Sol Genomics Network

SGN Marker C2_At2g34560

SGN-M4644
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	312033 (SGN) 132430 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197419	-	-	-
Lycopersicon Combined	Single	SGN-U214228	-	-	-
Solanum tuberosum	Multiple	SGN-U243806	-	-	-
Arabidopsis	Single	At2g34560 on TAIR	-	-	-

Mapped locations

Map: Tobacco N. acuminata
Map version 89 (location: 46469)
Chromosome 2
Position 40.10 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. acuminata

Map: Eggplant-COSII
Map version 63 (location: 42200)
Chromosome 2
Position 32.30 cM
Confidence F(LOD3)
Protocol CAPS

Eggplant-COSII

PCR data Exp. ID 43765

Forward primer (5'-3')

TAAGTGGGAGAGCATTAAAGGATT

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

TTCCTGTTCCAGGAGGGCCAA

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Pepper-COSII
Map version 58 (location: 41385)
Chromosome 2
Position 56.10 cM
Confidence F(LOD3)
Protocol dCAPS

Pepper-COSII

PCR data Exp. ID 43361

Forward primer (5'-3')

AGTTGTTAGCAAATGGCGTGGTG

Accessions and product sizes

Approximate temperature

63°C

Reverse primer (5'-3')

ACTGTTGATGTGTGTAGAAATGCCTG

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38358)
Chromosome 2
Position 38.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39611

Forward primer (5'-3')

AGTTGTTAGCAAATGGCGTGGTG

Accessions and product sizes

Solanum pennellii TA56

920

Solanum lycopersicum TA209

920

Approximate temperature

55°C

Reverse primer (5'-3')

TTCATCGAGAAAGATGGTTGAAGG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

920

Solanum lycopersicum TA209

600

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25815)
Chromosome 2
Position 14.57 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10777
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 920	Approximate temperature 55°C

PCR data Exp. ID 10778
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 920	Approximate temperature 55°C

PCR data Exp. ID 10779
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 920	Approximate temperature 55°C

PCR data Exp. ID 13019
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 950	Approximate temperature 55°C

PCR data Exp. ID 13020
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Solanum melongena TA2986: 950	Approximate temperature 55°C

PCR data Exp. ID 13021
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 850	Approximate temperature 55°C

PCR data Exp. ID 13022
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1100	Approximate temperature 55°C

PCR data Exp. ID 13023
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1100	Approximate temperature 55°C

PCR data Exp. ID 13024
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1100	Approximate temperature 55°C

PCR data Exp. ID 13025
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1300	Approximate temperature 55°C

PCR data Exp. ID 13026
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Physalis TA1367: 1400	Approximate temperature 55°C

PCR data Exp. ID 13027
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 950	Approximate temperature 55°C

PCR data Exp. ID 13028
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13029
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 1100	Approximate temperature 55°C

PCR data Exp. ID 13030
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Coffea canephora BP409: 300	Approximate temperature 55°C

PCR data Exp. ID 32942
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1100	Approximate temperature 55°C

PCR data Exp. ID 32943
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1100	Approximate temperature 55°C

PCR data Exp. ID 32944
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1100	Approximate temperature 55°C

PCR data Exp. ID 32945
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1300	Approximate temperature 55°C

PCR data Exp. ID 10780
Forward primer (5'-3') AGTTGTTAGCAAATGGCGTGGTG	Digested band sizes (using RsaI) Solanum lycopersicum LA925: 600 Solanum pennellii LA716: 920	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TTCATCGAGAAAGATGGTTGAAGG	Enzymes All possible enzymes for pennellii and and lycopersicum: RsaI, DraI, HaeIII
Accessions and product sizes Solanum lycopersicum LA925: 920 Solanum pennellii LA716: 920	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U214228

Overgo hybridization and physical mapping

C2_At2g34560 was used as an overgo probe on plate 13 [well A12]

Plausible BAC Matches: None

Overgo Sequences

A sequence

GGAAAGGTATCCTCCTTTTTGGCC

B sequence

TTTCCTGTTCCAGGAGGGCCAAAA

AB sequence

GGAAAGGTATCCTCCTTTTTGGCCCTCCTG

Marker sequence

ATGGCCGACGAACCTGCGTTGACTCGATGGACCTTTCCGNNNNNTTTGGG
AGGAGGAAGGTTCCTGCACGAGATGCAACTGACAATGGTGATTCTGTGCA
AAATGGAAATTCTTCAACTATGAATGGAAATGGATCTGTGCGGAACACTG
CAGAATTATCCATTTTCGAGCAGTATAATCAGGCTAATGGANNNNNGTTC
AGTCTGCCGGAGTGGATGGAAAACCNNNNNGGAAAAATCTCTACTTCCTC
CTTTCGAGTCTGCAGAAATGCGCACTTTAGCAGAAAGCTTAACCAGNNNN
NGGATATTCTTCGTGGTAATCCAGATGTTAAGTGGGAGAGCATTAAAGGA
TTAGAGACTGCCAAGCGTCTACTAAAAGAAGCAGTTGTCATGCCTATTAA
ATATCCAAANNNNNGTATTTTAAAGGTCTTTTAACTCCTTGGAAAGGTAT
CCTCCTTTTTGGCCCTCCTGGAACAGGAAAGNNNNNACCATGCTTGCGAA
GGCAGTTGCAACTGAATGCAATACCACATTTTTCAATATCTCAGCATCAT
CAGTTGTTAGCAAATGGCGTGNNNNNGTGATTCTGAAAAATTGATAAAAG
TGTTATTCGAGCTCGCTAGGCATCATGCTCCTTCAACCATCTTTCTCGAT
GAAATTGATGCCATTATCAGTCAACGCGGGGAAGCGCGCAGTGAGCATGA
ATCTAGTAGGCGTTTAAAAACAGAACTGCTCATACAGNNNNNATGGACGG
TTTGAATCGGACAGATGAACTTGTCTTTGTTCTTGCTGCAACAAATCTTC
CCTGGGAACTGGATGCAGCAATGCTCCGACGTCTTGAGAAGCGGNNNNNA
TCCTTGTGCCCCTTCCGGAGGCAGAAGCAAGGTGCGGGATGTTTGAGGAT
TTACTACCATCCCTTCCTGAAGAGGCGCCACTTCCATATGATTTATTGGT
AGAAAAGACAGAAGGCTTTTCTGGTTCTGATATTCGGCTATTATGCAAGG
AGGCTGCCATGCAACCATTACGACGTCTAATGGCAGAACTTGATAAGAGG
GAAGAATTGGTGCCTGAGGATGNNNNNAGTTGCCCAATGTTGGACCAATA
ACTGTGACAGATATCGAGGTGGCACTGAAGAACACGAGACCATCTGCACA
CCTACATGCACCTAGGTACGATAAGTTCAATTCAGATTATGGCAGCCATG
CTCTCCAGTGA

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