGCTTTAAGGCCCAAATCCTAA

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

BLASTX result of original unigene sequences against Arabidopsis protein database

Related Markers

Related Genotyped Markers: These markers have been genotyped and share a name with this marker

Genomic location of C2_At1g60200

%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D3919 marker 3919