Sol Genomics Network

SGN Marker C2_At2g38730

SGN-M4700
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	309875 (SGN) 131408 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U198818	-	-	-
Lycopersicon Combined	Single	SGN-U224513	-	-	-
Solanum tuberosum	Single	SGN-U253527	-	-	-
Arabidopsis	Single	At2g38730 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49235)
Chromosome 1
Position 79.36 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47166)
Chromosome 1
Position 88.14 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46642)
Chromosome 1
Position 50.30 cM
Confidence I(LOD2)
Protocol dCAPS

Tobacco N. tomentosiformis

Map: Tobacco N. acuminata
Map version 89 (location: 46472)
Chromosome 1
Position 26.40 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. acuminata

Map: Tomato-EXPEN 2000
Map version 52 (location: 38375)
Chromosome 1
Position 92.50 cM
Confidence F(LOD3)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39626

Forward primer (5'-3')

AGCGGACCAAACACTAATGGATG

Accessions and product sizes

Solanum lycopersicum TA209

500

Solanum pennellii TA56

550

Approximate temperature

55°C

Reverse primer (5'-3')

AGCCACATTCTCAATCTTCCTGAC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

550

Solanum pennellii TA56

500

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25871)
Chromosome 2
Position 16.20 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10828
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 550	Approximate temperature 55°C

PCR data Exp. ID 10829
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 500	Approximate temperature 55°C

PCR data Exp. ID 10830
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 500	Approximate temperature 55°C

PCR data Exp. ID 13065
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 650	Approximate temperature 55°C

PCR data Exp. ID 13066
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 850	Approximate temperature 55°C

PCR data Exp. ID 13067
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1100	Approximate temperature 55°C

PCR data Exp. ID 13068
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 550+1000	Approximate temperature 55°C

PCR data Exp. ID 13069
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13070
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1000	Approximate temperature 55°C

PCR data Exp. ID 13071
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1000	Approximate temperature 55°C

PCR data Exp. ID 13072
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 1000	Approximate temperature 55°C

PCR data Exp. ID 13073
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Physalis TA1367: 1200	Approximate temperature 55°C

PCR data Exp. ID 13074
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 550	Approximate temperature 55°C

PCR data Exp. ID 13075
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 580	Approximate temperature 55°C

PCR data Exp. ID 13076
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 580	Approximate temperature 55°C

PCR data Exp. ID 13077
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 550	Approximate temperature 55°C

PCR data Exp. ID 13078
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Coffea canephora BP409: 650	Approximate temperature 55°C

PCR data Exp. ID 32960
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 550+1000	Approximate temperature 55°C

PCR data Exp. ID 32961
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 32962
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1000	Approximate temperature 55°C

PCR data Exp. ID 32963
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1000	Approximate temperature 55°C

PCR data Exp. ID 10831
Forward primer (5'-3') AGCGGACCAAACACTAATGGATG	Digested band sizes (using amplicon difference) Solanum pennellii LA716: 500 Solanum lycopersicum LA925: 550	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGCCACATTCTCAATCTTCCTGAC	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference All possible enzymes for lycopersicum and pimpinellifolium: AluI
Accessions and product sizes Solanum pennellii LA716: 550 Solanum lycopersicum LA925: 500	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U224513
SGN-U279298

Overgo hybridization and physical mapping

C2_At2g38730 was used as an overgo probe on plate 13 [well H10]

Plausible BAC Matches: P214H10, P309C12, P309D12, P061L10, P194N05, P246F17, P019P03, P309E12

Non-Plausible BAC matches

P185G24, P160N24, P234D05, P320K06

Overgo Sequences

A sequence

CTGGTCGCATCAAGATGGAGCTTT

B sequence

GGAGTAATATCGGCGAAAAGCTCC

AB sequence

CTGGTCGCATCAAGATGGAGCTTTTCGCCG

Marker sequence

ATGGCGTCTGGCGGCGTGGGAGGAGGGGTGGTAGAATGGCACCTGAGGCC
ACAAGTACCAAAAAACCCAGTTGTATTTTTCGATGTAACAATCGGCAACA
TCCCTGCTGGTCGCATCAAGATGGAGCTTTTCGCCGATATTACTCCCAAA
ACTGCTGAGAATTTCAGGCAACTGTGCACGGGAGAATTTAGNNNNNGAAA
GCAGGAGTACCACAAGGCTTTAAGAATTGTCAGTTCCATAGGGTGATTAA
GGACTTCATGATCCAAGGTGGTGATTTCCTAAAGNNNNNGGAGATGGCAG
TGGATGTGTTTCCATATATGGAAGCAAGTTTGAGGATGAAAACTTTATTG
CCAAGCACACTGGTCCTGGCCTTTTATCAATGNNNNNGCAAATAGCGGAC
CAAACACTAATGGATGTCAGNNNNNTTTTTTGTCTCATGTGCCAAATGTG
AGTGGCTCGACAACAAGCATGTCGTTTTTGGGNNNNNCGTGTTCTTGGAG
ATGGTCTTTTAGTGGTCAGGAAGATTGAGAATGTGGCTGTTGGAGCAAAC
AACAAACCAAAGCTGGCATGTGTGATTGCTGAATGTGGAGAGATGTAA

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]
Forward amplicon sequence for S. hirtum 130005 plant #3, AB1 chromatogram - [View]
Forward amplicon sequence for S. hirtum 130005 plant #3, plain text
Forward amplicon sequence for S. quitoense SE plant #1, AB1 chromatogram - [View]
Forward amplicon sequence for S. quitoense SE plant #1, plain text

BLASTX result of original unigene sequences against Arabidopsis protein database