Sol Genomics Network

SGN Marker C2_At5g35360

SGN-M4661
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
Lycopersicon Combined	Single	SGN-U230893	-	-	-
Solanum tuberosum	Single	SGN-U251070	-	-	-
Arabidopsis	Single	At5g35360 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38841)
Chromosome 1
Position 21.30 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39956

Forward primer (5'-3')

AACAGATCCGTGTCGCTATGGGAG

Accessions and product sizes

Solanum lycopersicum TA209

150

Solanum pennellii TA56

100

Approximate temperature

53°C

Reverse primer (5'-3')

TTGAATGTCCTCTAAGCACAATATCCTC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27339)
Chromosome 5
Position 13.60 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11850
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 500	Approximate temperature 55°C

PCR data Exp. ID 11851
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 450	Approximate temperature 55°C

PCR data Exp. ID 11852
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 450	Approximate temperature 55°C

PCR data Exp. ID 13838
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 500	Approximate temperature 55°C

PCR data Exp. ID 13839
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 500	Approximate temperature 55°C

PCR data Exp. ID 13840
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 500	Approximate temperature 55°C

PCR data Exp. ID 13841
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 500	Approximate temperature 55°C

PCR data Exp. ID 13842
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 500	Approximate temperature 55°C

PCR data Exp. ID 13843
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 500	Approximate temperature 55°C

PCR data Exp. ID 13844
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Physalis TA1367: 500	Approximate temperature 55°C

PCR data Exp. ID 13845
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 500	Approximate temperature 55°C

PCR data Exp. ID 13846
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 500	Approximate temperature 55°C

PCR data Exp. ID 33253
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 500	Approximate temperature 55°C

PCR data Exp. ID 33254
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 500	Approximate temperature 55°C

PCR data Exp. ID 33255
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 500	Approximate temperature 55°C

PCR data Exp. ID 33256
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 500	Approximate temperature 55°C

PCR data Exp. ID 11853
Forward primer (5'-3') AACAGATCCGTGTCGCTATGGGAG	Digested band sizes (using amplicon difference) Solanum pennellii LA716: 500 Solanum lycopersicum LA925: 450	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTGAATGTCCTCTAAGCACAATATCCTC	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference All possible enzymes for lycopersicum and pimpinellifolium: AluI,MspI,RsaI,DraI,TaqI,RV,HaeIII,HinfI,DpnII,KpnI
Accessions and product sizes Solanum lycopersicum LA925: 450 Solanum pennellii LA716: 500	Approximate temperature 55°C

Overgo hybridization and physical mapping

C2_At5g35360 was used as an overgo probe on plate 13 [well D2]

Plausible BAC Matches: P305J13, P236O08, P244A10, P308B14, P076F15, P198N17, P030P13, P271N11, P105E12, P211B23, P162I22, P296H04, P253A12

Overgo Sequences

A sequence

GAATGCTGGTGTTCCAACTGTACC

B sequence

TAGTCCGTCACTTCCTGGTACAGT

AB sequence

GAATGCTGGTGTTCCAACTGTACCAGGAAG

Marker sequence

NNNNNGTGACATGCCGCGCCGAGAAAATTCTGGTGGCAAATAGAGGAGAG
ATTGTTGTTCGCGTGATCCGAACTGCCCATGAGATGGGAATTCCTTGTGT
TGCGGTTTATTCGACCATTGATAAAGATGCCTTACATGTGAAGCTAGCTG
ATGAATCTGTTTGCATTGGAGAAGCACCAAGTAATCAGTCNNNNNGTATT
TAGTGATCCCAAATGTCTTGTCTGCTGCTATCAGTCGCGGATGTACAATG
TTGCATCCTGGATATGGTTTCCTTTCTGAGAATGCAAGTTTTGTTGAGAT
GTGCAGAGAACATGGAATCAACTTTATTGGGCCAAATNNNNNCCAGACAG
CATAAGAGTCATGGGTGACAAAGCCACTGCTAGAGATACAATGAAGAATG
CTGGTGTTCCAACTGTACCAGGAAGTGACGGACTATTGCAGNNNNNAGTA
CTGAAGAAGGTGTAAAGCTTGCCGAGGAGATTGGTTACCCCGTGATGATT
AAGNNNNNGCAACAGCTGGTGGTGGTGGACGTGGAATGCGTCTTGCTAAA
GAACCTAATGAGTTCGTAAAATTATTGCAGNNNNNCAAGCTAAGAGTGAA
GCAGCAGCTGCATTTGGAAATGATGGCGTTTATCTGGAGAAGTACATCGT
AAATCCCAGGCACATTGAATTTCAGNNNNNGTTTTGGCGGACAAGTATGG
TAATGTTGTACACTTTGGAGAGCGTGATTGCAGTATTCAGNNNNNAGAAG
AAACCAAAAGTTGCTGGAGGAAGCACCATCCCCGGCATTGACACCAGAGC
TGAGGAAAGCCATGGGTGATGCAGCTGTGGCAGCAGCAGCATCTATAGGT
TACATTGGTGTTGGAACCATAGAGTTCCTATTGGATGAGAGAGGCTCCTT
TTACTTCATGGAAATGAACACTCGTATTCAGNNNNNGTAGAGCATCCGGT
GACAGAAATGATATCCTCTGTTGATCTGATAGAGGAACAGATCCGTGTCG
CTATGGGAGAAAAGCTCCCATACAAACAGNNNNNGAGGATATTGTGCTTA
GAGGACATTCAATTGAATGNNNNNNNNNNNNNNNNNNNNNNNNNN

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_At5g35360

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