Sol Genomics Network

SGN Marker C2_At5g44200

SGN-M4645
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	309104 (SGN) 129995 (CGN)	-	-	-
Lycopersicon Combined	Single	SGN-U227678	-	-	-
Solanum tuberosum	Single	SGN-U253465	-	-	-
Arabidopsis	Single	At5g44200 on TAIR	-	-	-

Mapped locations

Map: Tomato - Kazusa and SolCAP markers mapped to genome
Map version 105 (location: 49301)
Chromosome 2
Position 28.93 MB
Confidence uncalculated
Protocol CAPS

Tomato - Kazusa and SolCAP markers mapped to genome

Map: Kazusa F2-2000 genetic map
Map version 103 (location: 47241)
Chromosome 2
Position 13.00 cM
Confidence uncalculated
Protocol unknown

Kazusa F2-2000 genetic map

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46770)
Chromosome 5
Position 52.80 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Pepper-COSII
Map version 58 (location: 41536)
Chromosome 2
Position 0.00 cM
Confidence F(LOD3)
Protocol PCR

Pepper-COSII

PCR data Exp. ID 43512

Forward primer (5'-3')

TTATGGAAAATTGGTCCAAAAGGA

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

ATCTTCCCTGTGTCGCTTGCGATG

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38865)
Chromosome 2
Position 9.00 cM
Confidence I(LOD2)
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39970

Forward primer (5'-3')

TCGTGGAGGCTCTTATCGACATGG

Accessions and product sizes

Solanum pennellii TA56

150

Solanum lycopersicum TA209

150

Approximate temperature

50°C

Reverse primer (5'-3')

ATCTTCCCTGTGTCGCTTGCGATG

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

150

Solanum pennellii TA56

110

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 27422)
Chromosome 5
Position 17.82 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 11912
Forward primer (5'-3') TCGTGGAGGCTCTTATCGACATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCCCTGTGTCGCTTGCGATG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 150	Approximate temperature 50°C

PCR data Exp. ID 11913
Forward primer (5'-3') TCGTGGAGGCTCTTATCGACATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCCCTGTGTCGCTTGCGATG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 150	Approximate temperature 50°C

PCR data Exp. ID 11914
Forward primer (5'-3') TCGTGGAGGCTCTTATCGACATGG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCCCTGTGTCGCTTGCGATG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 150	Approximate temperature 50°C

PCR data Exp. ID 11915
Forward primer (5'-3') TCGTGGAGGCTCTTATCGACATGG	Digested band sizes (using HinfI) Solanum pennellii LA716: 110 Solanum lycopersicum LA925: 150	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') ATCTTCCCTGTGTCGCTTGCGATG	Enzymes All possible enzymes for pennellii and and lycopersicum: HinfI
Accessions and product sizes Solanum pennellii LA716: 150 Solanum lycopersicum LA925: 150	Approximate temperature 50°C

Unigene blast matches for primers

SGN-U227678

Overgo hybridization and physical mapping

C2_At5g44200 was used as an overgo probe on plate 13 [well B4]

Plausible BAC Matches: P165O24, P177F21, P038M12, P074H18, P023E12, P082H04, P210F16, P076J16, P073M09, P285H08, P191K05, P242F12, P216B16, P051E01, P117P22, P120B14, P019O07

Overgo Sequences

A sequence

ATGGTGGAAACCATGGTCGTGGAG

B sequence

CCATGTCGATAAGAGCCTCCACGA

AB sequence

ATGGTGGAAACCATGGTCGTGGAGGCTCTT

Marker sequence

NNNNNNNNNNNNNNNNNNNNGTGGATTATGGTACAGGATCGTTGGGCGCG
TACCCACCAGTTATGCCGCCACCTCNNNNNACTATGGTAGACATAATGGT
GGAAACCATGGTCGTGGAGGCTCTTATCGACATGGTAGAGNNNNNACTAT
CATCGCAAGCGACACAGGGAAGATGACCACCATCGGCCAGATTATCCAAA
GAGGACTTATGAGCGTGAATCTAGGAGAAACTCTGATCATGAATCTAGAC
CGNNNNNGAAAAGAATCCGCGTTTCCGTGAGAGTGGTGATTCTGATGAAG
AGGATGATGATGATAGGAAGCGGCGTACCTAG

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