Sol Genomics Network

SGN Marker C2_At5g49510

SGN-M3943
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	308601 (SGN) 130855 (CGN)	-	-	-
Lycopersicon Combined	Single	SGN-U217276	-	-	-
Solanum tuberosum	Single	SGN-U250583	-	-	-
Arabidopsis	Single	At5g49510 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49302)
Chromosome 5
Position 62.64 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47242)
Chromosome 5
Position 114.67 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46774)
Chromosome 5
Position 10.40 cM
Confidence F(LOD3)
Protocol dCAPS

Tobacco N. tomentosiformis

Map: Tomato-EXPEN 2000
Map version 52 (location: 38879)
Chromosome 5
Position 101.00 cM
Confidence F(LOD3)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39981

Forward primer (5'-3')

AAGCCAGTTTAGAGGTTCTTGTGG

Accessions and product sizes

Solanum lycopersicum TA209

500

Solanum pennellii TA56

600

Approximate temperature

55°C

Reverse primer (5'-3')

TTCTTTGGGAGTGGTAGCTTGTCG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

530

Solanum lycopersicum TA209

500

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27480)
Chromosome 5
Position 20.10 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11959
Forward primer (5'-3') AAGCCAGTTTAGAGGTTCTTGTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTTTGGGAGTGGTAGCTTGTCG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 600	Approximate temperature 55°C

PCR data Exp. ID 11960
Forward primer (5'-3') AAGCCAGTTTAGAGGTTCTTGTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTTTGGGAGTGGTAGCTTGTCG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 500	Approximate temperature 55°C

PCR data Exp. ID 11961
Forward primer (5'-3') AAGCCAGTTTAGAGGTTCTTGTGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTTTGGGAGTGGTAGCTTGTCG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 500	Approximate temperature 55°C

PCR data Exp. ID 11962
Forward primer (5'-3') AAGCCAGTTTAGAGGTTCTTGTGG	Digested band sizes (using amplicon difference) Solanum lycopersicum LA925: 500 Solanum pennellii LA716: 530	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCTTTGGGAGTGGTAGCTTGTCG	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference
Accessions and product sizes Solanum pennellii LA716: 600 Solanum lycopersicum LA925: 500	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U217276

Overgo hybridization and physical mapping

C2_At5g49510 was used as an overgo probe on plate 12 [well G11]

Plausible BAC Matches: None

Overgo Sequences

A sequence

TGTTCTTCATACACCGGTGAAGTG

B sequence

TACCTCTTCTCTCCGTCACTTCAC

AB sequence

TGTTCTTCATACACCGGTGAAGTGACGGAG

Marker sequence

ATGGCGGCGGCGGCGGCGTGTTCTTCATACACCGGTGAAGTGACGGAGAG
AAGAGGTATACCGGCGGCATCATTCGTACAAGACGTTCAGTCTTATCTCA
GCCAATCTGGTCTCGATGTTAACTCTGCTCTTGCATTCCTACAAGAAAGA
NNNNNCTNNNNNTCAGCAGTACCGAGTGGTTGAAATGAAACTTCTGGCCC
AGCAGAGGGATCTTCAGGNNNNNCAAAGATTCCTGACATAGAGAAATGCT
TGGATATAGTTGCTACTTTGCAAGCTAAGAAGGACAGCAATGAGGNNNNN
CACTAGTCGCTGATTTTGAAGTGTCAGAAGGTATTTATTCCCGGGCTAAG
ATTGAAGATGCTGAATCTGTGTGTTTATGGCTAGGGGCAAATGTCATGCT
ACAGTATTCATGCGAAGAGGNNNNNCTACTGCCCTTCTTCAAACAAACTT
GGAAAATGCAAAAGCCAGTTTAGAGGTTCTTGTGGCTGATCTACAATTTT
TGAGGGATCAAGTGACAATTACTCAGGTCNNNNNACAACTGCTCGTGTAT
ACAACTGGGATGTTCATCAACGTAGAGTTCGACAAGCTACCACTCCCAAA
GAATCATGA

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