Sol Genomics Network

SGN Marker C2_At3g54770

SGN-M4671
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
Capsicum annuum	Single	SGN-U200197	-	-	-
Lycopersicon Combined	Single	SGN-U223092	-	-	-
Solanum tuberosum	Single	SGN-U253485	-	-	-
Arabidopsis	Single	At3g54770 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49257)
Chromosome 4
Position 43.95 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47193)
Chromosome 4
Position 35.61 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46699)
Chromosome 5
Position 54.70 cM
Confidence CF(LOD3)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Tomato-EXPEN 2000
Map version 52 (location: 38568)
Chromosome 4
Position 55.30 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39767

Forward primer (5'-3')

ACCGGAAGATCCAAAGGCTATGG

Accessions and product sizes

Solanum lycopersicum TA209

250

Solanum pennellii TA56

250

Approximate temperature

50°C

Reverse primer (5'-3')

AGGGACGCGAGATTACAGTTGGC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

110

Solanum pennellii TA56

250

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26471)
Chromosome 3
Position 20.29 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11244
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 250	Approximate temperature 50°C

PCR data Exp. ID 11245
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 250	Approximate temperature 50°C

PCR data Exp. ID 11246
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 250	Approximate temperature 50°C

PCR data Exp. ID 13323
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 350	Approximate temperature 55°C

PCR data Exp. ID 13324
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 350	Approximate temperature 55°C

PCR data Exp. ID 13325
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 700	Approximate temperature 55°C

PCR data Exp. ID 13326
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 700	Approximate temperature 55°C

PCR data Exp. ID 13327
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 400	Approximate temperature 55°C

PCR data Exp. ID 13328
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Physalis TA1367: 280	Approximate temperature 55°C

PCR data Exp. ID 13329
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 480	Approximate temperature 55°C

PCR data Exp. ID 13330
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 480	Approximate temperature 55°C

PCR data Exp. ID 13331
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 480	Approximate temperature 55°C

PCR data Exp. ID 33060
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 480	Approximate temperature 55°C

PCR data Exp. ID 33061
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 350	Approximate temperature 55°C

PCR data Exp. ID 33062
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 700	Approximate temperature 55°C

PCR data Exp. ID 33063
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 700	Approximate temperature 55°C

PCR data Exp. ID 11247
Forward primer (5'-3') ACCGGAAGATCCAAAGGCTATGG	Digested band sizes (using EcoRV) Solanum pennellii LA716: 250 Solanum lycopersicum LA925: 110	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGGACGCGAGATTACAGTTGGC	Enzymes All possible enzymes for pennellii and and lycopersicum: EcoRV
Accessions and product sizes Solanum pennellii LA716: 250 Solanum lycopersicum LA925: 250	Approximate temperature 50°C

Unigene blast matches for primers

SGN-U223092
SGN-U281928

Overgo hybridization and physical mapping

C2_At3g54770 was used as an overgo probe on plate 13 [well E3]

Plausible BAC Matches: P311A10, P312A09, P046M10, P028I05, P028E02, P098K22, P043B14, P130G17, P032B09, P023F03, P313O11

Non-Plausible BAC matches

P080C23

Overgo Sequences

A sequence

GACGATGAGCAACATGGGTGATAC

B sequence

CACCTTTGTAAGCGTCGTATCACC

AB sequence

GACGATGAGCAACATGGGTGATACGACGCT

Marker sequence

ATGACGATGAGCAACATGGGTGATACGACGCTTACAAAGGTGTTTGTAGG
AGGGTTGGCATGGGAAACACCTAAGGAAGCCATGAAAGAACACTTTGACA
AGTATGGTGACATCTTGGAAGCTGTCATCATCTCCGATAAGATCACCGGA
AGATCCAAAGGCTATGGCTTTNNNNNGTGACCTTTAAGGATGCAGAATCA
GCCAAAAAAGCATGCGAGGATGCCACTCCAATTATCAACGGGCGCCGAGC
CAACTGTAATCTCGCGTCCCTCGGCGCCCGTCGTTCCCGCCCCTCTCCCT
CTATTACTCCCCCTCCTCCTCCTCCTCCTCAACAAGNNNNNGACCTAATG
TGGTTGGAGCAAGGGCTAATTCAGCATCACCTGCAAGTCACGTGCAGTGG
TACTATCCCCAAGCTGCACCTCCGGCTTCACCCTTTCACCATCATCAGCC
TCTTCCTTTCTATGGNNNNNGTATTCTCCAGCTTATATTGCCACAGACAT
GAACTACAATCATNNNNNAAAGTAAGCTACAATGGTGGGGGCTACGTGAA
TGGTCATTTTTCTCAAGTGTATCCAGGTCAGGCAATGATGCCAGTGTACC
ACCCATACTATCAGTTTCATCATCAGTCACAGACAATGGGCCTTCCAGCC
CATATCTATTCTCCAACACCTGCTGCCCCTATTCCAACCCTTATGTCAAA
GCCCACATCAANNNNNTTCCTCCTACTGCAGTTTGTTTGGCTGTGGAATA
G

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_At3g54770

%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D4671 marker 4671