Sol Genomics Network

SGN Marker C2_At5g42740

SGN-M4677
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	299909 (SGN) 123738 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U204994	-	-	-
Lycopersicon Combined	Single	SGN-U214848	-	-	-
Solanum tuberosum	Single	SGN-U244929	-	-	-
Arabidopsis	Single	At5g42740 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49300)
Chromosome 12
Position 5.27 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47240)
Chromosome 12
Position 54.60 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tobacco N. acuminata
Map version 89 (location: 46535)
Chromosome 9
Position 11.70 cM
Confidence CF(LOD3)
Protocol PCR

Tobacco N. acuminata

Map: Pepper Capsicum
Map version 65 (location: 42691)
Chromosome 3
Position 86.40 cM
Confidence uncalculated
Protocol PCR

Pepper Capsicum

Map: Pepper-COSII
Map version 58 (location: 41534)
Chromosome 3
Position 53.00 cM
Confidence I(LOD2)
Protocol PCR

Pepper-COSII

PCR data Exp. ID 43510

Forward primer (5'-3')

AGCACCATTTGAGAAAAATATACCTG

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

ATCCAAGGAATGAAACATTCCACAC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38861)
Chromosome 12
Position 54.50 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39967

Forward primer (5'-3')

AGCACCATTTGAGAAAAATATACCTG

Accessions and product sizes

Solanum pennellii TA56

450

Solanum lycopersicum TA209

450

Approximate temperature

55°C

Reverse primer (5'-3')

ATCCAAGGAATGAAACATTCCACAC

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27403)
Chromosome 5
Position 17.16 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11901
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 850	Approximate temperature 55°C

PCR data Exp. ID 11902
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 850	Approximate temperature 55°C

PCR data Exp. ID 11903
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 850	Approximate temperature 55°C

PCR data Exp. ID 13859
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 750	Approximate temperature 55°C

PCR data Exp. ID 13860
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Solanum melongena TA2986: 650	Approximate temperature 55°C

PCR data Exp. ID 13861
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1650	Approximate temperature 55°C

PCR data Exp. ID 13862
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1000	Approximate temperature 55°C

PCR data Exp. ID 13863
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1000	Approximate temperature 55°C

PCR data Exp. ID 13864
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1000	Approximate temperature 55°C

PCR data Exp. ID 13865
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1000	Approximate temperature 55°C

PCR data Exp. ID 13866
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Petunia axillaris subsp. parodii TA3310: 650	Approximate temperature 55°C

PCR data Exp. ID 13867
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 650	Approximate temperature 55°C

PCR data Exp. ID 13868
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Coffea canephora BP409: 550	Approximate temperature 55°C

PCR data Exp. ID 32658
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 750	Approximate temperature 55°C

PCR data Exp. ID 33261
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 750	Approximate temperature 55°C

PCR data Exp. ID 33262
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 750	Approximate temperature 55°C

PCR data Exp. ID 33263
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1000	Approximate temperature 55°C

PCR data Exp. ID 33264
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3347: 1000	Approximate temperature 55°C

PCR data Exp. ID 33265
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1000	Approximate temperature 55°C

PCR data Exp. ID 33266
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1000	Approximate temperature 55°C

PCR data Exp. ID 11904
Forward primer (5'-3') AGCACCATTTGAGAAAAATATACCTG	Digested band sizes (using AluI) Solanum lycopersicum LA925: 320+420 Solanum pennellii LA716: 320+520	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCCAAGGAATGAAACATTCCACAC	Enzymes All possible enzymes for pennellii and and lycopersicum: AluI
Accessions and product sizes Solanum lycopersicum LA925: 850 Solanum pennellii LA716: 850	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U214848
SGN-U270415

Overgo hybridization and physical mapping

C2_At5g42740 was used as an overgo probe on plate 13 [well E11]

Plausible BAC Matches: P208M14, P069M12, P036N05, P155M10, P018B15, P104J17, P176F21, P007F23, P163E02, P232P05, P315J01, P077B14, P279A21, P261F24, P131O19, P049O20, P061A01, P305E09, P309C07, P049J09, P199M12, P070K23, P216N06, P104H19, P069K15

