Sol Genomics Network

SGN Marker C2_At2g42810

SGN-M4003
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	304455 (SGN) 122559 (CGN)	-	-	-
Lycopersicon Combined	Single	SGN-U222683	-	-	-
Solanum tuberosum	Single	SGN-U245480	-	-	-
Arabidopsis	Single	At2g42810 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38388)
Chromosome 7
Position 45.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39637

Forward primer (5'-3')

TTGCCTTCAAGTGCATGTGTCC

Accessions and product sizes

Solanum pennellii TA56

1200

Solanum lycopersicum TA209

1200

Approximate temperature

55°C

Reverse primer (5'-3')

AGAGAGCTTCACGCCATCAACAC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

1200

Solanum lycopersicum TA209

560+520

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25924)
Chromosome 2
Position 17.82 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10852
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1200	Approximate temperature 55°C

PCR data Exp. ID 10853
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1200	Approximate temperature 55°C

PCR data Exp. ID 10854
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1200	Approximate temperature 55°C

PCR data Exp. ID 13089
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 800	Approximate temperature 55°C

PCR data Exp. ID 13090
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 600+700	Approximate temperature 55°C

PCR data Exp. ID 13091
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 650	Approximate temperature 55°C

PCR data Exp. ID 13092
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 650	Approximate temperature 55°C

PCR data Exp. ID 13093
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 650	Approximate temperature 55°C

PCR data Exp. ID 13094
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 650	Approximate temperature 55°C

PCR data Exp. ID 13095
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Physalis TA1367: 650	Approximate temperature 55°C

PCR data Exp. ID 13096
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 550	Approximate temperature 55°C

PCR data Exp. ID 13097
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 550	Approximate temperature 55°C

PCR data Exp. ID 13098
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 550	Approximate temperature 55°C

PCR data Exp. ID 32624
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1100	Approximate temperature 55°C

PCR data Exp. ID 32969
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: Multiple	Approximate temperature 55°C

PCR data Exp. ID 32970
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 650	Approximate temperature 55°C

PCR data Exp. ID 32971
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 650	Approximate temperature 55°C

PCR data Exp. ID 32972
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 650	Approximate temperature 55°C

PCR data Exp. ID 10855
Forward primer (5'-3') TTGCCTTCAAGTGCATGTGTCC	Digested band sizes (using TaqI) Solanum lycopersicum LA925: 520+560 Solanum pennellii LA716: 1200	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGAGAGCTTCACGCCATCAACAC	Enzymes All possible enzymes for pennellii and and lycopersicum: TaqI
Accessions and product sizes Solanum pennellii LA716: 1200 Solanum lycopersicum LA925: 1200	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U222683

Overgo hybridization and physical mapping

C2_At2g42810 was used as an overgo probe on plate 12 [well F12]

Plausible BAC Matches: P214H12, P302I05, P023C09

Overgo Sequences

A sequence

CACACAAGCGATTGAGTTGAACGG

B sequence

GTACACCGCATTCTCACCGTTCAA

AB sequence

CACACAAGCGATTGAGTTGAACGGTGAGAA

Marker sequence

ATGCCCGGTATGGAAGCTGAGAACTCAAACGCCTCCCGAGCTGAAGAACT
CAAGCAACTCGCAAATGAAGCATTCAAAGGGNNNNNCATAAGTATTCGCA
AGCTATTGATCTGTACACACAAGCGATTGAGTTGAACGGTGAGAATGCGG
TGTACTATGCTAACCGTGCGTTTGCTCACTCCAAATTGGAGGAATATGGA
AGCGCAATACAGGATGGAACTAGAGCTATTGAAATTGACCCTAGATATTC
AAAGGNNNNNGTTATTATAGGAGAGGAGCTGCATATTTGGCAATGGGGAA
GTTCAAAGATGCACTCAAGGATTTTCAACAGGTNNNNNCAAGAAATTATG
TCCAAACGACCCAGATGCTACCAAAAAATTGAAGGAATGTGAGAAAGCTG
TCATGAAGCTAAAATTTGAAGAAGCTATTTCTGTCCCAGAATCTCAGAGG
CGTTCAGTAGCTGACTCTATTGATTATCGTTCTGTAGNNNNNAGGTGGAG
CCTCAATATGCTGGTGCAAGAATAGAGGGAGATGTTGTAACATTAGATTT
TGTGAAGAAGATGCTGGATGACTTCAAAAACCAGAAGAACTTGCATAAGA
GGTATGNNNNNCCTACCAAATAGTACTGCAAACAAGAGAAATGTTGCGAG
CACTGCCCTCCCTTGTTGACATTGTTGTTCCCGAAGGGAAGCACTTCACT
GTATGTGGTGATGTACATGGTCAGNNNNNTTTTATGACCTCCTAAATATT
TTCGAGCTCAATGGGCTTCCATCAGAAGACAATCCGTATCTGTTCAATGG
TGATTTTGTTGATAGAGGGTCTTTCTCTCTAGAGGTCATATTGACATTAT
TTGCCTTCAAGTGCATGTGTCCATCAGNNNNNCTATACACCTGGCGAGAG
GAAATCACGAAAGCAAGAGCATGAACAAAATATATGGGTTTGAGGGCGAG
GTCAGATCCAAGTTAAGTGAAATATTTGTGGAACTCTTTGCAGAAGTGTT
CTGTTGCTTACCTTTGGCCCATGTCATAAATGAGAAAGTCTTTGTAGTAC
ATGGAGGTCTTTTTAGTGTTGATGGCGTGAAGCTCTCTGATATTAGAGCA
ATTGATCGGTTTTGTGAGCCCCCAGAAGAGGGNNNNNGTTAATGTGTGAA
TTNNNNNNNNNNNNNNN

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_At2g42810

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