Sol Genomics Network

SGN Marker C2_At5g01990

SGN-M4676
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	309442 (SGN) 127529 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U201301	-	-	-
Lycopersicon Combined	Multiple	SGN-U217820	-	-	-
Solanum tuberosum	Single	SGN-U254502	-	-	-
Arabidopsis	Single	At5g01990 on TAIR	-	-	-

Mapped locations

Map: Pepper-COSII
Map version 58 (location: 41503)
Chromosome 10
Position 54.10 cM
Confidence I
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43479

Forward primer (5'-3')

TATTGTTGGCCTTAGGAGGCAATC

Accessions and product sizes

Approximate temperature

63°C

Reverse primer (5'-3')

TGCAAACACAATCGCAACAGTTGTC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38735)
Chromosome 10
Position 39.20 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39901

Forward primer (5'-3')

TATTGTTGGCCTTAGGAGGCAATC

Accessions and product sizes

Solanum lycopersicum TA209

250

Solanum pennellii TA56

250

Approximate temperature

55°C

Reverse primer (5'-3')

TGCAAACACAATCGCAACAGTTGTC

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

250

Solanum lycopersicum TA209

150

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26997)
Chromosome 5
Position 0.38 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11616
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 250	Approximate temperature 55°C

PCR data Exp. ID 11617
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 250	Approximate temperature 55°C

PCR data Exp. ID 11618
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 250	Approximate temperature 55°C

PCR data Exp. ID 13604
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 280	Approximate temperature 55°C

PCR data Exp. ID 13605
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 250	Approximate temperature 55°C

PCR data Exp. ID 13606
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 280	Approximate temperature 55°C

PCR data Exp. ID 13607
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 250	Approximate temperature 55°C

PCR data Exp. ID 13608
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 250	Approximate temperature 55°C

PCR data Exp. ID 13609
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 250	Approximate temperature 55°C

PCR data Exp. ID 13610
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Physalis TA1367: 250	Approximate temperature 55°C

PCR data Exp. ID 13611
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 280	Approximate temperature 55°C

PCR data Exp. ID 13612
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 250	Approximate temperature 55°C

PCR data Exp. ID 13613
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 280	Approximate temperature 55°C

PCR data Exp. ID 13614
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Coffea canephora BP409: 200	Approximate temperature 55°C

PCR data Exp. ID 33157
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 280	Approximate temperature 55°C

PCR data Exp. ID 33158
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 250	Approximate temperature 55°C

PCR data Exp. ID 33159
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 250	Approximate temperature 55°C

PCR data Exp. ID 33160
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 250	Approximate temperature 55°C

PCR data Exp. ID 11619
Forward primer (5'-3') TATTGTTGGCCTTAGGAGGCAATC	Digested band sizes (using HaeIII) Solanum lycopersicum LA925: 150 Solanum pennellii LA716: 250	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGCAAACACAATCGCAACAGTTGTC	Enzymes All possible enzymes for pennellii and and lycopersicum: HaeIII
Accessions and product sizes Solanum lycopersicum LA925: 250 Solanum pennellii LA716: 250	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U217820
SGN-U217821

Overgo hybridization and physical mapping

C2_At5g01990 was used as an overgo probe on plate 13 [well E10]

Plausible BAC Matches: P236A04, P029I24, P228H03, P214E02, P156B03, P104J06, P109F07

Overgo Sequences

A sequence

ACCGAGTCATCCATCAGGTAGTTC

B sequence

TGGAACTTGCTCTGCAGAACTACC

AB sequence

ACCGAGTCATCCATCAGGTAGTTCTGCAGA

Marker sequence

ATGGATAGGGTGTCGAGGATTCTTTTTAGTGTTCTGACAGAACCGCAACG
AGGAGGACAGTCTTTCATCACGTCGATTAAGATTGCTGTTTTACCGATTG
CGAAAGTGTTTACACTATGCTTCTTGGGATTTTTGATGGCCTCCAAGTAT
GTCAATATTCTTCCAGCAAATGGACGGAAGCTTTTAAATGGGNNNNNTTG
GTGTTTTCACTTTTGCTGCCATGCTTGATATTCTCTCAACTTGGACAAGC
CATTACGTATGAGAAATTGCTTCAGTGNNNNNGTGGTTCATCCCTGTTAA
CATTGTTTTGGCCACCATATTTGGTTCTATTATTGGTTTAATTGTTGCTA
CGATAGTCCGTCCGCCATACCCTTATTTCAAGTTTACCATTATACAGATT
GGCATTGNNNNNGGAACATAGGAAATGTTCCACTTGTTCTGATAGCTGCG
TTATGTCGTGACCCATCAAATCCTTTTGGTGACTCTGAGATATGTGCGCG
AGATGGAAATGCATACATCTCTTTTGGACAGTGGNNNNNGTTGGTGCAAT
TATCCTCTACACCTTTGTATTCCAAATGCTCTCACCTCCTCCTGAAGGTT
CCTTCGATGTTGAAGATGCAAACCTTCCTATCAAGGTTCCTAACAAAGAA
AGATTACCGAGTCATCCATCAGGTAGTTCTGCAGAGCAAGTTCCATTACT
TGCAACAAATGTTGCACCAGCCGACTCTAGTAGTTCAAATAAAGAAAAGN
NNNNGTTAAACAGTTCTTTAAATTTCTCTATGAGACACTGAAGCTCAAGC
AACTTATTCAACCTCCCATTATAGCTTCTNNNNNATCATAGCGATTATCA
TAGGATGTGTGCCGGTCCTGAAACGCCTCATCTTTACTTCTGATGCTCCA
CTTTACTTCTTCACTGACAGCTGTTTAATTCTTGGNNNNNGGATGCCATG
ATTCCCTGCATATTGTTGGCCTTAGGAGGCAATCTCGTTGACGNNNNNGG
CCAGGACCTGGAAGTTCAAAAATTGGTCTTAAGACAACTGTTGCGATTGT
GTTTGCACGGTTGTGTTTGGTTCCTCCAACTGGACTCAGTATTGTCATGT
TAGCTGATAAGCTTGGCTTCCTTCCTGCTGATGATAAAATGTTCAGATTC
GTTCTTCTTCTTCAGTATTCAATGCCCACATCCATACTTGCTGGTGCGGT
TGCCAACTTGAGAGGGTGTGGGAAGGAGGCAGCTTCAATCTTGTTTTGGG
TTCATATATTTGCTGTGATCTCTATN

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. betaceum 6002061 plant #4, AB1 chromatogram - [View]
Forward amplicon sequence for S. betaceum 6002061 plant #4, plain text
Forward amplicon sequence for S. uniloba 6002078 plant #6, AB1 chromatogram - [View]
Forward amplicon sequence for S. uniloba 6002078 plant #6, plain text

BLASTX result of original unigene sequences against Arabidopsis protein database