Sol Genomics Network

SGN Marker C2_At3g10920

SGN-M4655
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	301995 (SGN) 124261 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197943	-	-	-
Lycopersicon Combined	Single	SGN-U215318	-	-	-
Solanum tuberosum	Single	SGN-U245568	-	-	-
Arabidopsis	Single	At3g10920 on TAIR	-	-	-

Mapped locations

Map: Pepper-COSII
Map version 58 (location: 41408)
Chromosome 5
Position 70.90 cM
Confidence F(LOD3)
Protocol dCAPS

Pepper-COSII

PCR data Exp. ID 43384

Forward primer (5'-3')

TGGCTTGGTGTGGACAAAGAGC

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

GATGAGCACTCATGAAAGTTGGACTTA

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38450)
Chromosome 6
Position 13.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39691

Forward primer (5'-3')

TGGCTTGGTGTGGACAAAGAGC

Accessions and product sizes

Solanum lycopersicum TA209

650

Solanum pennellii TA56

650

Approximate temperature

55°C

Reverse primer (5'-3')

TGCAAGTAGTATGCGTGTTCCC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

650

Solanum lycopersicum TA209

300

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26123)
Chromosome 3
Position 3.42 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11013
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 650	Approximate temperature 55°C

PCR data Exp. ID 11014
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 650	Approximate temperature 55°C

PCR data Exp. ID 11015
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 650	Approximate temperature 55°C

PCR data Exp. ID 13182
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 620	Approximate temperature 55°C

PCR data Exp. ID 13183
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 150	Approximate temperature 55°C

PCR data Exp. ID 13184
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 620	Approximate temperature 55°C

PCR data Exp. ID 13185
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 620	Approximate temperature 55°C

PCR data Exp. ID 13186
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 620+800	Approximate temperature 55°C

PCR data Exp. ID 13187
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Physalis TA1367: 620	Approximate temperature 55°C

PCR data Exp. ID 13188
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 620+1500	Approximate temperature 55°C

PCR data Exp. ID 13189
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 620+1500	Approximate temperature 55°C

PCR data Exp. ID 13190
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 620	Approximate temperature 55°C

PCR data Exp. ID 32632
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 700	Approximate temperature 55°C

PCR data Exp. ID 33010
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 700	Approximate temperature 55°C

PCR data Exp. ID 33011
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 700	Approximate temperature 55°C

PCR data Exp. ID 33012
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 620	Approximate temperature 55°C

PCR data Exp. ID 33013
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 620	Approximate temperature 55°C

PCR data Exp. ID 11016
Forward primer (5'-3') TGGCTTGGTGTGGACAAAGAGC	Digested band sizes (using HinfI) Solanum pennellii LA716: 650 Solanum lycopersicum LA925: 300	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAGTAGTATGCGTGTTCCC	Enzymes All possible enzymes for pennellii and and lycopersicum: HinfI
Accessions and product sizes Solanum pennellii LA716: 650 Solanum lycopersicum LA925: 650	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U215318
SGN-U270606

Overgo hybridization and physical mapping

C2_At3g10920 was used as an overgo probe on plate 13 [well C5]

Plausible BAC Matches: None

Overgo Sequences

A sequence

CTTGAACAGCTCCATGATGCCATC

B sequence

GAGCATCTCCTTTGGAGATGGCAT

AB sequence

CTTGAACAGCTCCATGATGCCATCTCCAAA

Marker sequence

ATGGCTCTTCGGACTTTAGTGAGCAGACGGACCTTAGCGGCAGGGCTAGG
GTTCCGCCAACAACTTCGTGGCGTTCAAACCTTTTCGCTCCCCGATCTCC
CATACGACTATGGCGCCCTGGAGCCGGCAATTAGCGGTGATATAATGCAG
CTCCACCACCAGAAGCATCATCAGACTTACATCACTAATTACAATAAGGC
CCTTGAACAGCTCCATGATGCCATCTCCAAAGGAGATGCTCCTGCCGTCG
CCAAATTGCACAGTGCCCTCAAATTTAACGGCGGAGNNNNNGTCATATTA
ATCACTCAATTTTCTGGAATAACCTTGCCCCTGTCAGCNNNNNGAAGGTG
GTGGGGAGCCTCCAAAGGGTTCTCTTGGCTGGGCTATTGACACTAACTTT
GGTTCACTGGAAGCTTTAGTAAAAAAGATGAACGCAGAAGGTGCTGCTTT
ACAGGGCTCTGGCTGGGTGNNNNNTGGCTTGGTGTGGACAAAGAGCTTAA
GCGCCTGGTGGTTGAAACCACTGCAAATCAGNNNNNGACCCTTTGGTTTC
TAAAGGAGCAAATTTGGTACCTCTTCTGGGTATAGACGTTTGGGAACACG
CATACTACTTGCAGNNNNNTACAAAAATGTAAGACCAGATTACCTGAAGA
ATATATGGAAAGTTATCAACTGGAAATATGCCAATGATGTTTACGAAAAT
GAGTGCCCCTGA

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_At3g10920

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