Sol Genomics Network

SGN Marker C2_At1g20050

SGN-M3982
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	301988 (SGN) 120126 (CGN)	-	-	-
Lycopersicon Combined	Single	SGN-U215678	-	-	-
Solanum tuberosum	Single	SGN-U244473	-	-	-
Arabidopsis	Single	At1g20050 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49202)
Chromosome 6
Position 44.86 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47132)
Chromosome 6
Position 110.00 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46563)
Chromosome 6
Position 84.30 cM
Confidence F(LOD3)
Protocol dCAPS

Tobacco N. tomentosiformis

Map: Tobacco N. acuminata
Map version 89 (location: 46430)
Chromosome 6
Position 97.30 cM
Confidence I(LOD2)
Protocol PCR

Tobacco N. acuminata

Map: Eggplant-COSII
Map version 63 (location: 42172)
Chromosome 6
Position 121.10 cM
Confidence F(LOD3)
Protocol CAPS

Eggplant-COSII

PCR data Exp. ID 43735

Forward primer (5'-3')

ATGATCTAAAATTGCCTGGTTTTG

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

AATAGCCCTCAAGGACCATGTGG

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Pepper-COSII
Map version 58 (location: 41310)
Chromosome 6
Position 139.40 cM
Confidence F(LOD3)
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43286

Forward primer (5'-3')

ATGATCTAAAATTGCCTGGTTTTG

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

AATAGCCCTCAAGGACCATGTGG

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38123)
Chromosome 6
Position 101.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39411

Forward primer (5'-3')

ATGATCTAAAATTGCCTGGTTTTG

Accessions and product sizes

Solanum pennellii TA56

1000

Solanum lycopersicum TA209

1000

Approximate temperature

55°C

Reverse primer (5'-3')

AATAGCCCTCAAGGACCATGTGG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

950

Solanum lycopersicum TA209

1000

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25070)
Chromosome 1
Position 6.95 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10063
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1000	Approximate temperature 55°C

PCR data Exp. ID 10064
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1000	Approximate temperature 55°C

PCR data Exp. ID 10065
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1000	Approximate temperature 55°C

PCR data Exp. ID 12480
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 900	Approximate temperature 55°C

PCR data Exp. ID 12481
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: Multiple	Approximate temperature 55°C

PCR data Exp. ID 12482
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 850	Approximate temperature 55°C

PCR data Exp. ID 12483
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: Multiple	Approximate temperature 55°C

PCR data Exp. ID 12484
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1200	Approximate temperature 55°C

PCR data Exp. ID 12485
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 1031	Approximate temperature 55°C

PCR data Exp. ID 12486
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Physalis TA1367: 900	Approximate temperature 55°C

PCR data Exp. ID 12487
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 900	Approximate temperature 55°C

PCR data Exp. ID 12488
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 900	Approximate temperature 55°C

PCR data Exp. ID 32594
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 900	Approximate temperature 55°C

PCR data Exp. ID 32715
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 900	Approximate temperature 55°C

PCR data Exp. ID 32716
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 900	Approximate temperature 55°C

PCR data Exp. ID 32717
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 850	Approximate temperature 55°C

PCR data Exp. ID 32718
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: Multiple	Approximate temperature 55°C

PCR data Exp. ID 32719
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1200	Approximate temperature 55°C

PCR data Exp. ID 10066
Forward primer (5'-3') ATGATCTAAAATTGCCTGGTTTTG	Digested band sizes (using DraI) Solanum lycopersicum LA925: 1000 Solanum pennellii LA716: 950	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AATAGCCCTCAAGGACCATGTGG	Enzymes All possible enzymes for pennellii and and lycopersicum: DraI, EcoRV, HaeIII
Accessions and product sizes Solanum lycopersicum LA925: 1000 Solanum pennellii LA716: 1000	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U215678

Overgo hybridization and physical mapping

C2_At1g20050 was used as an overgo probe on plate 12 [well H10]

Plausible BAC Matches: P055E18, P275G06, P060A01, P071M21, P115F17, P165G21, P154J16, P072B24, P220H19, P203H13, P148A07, P254L24, P148I02, P254C07, P148B07, P017H05

Overgo Sequences

A sequence

AAGACTGACAGGGTACTCATGTGC

B sequence

CCGTGAAAATCCACCAGCACATGA

AB sequence

AAGACTGACAGGGTACTCATGTGCTGGTGG

Marker sequence

ATGGCAAGCCAGGGAGAAGCTCACCCCTACGTTCCACATGATCTAAAATT
GCCTGGTTTTGTTCCCCTATTCCTCTCACAGTCAGAAATTGTTGGTGTAT
ATGGCATCTCATCCGTACTGGTTGTGGTGTTCATGTGGATATTCTCAGGN
NNNNATTTGTTCCTAAATTATCAAAGACTGACAGGGTACTCATGTGCTGG
TGGATTTTCACGGGCCTAACCCACATGGTCCTTGAGGGCTATTTCGTTTT
TACTCCAGATTTCTACCAAAAGACTAGTCCCGTTTACCTTGCTGAAGTCT
GNNNNNGAAAGAATACAGCAAAGGTGATTCAAGATACGTAGGCCGAGATG
CTGCAGTTGTTAGTGTTGAAGGGGTCACAGCTGTCATAGAGGGGCCAGCG
TGCCTTCTTGCAGTNNNNNGTATGCTATAGCTACTAAGAAGGCATACAGG
CACGTACTTCAACTATCCATTTGTTTGGGGCAGCTCTATGGCACGGCTAT
ATACTTCATAACAGCTCTTTTGGAAGGCGATAATTTTTCTACAAGCCCCT
TCTATTACTACGCTTACTATGTCTTTGCAAATCATTTCTGGGTTTGGATA
CCAAGTCTCATAGTGATCCACTGCTGGAAGAAAATATGTGCTGCTGTCCG
CGTCCACGAGCAGAAGACCAAGACCCGCTGA

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
Forward amplicon sequence for S. hirtum 120062 plant #28, AB1 chromatogram - [View]
Forward amplicon sequence for S. hirtum 120062 plant #28, plain text
Forward amplicon sequence for S. quitoense plant #3, AB1 chromatogram - [View]
Forward amplicon sequence for S. quitoense plant #3, plain text

BLASTX result of original unigene sequences against Arabidopsis protein database