Sol Genomics Network

SGN Marker C2_At1g44575

SGN-M4649
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	299798 (SGN) 120341 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197157	-	-	-
Lycopersicon Combined	Single	SGN-U213287	-	-	-
Solanum tuberosum	Multiple	SGN-U243646	-	-	-
Arabidopsis	Single	At1g44575 on TAIR	-	-	-

Mapped locations

Map: Tomato-EXPEN 2000
Map version 52 (location: 38179)
Chromosome 6
Position 39.20 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39460

Forward primer (5'-3')

AGCTATTTGTTGGCCGTGTTGC

Accessions and product sizes

Solanum pennellii TA56

750

Solanum lycopersicum TA209

750

Approximate temperature

55°C

Reverse primer (5'-3')

TGCCTCTGTCTCCCAAAGCTCC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

450

Solanum pennellii TA56

750

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25213)
Chromosome 1
Position 16.87 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10203
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 750	Approximate temperature 55°C

PCR data Exp. ID 10204
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 750	Approximate temperature 55°C

PCR data Exp. ID 10205
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 750	Approximate temperature 55°C

PCR data Exp. ID 12622
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 700	Approximate temperature 55°C

PCR data Exp. ID 12623
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 580	Approximate temperature 55°C

PCR data Exp. ID 12624
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 680	Approximate temperature 55°C

PCR data Exp. ID 12625
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1000	Approximate temperature 55°C

PCR data Exp. ID 12626
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1000	Approximate temperature 55°C

PCR data Exp. ID 12627
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1100	Approximate temperature 55°C

PCR data Exp. ID 12628
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 750	Approximate temperature 55°C

PCR data Exp. ID 12629
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 800	Approximate temperature 55°C

PCR data Exp. ID 12630
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Physalis TA1367: 1100	Approximate temperature 55°C

PCR data Exp. ID 12631
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 800	Approximate temperature 55°C

PCR data Exp. ID 12632
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 800	Approximate temperature 55°C

PCR data Exp. ID 12633
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 800	Approximate temperature 55°C

PCR data Exp. ID 12634
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 800	Approximate temperature 55°C

PCR data Exp. ID 12635
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Coffea canephora BP409: 1000	Approximate temperature 55°C

PCR data Exp. ID 32766
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1000	Approximate temperature 55°C

PCR data Exp. ID 32767
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1000	Approximate temperature 55°C

PCR data Exp. ID 32768
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1100	Approximate temperature 55°C

PCR data Exp. ID 32769
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 750	Approximate temperature 55°C

PCR data Exp. ID 10206
Forward primer (5'-3') AGCTATTTGTTGGCCGTGTTGC	Digested band sizes (using HinfI) Solanum lycopersicum LA925: 450 Solanum pennellii LA716: 750	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCCTCTGTCTCCCAAAGCTCC	Enzymes All possible enzymes for pennellii and and lycopersicum: DraI, EcoRV, HaeIII, HinfI All possible enzymes for lycopersicum and pimpinellifolium: HaeIII, HinfI
Accessions and product sizes Solanum pennellii LA716: 750 Solanum lycopersicum LA925: 750	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U213287
SGN-U268879

Overgo hybridization and physical mapping

C2_At1g44575 was used as an overgo probe on plate 13 [well B9]

Plausible BAC Matches: P216P21

Overgo Sequences

A sequence

CTTCTTGGAGCCATTGGAGCTTTG

B sequence

ATTTGCCTCTGTCTCCCAAAGCTC

AB sequence

CTTCTTGGAGCCATTGGAGCTTTGGGAGAC

Marker sequence

ATGGCTCAAACAATGTTGTTAACAGCCAATGCCAAAGTTGATTTAAGGAG
TAAAGAATCTTTAGTTGAAAGACTAAAACCAAAGCCTTTGTCTTCTTTGT
TCCTACCTTCTCTTCCTTTGAGATTTTCTTCTTCTTCCACTAATGCTTCT
TCTTCAAAATTCACTAGTACTACTGTTGCTCTATTCAAGTCAAAAGCTAA
AGCTCCTCCCAAAAAGNNNNNGTTGCACCACCAAAGGAAAAGCAAAAGGT
GGAGGATGGGATTTTTGGTACCTCCGGAGGAATTGGCTTCACTAAGCAAA
ATGAGCTATTTGTTGGCCGTGTTGCTATGATTGGTTTTGCTNNNNNGCCT
CTTTGTTGGGAGAAGCAATAACAGGAAAAGGTATTTTGGCACAATTAAAT
CTTGAAACTGGAATTCCAATCTATGAAGCAGAGCCACTTCTATTGTTCTT
CATTCTATTCAATCTTCTTGGAGCCATTGGAGCTTTGGGAGACAGAGGCA
AATTTGTTGATGACCCTACCCCTCCTACTGGCCTTGAAAAGGCTGTTATC
CCTCCTGGCAAATCCTTCAAATCTGCTTTGGGACTCAGTGAAGGAGNNNN
NGTCCATTGTTTGGATTCACAAAGGCAAATGAGTTGTTTGTAGGGAGATT
GGCACAATTGGGAATTGCATTTTCCATTATAGGTGAAATTATTACAGGGA
AAGGAGCATTGGCACAATTGAACTTTGAGACAGGTGTCCCAATCAATGAG
ATTGAGCCTCTTTTGTTGTTTAACATTGCCTTCTTCTTCTTTGCTGCTAT
AAATCCTGGTACTGGCAAATTTATCACTGATGAGGAAGAAGATTAG

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]