Sol Genomics Network

SGN Marker C2_At5g37360

SGN-M4695
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	308912 (SGN) 126457 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U202689	-	-	-
Lycopersicon Combined	Single	SGN-U219292	-	-	-
Solanum tuberosum	Multiple	SGN-U248077	-	-	-
Arabidopsis	Single	At5g37360 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49298)
Chromosome 4
Position 46.42 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47238)
Chromosome 4
Position 35.63 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46766)
Chromosome 5
Position 56.50 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Tobacco N. acuminata
Map version 89 (location: 46534)
Chromosome 5
Position 50.80 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. acuminata

Map: Tomato-EXPEN 2000
Map version 52 (location: 38848)
Chromosome 4
Position 56.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39958

Forward primer (5'-3')

TGCAGCATTTGATCTTTCAAATGG

Accessions and product sizes

Solanum pennellii TA56

1200

Solanum lycopersicum TA209

1300

Approximate temperature

55°C

Reverse primer (5'-3')

TGATTTTTGAGAGCCTGTCAATGAG

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

1300

Solanum pennellii TA56

1200

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27353)
Chromosome 5
Position 14.82 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11861
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1300	Approximate temperature 55°C

PCR data Exp. ID 11862
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1300	Approximate temperature 55°C

PCR data Exp. ID 11863
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1300	Approximate temperature 55°C

PCR data Exp. ID 13847
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1500	Approximate temperature 55°C

PCR data Exp. ID 13848
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1250	Approximate temperature 55°C

PCR data Exp. ID 13849
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1200	Approximate temperature 55°C

PCR data Exp. ID 13850
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1200	Approximate temperature 55°C

PCR data Exp. ID 13851
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1200	Approximate temperature 55°C

PCR data Exp. ID 13852
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1200	Approximate temperature 55°C

PCR data Exp. ID 13853
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 1200+1400	Approximate temperature 55°C

PCR data Exp. ID 13854
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 1200	Approximate temperature 55°C

PCR data Exp. ID 13855
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 1200	Approximate temperature 55°C

PCR data Exp. ID 13856
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 1200	Approximate temperature 55°C

PCR data Exp. ID 13857
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 1200	Approximate temperature 55°C

PCR data Exp. ID 13858
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Coffea canephora BP409: 1300	Approximate temperature 55°C

PCR data Exp. ID 33257
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1200	Approximate temperature 55°C

PCR data Exp. ID 33258
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1200	Approximate temperature 55°C

PCR data Exp. ID 33259
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1200	Approximate temperature 55°C

PCR data Exp. ID 33260
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1200	Approximate temperature 55°C

PCR data Exp. ID 11864
Forward primer (5'-3') TGCAGCATTTGATCTTTCAAATGG	Digested band sizes (using AluI) Solanum pennellii LA716: 400+500 Solanum lycopersicum LA925: 850	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGATTTTTGAGAGCCTGTCAATGAG	Enzymes All possible enzymes for pennellii and and lycopersicum: AluI, DraI, HinfI
Accessions and product sizes Solanum lycopersicum LA925: 1300 Solanum pennellii LA716: 1300	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U202689
SGN-U219292
SGN-U274071

Overgo hybridization and physical mapping

C2_At5g37360 was used as an overgo probe on plate 13 [well H2]

Plausible BAC Matches: P077J20, P177P12, P309I09, P177N21, P320O12, P180P17, P198L24, P248O07

Overgo Sequences

A sequence

TCGAGCATGGGAAATGGCTGATAC

B sequence

AGCTGTGGACGTTGATGTATCAGC

AB sequence

TCGAGCATGGGAAATGGCTGATACATCAAC

Marker sequence

ATGGCTTCCTCTATCTCACTTCATCAACACTCGTCTATCTATTGTCTCTT
TTCTACTCCTACTCTTCGTTTTGGCAAACACCCACATCATATCATCTCCA
TCCTTCCATCATTTCGCAAGAATTTCCTCAAATTTCATACACGTACAACA
GTACCGTTTGCTGTTACTGAATCTGATTCCCCCAAATCTCTTGAACCAAA
CCCTCAAACACTTGTACAGGAAATCGCTNNNNNGAGAGTTTTGTTCTACC
TGCAGACTTTTTTTCGCAGCTTCCCAGTGATCTTCGCTTAGATNNNNNCT
GAATGATGCAGCATTTGATCTTTCAAATGGGCCAGTTAAAGTTGAGNNNN
NTGTGGTGAAGAGGTTGGAGAGACATTGTTAAATATAAGTCGAGCATGGG
AAATGGCTGATACATCAACGTCCACAGCTTTAGTGGACAAGCTGCCTTTA
TTGGTTGGCTCATTGACAGGCTCTCAAAAATCATTAGNNNNNCATTTGGA
AGGCGCTTGTTATCAGCTGGAAAAAGGTTCCAGTCCATGGGACAATATGG
CGAAGGTGAAGTGCAGAANNNNNNGTATCTGGGGTTGATGTTGAAGAATT
TAAGCAGCAAACCAGGATGTTCAAGNNNNNTTTGGGGATCTTCAGGTTGA
ATTGACCTCTGGAAAGGCCTACACTGGAGCTGCCATTGCATTCATCTTTA
GNNNNNTTTTCTTTCTTGGGAATTGGGCCAAGGCATACAGAGCATACCGG
AGAGCTCATTACAGTATGCAAATGACAATGCTTTATTGCTTGCTAAGNNN
NNTCTCTGCGAGCATCTCTGCTTGTGATGTCCTATTCATCAACCGTTTTA
GCTGCTTTTGCAATGGTGGGACTTATTTTACTTGGGGGACAACTTAAGTC
GGAAAATAAGTGA

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