Sol Genomics Network

SGN Marker C2_At4g15520

SGN-M3786
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	300792 (SGN) 121467 (CGN)	-	-	-
Lycopersicon Combined	Single	SGN-U224862	-	-	-
Solanum tuberosum	Single	SGN-U245444	-	-	-
Arabidopsis	Single	At4g15520 on TAIR	-	-	-

Mapped locations

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46717)
Chromosome 9
Position 44.30 cM
Confidence CF(LOD3)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Tomato-EXPEN 2000
Map version 52 (location: 38641)
Chromosome 1
Position 47.10 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39825

Forward primer (5'-3')

TCCGTTTCCGCCACTTCCAC

Accessions and product sizes

Solanum lycopersicum TA209

850

Solanum pennellii TA56

850

Approximate temperature

55°C

Reverse primer (5'-3')

ATTCAATGAAGCAGTACCACACCC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

370+450

Solanum pennellii TA56

280

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26694)
Chromosome 4
Position 8.86 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11409
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 850	Approximate temperature 55°C

PCR data Exp. ID 11410
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 850	Approximate temperature 55°C

PCR data Exp. ID 11411
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 850	Approximate temperature 55°C

PCR data Exp. ID 13415
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 720	Approximate temperature 55°C

PCR data Exp. ID 13416
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13417
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 720+900	Approximate temperature 55°C

PCR data Exp. ID 13418
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 900	Approximate temperature 55°C

PCR data Exp. ID 13419
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 900	Approximate temperature 55°C

PCR data Exp. ID 13420
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Physalis TA1367: 350+450	Approximate temperature 55°C

PCR data Exp. ID 13421
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13422
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 700	Approximate temperature 55°C

PCR data Exp. ID 13423
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 700	Approximate temperature 55°C

PCR data Exp. ID 32641
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 800	Approximate temperature 55°C

PCR data Exp. ID 33094
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 800	Approximate temperature 55°C

PCR data Exp. ID 33095
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 800	Approximate temperature 55°C

PCR data Exp. ID 33096
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 720+900	Approximate temperature 55°C

PCR data Exp. ID 33097
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 900	Approximate temperature 55°C

PCR data Exp. ID 11412
Forward primer (5'-3') TCCGTTTCCGCCACTTCCAC	Digested band sizes (using HinfI) Solanum pennellii LA716: 280 Solanum lycopersicum LA925: 450+370	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATTCAATGAAGCAGTACCACACCC	Enzymes All possible enzymes for pennellii and and lycopersicum: HinfI
Accessions and product sizes Solanum pennellii LA716: 850 Solanum lycopersicum LA925: 850	Approximate temperature 55°C

Overgo hybridization and physical mapping

C2_At4g15520 was used as an overgo probe on plate 12 [well H11]

Plausible BAC Matches: None

Overgo Sequences

A sequence

TTTGGGCTGGATTCTCCGAGAGAA

B sequence

TTGTTCCCTTCACGTGTTCTCTCG

AB sequence

TTTGGGCTGGATTCTCCGAGAGAACACGTG

Marker sequence

ATGGAAAATGAGAAGAAACTAGAGAGCTTCGTGCTGGTACATAATATAGC
AAAGAGACACAACGTCGGAACCTTAGCTCGTAGCGCCACGGCGTTCGGCG
TCTCGGAGATGATACTCGTCGGCCGTAGAGATTTCAACGCTTTCGGTAGC
CACGGCTCCACTTCTCACGTCCGTTTCCGCCACTTCCACTCCCTTGCCGA
TGCTAAAACCTTCCTCAAGGNNNNNAAAGAGATTGTGATATATGTGGAGT
TGAAATTACAGAAAATGCGGTTGCTGTAAATGAACATCCTTTTAAGAGAA
GTACTGCTTTCCTGCTGGGCAATGAGGNNNNNGTACTGGACTTTCTGCAA
AAGAGTGTGAGATATGTGATTTCTTTGTATATATTCCACAATATGGGTGT
GGTACTGCTTCATTGAATGTGACTGTTGCTGCTTCCATTGTTCTACATCA
ATTTGGAGNNNNNTTTGGGCTGGATTCTCCGAGAGAACACGTGAAGGGAA
CAAGTTCATTGTGGCTGAAAGACATTTCAAACAGGCAAAGAAAAATTACT
GCATGGAATCATCTGAATCTGTTGCTGAGGAGCGAAGACTGAAGAGGGAA
AATCTTTCAAATGGGTTCTTTGAAGATGCTGGAAAAGAGGAATCTCCTTC
AAATCTTTTAGATACCTTGTTCGATGACTAG

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

BLASTX result of original unigene sequences against Arabidopsis protein database

Related Markers

Related Genotyped Markers: These markers have been genotyped and share a name with this marker

Genomic location of C2_At4g15520

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