Sol Genomics Network

SGN Marker C2_At5g12200

SGN-M4684
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	311782 (SGN) 132417 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U204962	-	-	-
Lycopersicon Combined	Single	SGN-U226142	-	-	-
Arabidopsis	Single	At5g12200 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49291)
Chromosome 11
Position 47.32 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47232)
Chromosome 11
Position 70.10 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46751)
Chromosome 11
Position 84.50 cM
Confidence F(LOD3)
Protocol PCR

Tobacco N. tomentosiformis

Map: Tomato-EXPEN 2000
Map version 52 (location: 38780)
Chromosome 11
Position 53.50 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39922

Forward primer (5'-3')

TCCTGACTTCCATTTTGCAGCAAG

Accessions and product sizes

Solanum lycopersicum TA209

150

Solanum pennellii TA56

150

Approximate temperature

55°C

Reverse primer (5'-3')

TGCTCTGATTGGTGGGCTCATGAC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

250

Solanum lycopersicum TA209

210

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27120)
Chromosome 5
Position 3.94 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11696
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 150	Approximate temperature 55°C

PCR data Exp. ID 11697
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 150	Approximate temperature 55°C

PCR data Exp. ID 11698
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 150	Approximate temperature 55°C

PCR data Exp. ID 13687
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 200	Approximate temperature 55°C

PCR data Exp. ID 13688
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 200	Approximate temperature 55°C

PCR data Exp. ID 13689
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 200	Approximate temperature 55°C

PCR data Exp. ID 13690
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 200	Approximate temperature 55°C

PCR data Exp. ID 13691
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 200	Approximate temperature 55°C

PCR data Exp. ID 13692
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 200	Approximate temperature 55°C

PCR data Exp. ID 13693
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 200	Approximate temperature 55°C

PCR data Exp. ID 13694
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 200	Approximate temperature 55°C

PCR data Exp. ID 13695
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Physalis TA1367: 200	Approximate temperature 55°C

PCR data Exp. ID 13696
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 200	Approximate temperature 55°C

PCR data Exp. ID 13697
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 200	Approximate temperature 55°C

PCR data Exp. ID 13698
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 200	Approximate temperature 55°C

PCR data Exp. ID 33194
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 200	Approximate temperature 55°C

PCR data Exp. ID 33195
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 200	Approximate temperature 55°C

PCR data Exp. ID 33196
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 200	Approximate temperature 55°C

PCR data Exp. ID 33197
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 200	Approximate temperature 55°C

PCR data Exp. ID 11699
Forward primer (5'-3') TCCTGACTTCCATTTTGCAGCAAG	Digested band sizes (using RsaI) Solanum pennellii LA716: 250 Solanum lycopersicum LA925: 210	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCTCTGATTGGTGGGCTCATGAC	Enzymes All possible enzymes for pennellii and and lycopersicum: RsaI
Accessions and product sizes Solanum pennellii LA716: 150 Solanum lycopersicum LA925: 150	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U204962
SGN-U226142

Overgo hybridization and physical mapping

C2_At5g12200 was used as an overgo probe on plate 13 [well F11]

Plausible BAC Matches: P266K10, P070D14, P047M18, P045J15, P163L12, P119D16, P200A13, P017I01, P129P04, P294F14, P267K10, P235M22, P238L19, P287F05, P065E22, P033K21

Overgo Sequences

A sequence

AATCAGAGCAGCAGGTCATGGAAC

B sequence

AGCTGCTTGAAGAGCTGTTCCATG

AB sequence

AATCAGAGCAGCAGGTCATGGAACAGCTCT

Marker sequence

ATGAGTATTGACGCGATGGAAGAAATTGCCAGAGCTCGGAAGTCAGNNNN
NGTCAAAGAATTGTTGGGGAGCCAGTCGTTTCAGGTTTACTTCTTAATGA
TTCAGTACTTTGGGATCCTGACTTCCATTTTGCAGCAAGNNNNNGTACGT
CATGAGCCCACCAATCAGAGCAGCAGGTCATGGAACAGCTCTTCAAGCAG
CTCTTGCTGCAGGGGTTCTGCAGNNNNNCTGGTAGGAACTGATCACTGCA
CCTTCAACTCAACTCAGAAAGCGCTAGGAATTGGTGATTTCCGGAAAATA
CCAAATGGTGTTAATGNNNNNGTATGGAGGAGAGAATGCATTTGGTTTGG
AATACAATGGTGNNNNNGCTTCTGGTCAGATATCTGTCACTGATTATGTT
CGCATAACAAGCACAGAATGNNNNNTGCTCGGATTTTCAATATCTATCCA
AGGAAGGGAGCAATACTTGTTGGGTCTGATGCAGATATAATCATTTTAAA
TCCCAATTCAAGCTTCAAGATTAGTTCAAAGTCACACCATTATAGGACAG
ATACCAATGTCTATGAGGGTTGGACAGGCATGNNNNNGGAAAGGTTGAAA
CTACAATTGCAGGAGGAAGGGTTGTTTGGGAAAATGATGAGCTGAAAGTC
ATCCCTGGTGCTGGCAAGTACATTGAAATGCCACCTTTCAGTTATCTTTT
TGACGGGATAGACAAGGCAGATGCAAAGTACCTCTCTTCCTTAAGAGCAC
CCGTAGAACGATCAACGACTTGA

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]

BLASTX result of original unigene sequences against Arabidopsis protein database

Input file for PAUP, NEXUS format
Phylogenetic tree
Phylogenetic tree | [View]

Related Markers

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

Genomic location of C2_At5g12200

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