Sol Genomics Network

SGN Marker C2_At4g22260

SGN-M4685
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	302905 (SGN) 121182 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U205149	-	-	-
Lycopersicon Combined	Single	SGN-U218630	-	-	-
Solanum tuberosum	Single	SGN-U262956	-	-	-
Arabidopsis	Single	At4g22260 on TAIR	-	-	-

Mapped locations

Map: Eggplant-COSII
Map version 63 (location: 42241)
Chromosome 11
Position 5.00 cM
Confidence I(LOD2)
Protocol PCR

Eggplant-COSII

PCR data Exp. ID 43808

Forward primer (5'-3')

CACGTTGAGCAATGCATCAGCATTC

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

AGGAACTCTTGCAATTGTTTCCAGAAC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Pepper-COSII
Map version 58 (location: 41481)
Chromosome 12
Position 0.00 cM
Confidence F(LOD3)
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43457

Forward primer (5'-3')

TCCTCTAACGGTCTAGAGAAATGGG

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

AGGAACTCTTGCAATTGTTTCCAGAAC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38669)
Chromosome 11
Position 37.00 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39846

Forward primer (5'-3')

TCCTCTAACGGTCTAGAGAAATGGG

Accessions and product sizes

Solanum pennellii TA56

650

Solanum lycopersicum TA209

650

Approximate temperature

55°C

Reverse primer (5'-3')

AGGAACTCTTGCAATTGTTTCCAGAAC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

100

Solanum pennellii TA56

400

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 26769)
Chromosome 4
Position 11.77 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11460
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 650	Approximate temperature 55°C

PCR data Exp. ID 11461
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 650	Approximate temperature 55°C

PCR data Exp. ID 11462
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 650	Approximate temperature 55°C

PCR data Exp. ID 13439
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 700	Approximate temperature 55°C

PCR data Exp. ID 13440
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 650	Approximate temperature 55°C

PCR data Exp. ID 13441
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1200	Approximate temperature 55°C

PCR data Exp. ID 13442
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 400	Approximate temperature 55°C

PCR data Exp. ID 13443
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 13444
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 550	Approximate temperature 55°C

PCR data Exp. ID 13445
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 500	Approximate temperature 55°C

PCR data Exp. ID 13446
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 550	Approximate temperature 55°C

PCR data Exp. ID 13447
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Physalis TA1367: 650	Approximate temperature 55°C

PCR data Exp. ID 13448
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 900	Approximate temperature 55°C

PCR data Exp. ID 13449
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 850	Approximate temperature 55°C

PCR data Exp. ID 13450
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 650	Approximate temperature 55°C

PCR data Exp. ID 13451
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Coffea canephora BP409: 580	Approximate temperature 55°C

PCR data Exp. ID 33103
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 400	Approximate temperature 55°C

PCR data Exp. ID 33104
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: Multiple	Approximate temperature 55°C

PCR data Exp. ID 33105
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 550	Approximate temperature 55°C

PCR data Exp. ID 33106
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 500	Approximate temperature 55°C

PCR data Exp. ID 11463
Forward primer (5'-3') TCCTCTAACGGTCTAGAGAAATGGG	Digested band sizes (using HinfI) Solanum lycopersicum LA925: 100 Solanum pennellii LA716: 400	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') AGGAACTCTTGCAATTGTTTCCAGAAC	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: 650 Solanum lycopersicum LA925: 650	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U218630

Overgo hybridization and physical mapping

C2_At4g22260 was used as an overgo probe on plate 13 [well F12]

Plausible BAC Matches: P015A13

Overgo Sequences

A sequence

GAAGTAATGGGAAGCCACCAGATG

B sequence

CCGTTAGAGGATGAATCATCTGGT

AB sequence

GAAGTAATGGGAAGCCACCAGATGATTCAT

Marker sequence

ATGGCGATTTCGATTTCTGCTATGAGTTTTGGAACCTCAGTTTCTTCACA
TTCTTGTTTTAGAGCTAGGAGTTTTGAGAAGTCATCAGTTTTATGCAATT
CCCAGAACCCATGTCGGTTTAATTCTGTTTTTCCGATTCGGAAATCTGAT
GGGGCTTCACGGTGTTCTGTTTCTAGNNNNNGAAATCATGTAGAGTTCGA
GCAACGTTGTTACAAGAGAATGAAGAAGAAGTGGTTGTGGAGAAATCTTT
TGCACCTAAGAGTTTTCCTGATAACGTGGGAGGGGGAAGTAATGGGAAGC
CACCAGATGATTCATCCTCTAACGGTCTAGAGAAATGGGTTATAAAGCTT
GAGCAGTCTGTAAATATCTTACTCACGNNNNNGATTCAGTGATAAAGATT
CTTGACACTTTGTATCACAACCGAAACTATGCGAGGTTTTTTGTTCTGGA
AACAATTGCAAGAGTTCCTTATTTTGNNNNNCATTTATATCGGTTCTTCA
CATGTATGAGAGCTTTGGCTGGTGGAGAAGGGCAGATTATATGAAAGTGC
ATTTTGCTGAAAGCTGGAATGAGATGCACCATTTGCTCATTATGGAANNN
NNGAATTAGGGGGAAATGCTTGGTGGTTTGATCGATTTCTTGCACAACAT
ATAGCTATATTCTATTATTTCATGACAGTCTTGATGTATGCTTTGAGCCC
GAGAATGGCATNNNNNATCATTTCTCTGAATGTGTGGAGAGCCATGCATA
CGAGACTTACGATAAATTCATCAAGGATCAAGGAGNNNNNAGGAATTGAA
GAATTTGCCCGCTCCAAAGATTGCAGTGGACTACTACACGGGAGGTGACT
TATATTTATTTGNNNNNATGAGTTTCAAACTTCACGAGAGCCTAATACTC
GAAGACCAAAAATAGNNNNNATAATCTCTATGACGTATTCATGAACATTA
GAGATGACGAAGCAGAGCATTGTAAAACGATGAAAGCCTGTCAAACTCAC
GGGAGCCTTCGTTCTCCACACACAGATCCATGCGATGATTCTGAAGATGA
TACAGGGTGTTCCGTACCTCAAGCTGATTGTATAGGTATCGTGGATTGTA
TAAAGAAGTCAGTCACCGATACTCAAGTAACCAAAAGGTAG

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]

BLASTX result of original unigene sequences against Arabidopsis protein database

Input file for PAUP, NEXUS format
Phylogenetic tree
Phylogenetic tree | [View]

Related Markers

Related Genotyped Markers: These markers have been genotyped and share a name with this marker

Genomic location of C2_At4g22260

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