Sol Genomics Network

SGN Marker C2_At4g29490

SGN-M4673
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	306923 (SGN) 130498 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U199794	-	-	-
Lycopersicon Combined	Multiple	SGN-U214068	-	-	-
Solanum tuberosum	Single	SGN-U246158	-	-	-
Arabidopsis	Single	At4g29490 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38685)
Chromosome 7
Position 22.30 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39862

Forward primer (5'-3')

AAGAGCAAACTCGACATTGCACC

Accessions and product sizes

Solanum lycopersicum TA209

530

Solanum pennellii TA56

530

Approximate temperature

55°C

Reverse primer (5'-3')

ACAAGTAGGCGAAATAGCTCTCCTG

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

200+250

Solanum pennellii TA56

350

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26844)
Chromosome 4
Position 14.49 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11515
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 530	Approximate temperature 55°C

PCR data Exp. ID 11516
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 530	Approximate temperature 55°C

PCR data Exp. ID 11517
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 530	Approximate temperature 55°C

PCR data Exp. ID 13477
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 510	Approximate temperature 55°C

PCR data Exp. ID 13478
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Solanum melongena TA2986: 500	Approximate temperature 55°C

PCR data Exp. ID 13479
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 250	Approximate temperature 55°C

PCR data Exp. ID 13480
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 150	Approximate temperature 55°C

PCR data Exp. ID 13481
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 200	Approximate temperature 55°C

PCR data Exp. ID 13482
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 150	Approximate temperature 55°C

PCR data Exp. ID 13483
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 200	Approximate temperature 55°C

PCR data Exp. ID 13484
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Physalis TA1367: 500	Approximate temperature 55°C

PCR data Exp. ID 13485
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 550	Approximate temperature 55°C

PCR data Exp. ID 33115
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 150	Approximate temperature 55°C

PCR data Exp. ID 33116
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 200	Approximate temperature 55°C

PCR data Exp. ID 33117
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 150	Approximate temperature 55°C

PCR data Exp. ID 11518
Forward primer (5'-3') AAGAGCAAACTCGACATTGCACC	Digested band sizes (using TaqI) Solanum pennellii LA716: 350 Solanum lycopersicum LA925: 200+250	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ACAAGTAGGCGAAATAGCTCTCCTG	Enzymes All possible enzymes for pennellii and and lycopersicum: TaqI
Accessions and product sizes Solanum pennellii LA716: 530 Solanum lycopersicum LA925: 530	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U214068
SGN-U272681

Overgo hybridization and physical mapping

C2_At4g29490 was used as an overgo probe on plate 13 [well E7]

Plausible BAC Matches: P149C03, P153J18, P049M11, P272H07, P158J17, P197C14, P058P20, P308P13, P069K12, P290B10, P196H16, P302E19, P169F22, P251O12, P166N17, P313P01, P138N20, P308P12, P037K05, P054J09, P001A24, P119P02, P120B09, P108F03, P308O12, P048D18, P112M13

Non-Plausible BAC matches

P076F20, P077F10

Overgo Sequences

A sequence

CGAGAGAAGCTCTTCAACTCTCTG

B sequence

AAGTGAGGTGGTTACGCAGAGAGT

AB sequence

CGAGAGAAGCTCTTCAACTCTCTGCGTAAC

Marker sequence

ATGTCTCCTCCGATGATTCGCATGGAACTCCATTCACTTAATCGAGAGAA
GCTCTTCAACTCTCTGCGTAACCACCTCACTTCATGCGCTCGTCCTCTCC
AAGGCTTTGTTCTCTTACAGNNNNNGGTGGCGAAGAGCAAACTCGACATT
GCACCGATCACCTAGAACTGTTCAGNNNNNACAGGAGAGCTATTTCGCCT
ACTTGTTTGGAGTGGAAGAGCCTGGATTTTACGGAACTATTNNNNNGATA
TAGCAAGTGGGAAATCTATGCTCTTTATTCCTAGGTTACCCGCTGACTAT
GCTGTTTGGATGGGAGAAATACAACCACCTTCTCACTTCCAGNNNNNGAA
AAGTACAAGGTTACCCAGGTCTTCTATACTGATGAGATTAAGGAAGTTTT
GGTTGATCAGTACCAAGCGACAGGAGCAGCATTACTATTTCTCTTGCATG
GGCTTAATACTGATAGCAACAAGTATTTTAAACCAGCAGAATTTCAGNNN
NNGGTATTGAGAAGTTCCAGACAGATCTAAGCACATTGCATCCTATCCTA
ACTGAATGCCGTGTTATAAAGTCCGATTTAGAGCTTGCTCTCATTCAATA
TGCAAATGACATAAGCTCTGAAGCTCATGTTGAGNNNNNGTTATGAGGAA
AACAAAAGTAGGGATGAAAGAATATCAGTTAGAAAGCATGTTTCTTCACC
ATACCTACATGTATGGCGGCTGTAGGCATTGTTCATACACATGTATATGT
GCTACTGGCGATAATAGNNNNNTGCTGTACTCCATTATGGTCATGCAGCA
GCTCCAAATGACAAGNNNNNACATTGCAAGAGGGAGATATGGCACTTCTA
GATATGGGAGCTGAGTACCACTTTTATGGGTCCGACATAACTTGTTCCTT
TCCANNNNNGTAAATGGGAAATTTACTCGTGACCAGTCACTTTTATATAC
TGCTGTTCTTGATGCTCATGATGCTGTCATTTCTGCCATGAAGCCTGGAG
TGAGCTGGGTCGATATGCATAAATTAGCTGAAAGGGTCATTTTGGAATCA
CTGAAGAAAGGGAACCTACTTGTTGGGGATGTTGATAAAATGATGGCCGA
GCGACTTGGTGCTGTTTTCATGCCTCATGGATTGGGGCACCTTCTTGGAA
TTGATACTCATGATCCTGGGGGTTACTTGAAGGGAGCTAAAAGACCAAAA
GAACCTGGATTGAGCTCTCTACGTACGAGCAGAAAGCTCTTAAAGGGAAT
GGTGATCACTGTGGAGCCTGGTTGTTACTTCATTGATGCCTTGCTACTTC
CTGCCTTGAAGAGTCCAGCAGTTTCAGAGTTTTTCAATCGTGTTGAGATC
AACAGGTTTAGACCTTTTGGTGGAGTCAGAATTGAAAGTGATGTGTGTGT
TACTTCCATTGGATGCATTAACATGAGCAAATGTCCGCGGAAGATTGAAG
AGATAGAGGCAGTGATGGCGGGGGCTCCTTGGCCGATAGAAAAGACTACC
TTTCTATCTGGAAATGGACAAGTGTAATTCTCCCAAATATTGCATGACAT
CAAGAAACTAGAATAA

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_At4g29490

%2Fsearch%2Fmarkers%2Fmarkerinfo.pl%3Fmarker_id%3D4673 marker 4673

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

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