Sol Genomics Network

SGN Marker C2_At4g39660

SGN-M4680
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
Capsicum annuum	Single	SGN-U204579	-	-	-
Lycopersicon Combined	Single	SGN-U220644	-	-	-
Solanum tuberosum	Single	SGN-U247528	-	-	-
Arabidopsis	Single	At4g39660 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49287)
Chromosome 4
Position 51.44 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47227)
Chromosome 4
Position 39.80 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Pepper-COSII
Map version 58 (location: 41500)
Chromosome 12
Position 56.50 cM
Confidence F(LOD3)
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43476

Forward primer (5'-3')

ACAGGGAGCCACTACTGGGGTTT

Accessions and product sizes

Approximate temperature

63°C

Reverse primer (5'-3')

ACATAACCAACAAATAAGGTGCACG

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38729)
Chromosome 4
Position 58.70 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39898

Forward primer (5'-3')

TCCTGATATAGTTACAATGGCAAAG

Accessions and product sizes

Solanum pennellii TA56

500

Solanum lycopersicum TA209

500

Approximate temperature

55°C

Reverse primer (5'-3')

TTTAAGTACTGCATGTCCACCAGC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

500

Solanum lycopersicum TA209

450

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26971)
Chromosome 4
Position 18.41 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11608
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 500	Approximate temperature 55°C

PCR data Exp. ID 11609
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 500	Approximate temperature 55°C

PCR data Exp. ID 11610
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 500	Approximate temperature 55°C

PCR data Exp. ID 13590
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 500	Approximate temperature 55°C

PCR data Exp. ID 13591
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 500	Approximate temperature 55°C

PCR data Exp. ID 13592
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 500	Approximate temperature 55°C

PCR data Exp. ID 13593
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 500	Approximate temperature 55°C

PCR data Exp. ID 13594
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 500	Approximate temperature 55°C

PCR data Exp. ID 13595
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 500	Approximate temperature 55°C

PCR data Exp. ID 13596
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 500	Approximate temperature 55°C

PCR data Exp. ID 13597
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 500	Approximate temperature 55°C

PCR data Exp. ID 13598
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Physalis TA1367: 500	Approximate temperature 55°C

PCR data Exp. ID 13599
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 500	Approximate temperature 55°C

PCR data Exp. ID 13600
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 500	Approximate temperature 55°C

PCR data Exp. ID 13601
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 500	Approximate temperature 55°C

PCR data Exp. ID 13602
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 500	Approximate temperature 55°C

PCR data Exp. ID 13603
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Coffea canephora BP409: 500	Approximate temperature 55°C

PCR data Exp. ID 33153
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 500	Approximate temperature 55°C

PCR data Exp. ID 33154
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 500	Approximate temperature 55°C

PCR data Exp. ID 33155
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 500	Approximate temperature 55°C

PCR data Exp. ID 33156
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 500	Approximate temperature 55°C

PCR data Exp. ID 11611
Forward primer (5'-3') TCCTGATATAGTTACAATGGCAAAG	Digested band sizes (using HinfI) Solanum pennellii LA716: 500 Solanum lycopersicum LA925: 450	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTTAAGTACTGCATGTCCACCAGC	Enzymes All possible enzymes for pennellii and and lycopersicum: HinfI All possible enzymes for lycopersicum and pimpinellifolium: HinfI
Accessions and product sizes Solanum pennellii LA716: 500 Solanum lycopersicum LA925: 500	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U220644

Overgo hybridization and physical mapping

C2_At4g39660 was used as an overgo probe on plate 13 [well F4]

Plausible BAC Matches: P195C08, P075O04, P098K19

Overgo Sequences

A sequence

AGGTGGTTCTCCAATGAGGGATTG

B sequence

GACCGGAAAAATGCCTCAATCCCT

AB sequence

AGGTGGTTCTCCAATGAGGGATTGAGGCAT

Marker sequence

TTACAGAGGAAATTAATAAATGGGTGTGCCGGAATTACCAAGTTAAGGTG
GTTCTCCAATGAGGGATTGAGGCATTTTTCCGGTCAAGTGGCGGCGCCGA
CGGAATTGCCGCCGTTCGACTACCAACCAAAGCCGTATAAAGGGCCTTTG
GCTGATGCAGTGTTGGAGAAAAGAAGAAAGTTTTTGGGTCCTTCACTCTT
CTATTTCTACGAAAAACCTNNNNNCTAAATATTGTTGAAGGGAAGATGCA
ATATTTGTATGATGAGAATGGAAAACGTTATCTCGATGCTTTTGCTGGAA
TAGTTACTGTCTCATGTGGTCATTGTCATCCTGAAGTGTTGAATGCCATC
ATTGAGCAAAGCAAGCTTCTTCAACATGCTACAACCATTTATCTACATCA
TGCAATAGCCGATTTTGCCGAAGCATTGGCATCTAAGATGCCAGGAAACC
TCAAGNNNNNGTAGTATATTTTGTAAATTCAGGGACAGAAGCAAATGAAT
TAGCAATGTTGATGGCACGATTGTACAGCGGTCACTTAAATATGATTGCC
TTGAGGAATGCATATCATGGTGGAAGCTCTAACACGATTGGGCTAACTGC
TCTTAACACATGGAAGTACCCTATTCCACAGNNNNNGGTGAAATCCATCA
CGTTATGAATCCTAACCCATATCGTGGAGCATTTGGATCCGATGCTAAAC
GATATGCTGAAGATGTACAGAATCACATTGATCATGGTACTTCAGGAAAG
GTTGCTGGTTTTATTGCTGAAACAATTCAGNNNNNGGGGTTGGAGGAACA
GTTGAATTAGCCCCTGGATACTTGAAGTTGGTTTATGATATTGTTCGCAA
AGCGGGAGGCGTTTGTATTGCTGACGAAGTACAAACCGGCTTTGGTCGAA
CAGGGAGCCACTACTGGGGTTTTCAGACACAGGGTGTAACTCCTGATATA
GTTACAATGGCAAAGNNNNNGGTATTGGAAATGGCTTACCGCTTGGAGCT
GTTGTCACAACGCCAGAAATTGCAAGTGTTATGGCTCAAAAGATTCAATT
TAATACATATGGTGGAAACCCTGTTTGCTCTGCTGGTGGACATGCAGTAC
TTAAAGTTATTGAGAAGGAACAACGCCAAAAGCATTGTGCTGAGGTTGGC
TCACACTTGTTTGGGCGGCTGAGGGATCTAGAGGAAAAGAACGACANNNN
NTAATTGGAGATGTGAGAGGCAGAGGTTTGATGGTTGGTATTGAACTGGT
AACTGACAGAAAAGAGAAGACACCCGCCAAGGCAGAAACTGGAGTTCTCT
TTGAGAAGCTTAAAGNNNNNATCTTGGTGTTCTAGTAGGGAAAGGTGGTA
TACATGGAAATGTTTTCAGAATAAAGCCTCCCATGTGTTTCAGCAAGGAT
GATGCAGNNNNNATTTCCTAGTTGATGCACTGGACTATTCTCTTTCAAAG
TTGTGA

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