Sol Genomics Network

SGN Marker C2_At3g04780

SGN-M4681
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	302257 (SGN) 125074 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197300	-	-	-
Lycopersicon Combined	Multiple	SGN-U213344	-	-	-
Solanum tuberosum	Single	SGN-U249608	-	-	-
Arabidopsis	Single	At3g04780 on TAIR	-	-	-

Mapped locations

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46654)
Chromosome 1
Position 49.70 cM
Confidence I(LOD2)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Tomato-EXPEN 2000
Map version 52 (location: 38426)
Chromosome 1
Position 98.50 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39671

Forward primer (5'-3')

ACTATTGTCAATGCCCTCAAACAGG

Accessions and product sizes

Solanum pennellii TA56

1650

Solanum lycopersicum TA209

1650

Approximate temperature

55°C

Reverse primer (5'-3')

ATGCAGTTTGATGACTTGATTAAAAGG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

900

Solanum lycopersicum TA209

1200

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26039)
Chromosome 3
Position 1.31 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10957
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1650	Approximate temperature 55°C

PCR data Exp. ID 10958
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1650	Approximate temperature 55°C

PCR data Exp. ID 10959
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1650	Approximate temperature 55°C

PCR data Exp. ID 13124
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1750	Approximate temperature 55°C

PCR data Exp. ID 13125
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1600	Approximate temperature 55°C

PCR data Exp. ID 13126
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 2200	Approximate temperature 55°C

PCR data Exp. ID 13127
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 2200	Approximate temperature 55°C

PCR data Exp. ID 13128
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1650	Approximate temperature 55°C

PCR data Exp. ID 13129
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1650	Approximate temperature 55°C

PCR data Exp. ID 13130
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 1100	Approximate temperature 55°C

PCR data Exp. ID 13131
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 1200	Approximate temperature 55°C

PCR data Exp. ID 13132
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 1200	Approximate temperature 55°C

PCR data Exp. ID 13133
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 1100	Approximate temperature 55°C

PCR data Exp. ID 32986
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 2200	Approximate temperature 55°C

PCR data Exp. ID 32987
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 2200	Approximate temperature 55°C

PCR data Exp. ID 32988
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1650	Approximate temperature 55°C

PCR data Exp. ID 32989
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1650	Approximate temperature 55°C

PCR data Exp. ID 10960
Forward primer (5'-3') ACTATTGTCAATGCCCTCAAACAGG	Digested band sizes (using RsaI) Solanum pennellii LA716: 900 Solanum lycopersicum LA925: 1200	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATGCAGTTTGATGACTTGATTAAAAGG	Enzymes All possible enzymes for pennellii and and lycopersicum: RsaI
Accessions and product sizes Solanum pennellii LA716: 1650 Solanum lycopersicum LA925: 1650	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U213344
SGN-U273002

Overgo hybridization and physical mapping

C2_At3g04780 was used as an overgo probe on plate 13 [well F7]

Plausible BAC Matches: P319D11, P166C09, P089M01

Non-Plausible BAC matches

P155P21

Overgo Sequences

A sequence

TTGTAGACTGGTCTGGCGTCGAAT

B sequence

CCACTTTGGTTAAGGCATTCGACG

AB sequence

TTGTAGACTGGTCTGGCGTCGAATGCCTTA

Marker sequence

ATGGCTGCCGAATCTGCTTTTGCAATTCCCAAAGGCCAANNNNNGTTGAT
TTGATGGACTTTGTAGACTGGTCTGGCGTCGAATGCCTTAACCAAAGTGG
CAGCAACACTATTGTCAATGCCCTCAAACAGNNNNNGGTTACAGAGAAGA
CGAGGGCTTGAACCTGGTGAGTGATGCAGATGAACAGCTATTGATTTACA
TACCTTTTAATCAAGTCATCAAACTGCATTCAATCGTTATCAAAGGACCT
GAGGAGGAAGNNNNNGTCCTAAAACTGTGAAGCTGTTTTCTAACAAGGAG
CACATGGGATTTAGNNNNNTAATGTTAATGATTACCCTCCAAGTGACACA
GTTGTTTTATCTGAAGATAACCTCAAGNNNNNGGAAAACCAGTTACCTTG
AAGTATGTCAAGTTTCAAAATGTTCGCAGNNNNNTGTGACCATTTTTATT
GAGGATAATCAACATGATGGGGAAACTACAAATGTTCAAAAAATTGTTTT
GTATGGATCAACNNNNNGGTGGAAACAACAGATATGAAAGGCTTGAAGAA
GATTGAGGACCACTGA

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_At3g04780

%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D4681 marker 4681