Sol Genomics Network

SGN Marker C2_At3g16150

SGN-M4656
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	301023 (SGN) 124533 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U196433	-	-	-
Lycopersicon Combined	Single	SGN-U218429	-	-	-
Solanum tuberosum	Multiple	SGN-U245845	-	-	-
Arabidopsis	Single	At3g16150 on TAIR	-	-	-

Mapped locations

Map: Pepper-COSII
Map version 58 (location: 41418)
Chromosome 4
Position 122.90 cM
Confidence I
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43394

Forward primer (5'-3')

AAGCAACTCCTTACTCGTTGCC

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

CTAGCTTCAGCATACCAACATTGTC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38473)
Chromosome 4
Position 97.50 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39712

Forward primer (5'-3')

AAGCAACTCCTTACTCGTTGCC

Accessions and product sizes

Solanum pennellii TA56

400

Solanum lycopersicum TA209

400

Approximate temperature

55°C

Reverse primer (5'-3')

TGGAGATACCAGAAACGGCG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

150+200

Solanum lycopersicum TA209

100+150

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26184)
Chromosome 3
Position 5.47 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11062
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 400	Approximate temperature 55°C

PCR data Exp. ID 11063
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 400	Approximate temperature 55°C

PCR data Exp. ID 11064
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 400	Approximate temperature 55°C

PCR data Exp. ID 13228
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 400	Approximate temperature 55°C

PCR data Exp. ID 13229
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 600	Approximate temperature 55°C

PCR data Exp. ID 13230
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 600	Approximate temperature 55°C

PCR data Exp. ID 13231
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes
Accessions and product sizes Physalis TA1367: 400	Approximate temperature 55°C

PCR data Exp. ID 33028
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 600	Approximate temperature 55°C

PCR data Exp. ID 33029
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 600	Approximate temperature 55°C

PCR data Exp. ID 11065
Forward primer (5'-3') AAGCAACTCCTTACTCGTTGCC	Digested band sizes (using HinfI) Solanum lycopersicum LA925: 150+100 Solanum pennellii LA716: 200+150	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGGAGATACCAGAAACGGCG	Enzymes All possible enzymes for pennellii and and lycopersicum: HinfI All possible enzymes for lycopersicum and pimpinellifolium: HinfI
Accessions and product sizes Solanum lycopersicum LA925: 400 Solanum pennellii LA716: 400	Approximate temperature 55°C

Overgo hybridization and physical mapping

C2_At3g16150 was used as an overgo probe on plate 13 [well C8]

Plausible BAC Matches: P297M18, P165C11, P018K15, P206I03, P171B21, P308D07, P316E10, P145G05, P147G09, P214C02, P214B18, P068A12, P122I24

Overgo Sequences

A sequence

ACATTGGAATCTCCGCTCTTCGCT

B sequence

ATGGCAGGTAGAGAAGAGCGAAGA

AB sequence

ACATTGGAATCTCCGCTCTTCGCTCTTCTC

Marker sequence

ATGGGCGGTTGGGCTATAGCGGTGCACGGTGGCGCTGGTGTGGACCCAAA
TCTCCCAGATGAACGTCAACAACAAGCTAAGCAACTCCTTACTCGTTGCC
TTAACATTGGAATCTCCGCTCTTCGCTCTTCTCTACCTGCCATTGATGTC
GTTGAACTCGTTNNNNNGTGAGAGAACTTGAAAGTGATCCTCTATTCAAT
TCGGGTCGTGGATCTGCATTAACTGCAAATAGAACAGTGGAAATGGAGGC
GAGCATTATGGACGGCGATGGTAGACGATGCGGCGCCGTTTCTGGTATCT
CCACCGTGAAAAACCCAATTTCTCTCGCTCGCCTTGTCATGGATAAATCC
CCTCATTCTTACCTCGGTTTCTCCGGCGCCGAAGAATTCGCCAAACAACA
GNNNNNGGCGTGGAAATGGTAGACAATGAATATTTCATAACTGAGGACAA
TGTTGGTATGCTGAAGCTAGCCAAAGAGGCTAACACCATTTTGNNNNNTT
CGATTACAGAATTCCATTAACTGGATTGGATTCGTGTGCGGCATCCGTTG
AAAGCCCAATTCACATGAACGGATTACCGATAAATATTTATGCACCGGAG
ACGGTCGGATGTGTGGTGGTAGACCGGCAAGGCAGGTGCGCCGCCGGTAC
TTCCACCGGTGGTTTAATGAACAAAATGACCGGTCGGATCGGTGATTCAC
CTCTGATTGGTGCTGGGACCTACGCCGGTGAGCTTTGTGGGGTGTCATGT
ACAGGTGAAGGAGAAGCTATCATACGTGGTACCCTAGCACGTGACGTGGC
AGCAGTTATGGAATACAAGGAATTGGGTCTTCAAGACGCAGTAAACTTTG
TGATTAAGAAGAGATTGGATAAAGGTTTCGCTGGGCTTATTGCTGTGTCT
AACAAGGGNGAAGTGGCTTTTGGGTTTAATTGTAATGGAATGTTTAGAGG
ATGTGCTACTGAAGATGGATTTATGGATGTTGGTATTTGGTAA

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