Sol Genomics Network

SGN Marker C2_At5g56130

SGN-M4683
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	307866 (SGN) 128346 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U201794	-	-	-
Lycopersicon Combined	Single	SGN-U223085	-	-	-
Solanum tuberosum	Single	SGN-U248284	-	-	-
Arabidopsis	Single	At5g56130 on TAIR	-	-	-

Mapped locations

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46779)
Chromosome 7
Position 50.80 cM
Confidence CF(LOD3)
Protocol dCAPS

Tobacco N. tomentosiformis

Map: Eggplant-COSII
Map version 63 (location: 42262)
Chromosome 7
Position 111.60 cM
Confidence I
Protocol dCAPS

Eggplant-COSII

PCR data Exp. ID 43831

Forward primer (5'-3')

CTTCGTCCTCTTTCTACTGCATGAAT

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

TAGGTTTAAACTTGCGAACATCC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38893)
Chromosome 7
Position 108.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39995

Forward primer (5'-3')

ACATATAGCTGTTGGGAACAGGG

Accessions and product sizes

Solanum pennellii TA56

350

Solanum lycopersicum TA209

350

Approximate temperature

55°C

Reverse primer (5'-3')

TAGGTTTAAACTTGCGAACATCC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

300

Solanum pennellii TA56

220

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27564)
Chromosome 5
Position 22.74 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 12027
Forward primer (5'-3') ACATATAGCTGTTGGGAACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGGTTTAAACTTGCGAACATCC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 350	Approximate temperature 55°C

PCR data Exp. ID 12028
Forward primer (5'-3') ACATATAGCTGTTGGGAACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGGTTTAAACTTGCGAACATCC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 350	Approximate temperature 55°C

PCR data Exp. ID 12029
Forward primer (5'-3') ACATATAGCTGTTGGGAACAGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGGTTTAAACTTGCGAACATCC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 350	Approximate temperature 55°C

PCR data Exp. ID 12030
Forward primer (5'-3') ACATATAGCTGTTGGGAACAGGG	Digested band sizes (using RsaI) Solanum pennellii LA716: 220 Solanum lycopersicum LA925: 300	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TAGGTTTAAACTTGCGAACATCC	Enzymes All possible enzymes for pennellii and and lycopersicum: RsaI All possible enzymes for lycopersicum and pimpinellifolium: RsaI
Accessions and product sizes Solanum lycopersicum LA925: 350 Solanum pennellii LA716: 350	Approximate temperature 55°C

Overgo hybridization and physical mapping

C2_At5g56130 was used as an overgo probe on plate 13 [well F10]

Plausible BAC Matches: None

Overgo Sequences

A sequence

TTAAAGGGTCACACCGACAGTGTG

B sequence

CCCAACATAACTGGTCCACACTGT

AB sequence

TTAAAGGGTCACACCGACAGTGTGGACCAG

Marker sequence

ATGGCGGAAACAATACCCTTCAAAAATCTTCATAGCAGAGAGTACCAGGG
ACACAAGAAGAAGNNNNNGTGCATTCGGTGGCATGGAACTGCAGTGGCAC
GAAATTAGCTTCAGGTTCTGTGGATCAAACAGCTCGTATTTGGCAAATTG
AGCCTCATGGTCATNNNNNGGAAAGGTAAAAGATGTTGAATTAAAGGGTC
ACACCGACAGTGTGGACCAGTTATGTTGGGATCCAAAACATGCAGAATTG
ATAGCTACAGCATCTGGTGACAAGACAGTTCGATTATGGGATGCCCGTAN
NNNNGTGGGAAATGCTCACAGCAAGTTGAACTCAGTGGGGAAAATATCAA
TATCACTTACAAGCCTGATGGGACACATATAGCTGTTGGGAACAGGNNNN
NGATGATGAGCTAACAATCTTGGATGTTCGCAAATTTAAGCCTATTCATA
AGCGCAAGTTTAATTATGAGNNNNNGTAAATGAGATTGCATGGAACACGG
GTGGCGATATGTTCTTTCTTACAACTGGAAATGNNNNNGAACTGTGGAAG
TCTTAGCTTATCCGTCTCTACAAGCTGTTAACACGCTTAATGCTCACACT
GCTGGTTGTTACTGCATTGCAATTGATCCACTAAGAAGNNNNNATATTTT
GCTGTTGGAAGTGCTGATTCATTGGTCAGCCTTTGGAGCATCAAGGAGAT
GCTATGTCTTCGAACATTTACAAAACTTGANNNNNGTGGCCAGTTCGGAC
AATAAGTTTCAATCACACAGGAGACTACATTGCCTCTGCTAGTGAAGATT
TGTTTATTGATATTNNNNNGCTAATGTCCAATCTGGACGGTCAGTTCACC
AAATTCCATGTCGTGCTGCCATGAACAGTGGTGAATGGAATCCAAAACAC
AACTTGCTTGCCTTTGCCGGGGATGATAAGAACAAATACCAGGCTGATGA
AGNNNNNGTGTGTTTCGCATATTTGGCTTTGAGAGCGCATAG

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 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

Related Markers

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

Genomic location of C2_At5g56130

%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D4683 marker 4683

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Accessions	Seedlots
Accessions		Breeding Program	Seedlot Name	Contents	Seedlot Location	Count	Weight(g)

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