Overgo Sequences

A sequence

TGGTATAGGTGGCAGTTTCTTGGG

B sequence

GTGTACGAACAAAGGGCCCAAGAA

AB sequence

TGGTATAGGTGGCAGTTTCTTGGGCCCTTT

Marker sequence

ATGGCTTCATCTGCTTTAATTAGCGATACTCAGTCATGGAAGGATTTGCG
AGCTCATGTTGAAGAAATTAACAAAACTCATTTGCGTGATTNNNNNTGTT
GAATCACACTGATCGATGTCAATCAATGATGGTGGAGTTTGATGGGATTC
TGNNNNNATCGATTACTCGAGACAAAGAGCCACCCTTGATACATTGAAAA
AGCTCTTCAATTTAGCTGAGGCAGCACATGTTAANNNNNGGAGAAGATTA
TTCGGATGTTCAATGGAGAGCATATAAACAGCACAGAAAACAGACCCGTT
CTTCATGTTGCACTGCGTGCTNNNNNCCAAGGGATGCAGTCATAAATAGT
GACGGGAAGAATGTTGTTCCTGAGNNNNNGTTTGGCATGTACTTGATAAG
ATCCGAGACTTCTCTGAGAGGGTTCGCAGTGGTTCCTGGGTTGGAGCCAC
AGGAAAAGCATTGAAAGATGTTGTAGCTGTTGGTATAGGTGGCAGTTTCT
TGGGCCCTTTGTTCGTACACACAGCACTTCAAACANNNNNGAAGCGGAGG
CTAGTGAGTGTGCAAGAGGGCGCCAGTTGCGATTTCTCGCGAATGTTGAT
CCAATTGATGTAGCCCGAAATATAACAGGCTTGAATCNNNNNCTGAAACA
ACTCTAGTTGTGGTGGTCTCAAAGACTTTTACTACNNNNNAGCCGAGACA
ATGCTAAATGCCCGTACAATGAGGGAATGGATCTCCTCTGCATTAGGACC
TCAGGCAGNNNNNTTGCAAAGCATATGGTTGCAGTTAGTACCAATCTTAA
GCTCGTAGAACAATTTGGCATTGATCCAAATAATGCATTCGCTTTCTGNN
NNNGGACTGGGTAGGAGGTCGATTTAGTGTCTGCAGTGCAGTTGGAGTAT
TGNNNNNCCTCTTTCTCTGCAATATGGTTTTTCCATTGTTGAGAAATTTC
TGAAGGGAGCTTCAAGTGTTGATCAGCATTNNNNNTCCTCTCAGCACCAT
TTGAGAAAAATATACCTGTGCTTTTAGGCTTGCTGAGTGTGTGGAANNNN
NTGTTTCATTCCTTGGATATCCAGCAAGAGCAATATTACCCTATTCTCAA
GCACTGGAGAAGTTGGCANNNNNCCTCATATTCAACAGGTCAGTATGGAG
AGTAATGGGAAAGGGGTGTCAATTGATGGTNNNNNGTCCCTCTTCCTTAT
CAGACTGGTGAAATTGACTTTGGTGAACCAGGGACGAATNNNNNGGCCAA
CACAGCTTTTACCAATTAATTCACCAGGGCCGTGTTATTCCTTGTGATTT
TATTGGTGTTGTTAAGAGTCAGCAGCCTATTTACCTAAAAGATGAAGTGG
TGAATAACCATGATGAGCTCATGNNNNNTCGAACTTCTTTGCGCAGCCAG
ATGCCCTTGCTTATGGGAAGACACCAGAGCAGTTGCAAAAGGNNNNNAGA
ATATTCCTGAGCATCTTGTTTCTCATAAGACATTTTCTGGAAATCGACCT
TCTCTAAGTATACTACTTCCANNNNNTCATTGTCTGCTTACAATATTGGA
CAGTTACTGGCCATCTACGAGCACAGAGTTNNNNNGCAGTCCAAGGCTTC
GTATGGGGTATCAATTCTTTTGATCAGTGGGGTGTGGAGCTAGGAAAGTC
TCTANNNNNGCGACTCAAGTTAGAAAGCAACTTCATGCATCTCGTAAGAA
AGGAGAATCAGTTGAAGGCTTCAATTTCAGCACCAAAATGTTGATAACAA
GATATCTCGAGGCAAGTGCTGATGTTCCTTCTGATCCTTCAACTCTTCTG
CCAAATATATGANNNNN

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