Sol Genomics Network

SGN Marker C2_At1g07080

SGN-M4694
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	300364 (SGN) 119605 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197797	-	-	-
Lycopersicon Combined	Multiple	SGN-U216215	-	-	-
Solanum tuberosum	Single	SGN-U247392	-	-	-
Arabidopsis	Single	At1g07080 on TAIR	-	-	-

Mapped locations

Map: Eggplant-RAD 2012
Map version 174 (location: 132171)
Chromosome 6
Position 31.33 cM
Confidence uncalculated
Protocol CAPS

Eggplant-RAD 2012

Map: Pepper-COSII
Map version 58 (location: 41290)
Chromosome 6
Position 130.90 cM
Confidence F(LOD3)
Protocol CAPS

Pepper-COSII

PCR data Exp. ID 43266

Forward primer (5'-3')

TTGTGCCATGGGTTGTTGTTGATG

Accessions and product sizes

Approximate temperature

55°C

Reverse primer (5'-3')

TGTAAGCTTTGCAAATGTAGCTTATG

Digested band sizes (using unknown enzyme)

Mg⁺² concentration

Unknown

Enzymes

Map: Tomato-EXPEN 2000
Map version 52 (location: 38070)
Chromosome 6
Position 3.50 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39371

Forward primer (5'-3')

TTGTGCCATGGGTTGTTGTTGATG

Accessions and product sizes

Solanum lycopersicum TA209

650

Solanum pennellii TA56

650

Approximate temperature

53°C

Reverse primer (5'-3')

TGTAAGCTTTGCAAATGTAGCTTATG

Digested band sizes (using amplicon difference)

Solanum pennellii TA56

200+300

Solanum lycopersicum TA209

500

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 24929)
Chromosome 1
Position 2.17 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 9943
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 650	Approximate temperature 53°C

PCR data Exp. ID 9944
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 650	Approximate temperature 53°C

PCR data Exp. ID 9945
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 650	Approximate temperature 53°C

PCR data Exp. ID 12374
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 400+750	Approximate temperature 55°C

PCR data Exp. ID 12375
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 650	Approximate temperature 55°C

PCR data Exp. ID 12376
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 300+650	Approximate temperature 55°C

PCR data Exp. ID 12377
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 650	Approximate temperature 55°C

PCR data Exp. ID 12378
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 650	Approximate temperature 55°C

PCR data Exp. ID 12379
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: Multiple	Approximate temperature 55°C

PCR data Exp. ID 12380
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Physalis TA1367: 300+500	Approximate temperature 55°C

PCR data Exp. ID 12381
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Petunia axillaris TA3309: 600	Approximate temperature 55°C

PCR data Exp. ID 12382
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 600	Approximate temperature 55°C

PCR data Exp. ID 12383
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Petunia integrifolia TA3312: 600	Approximate temperature 55°C

PCR data Exp. ID 32591
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 650	Approximate temperature 55°C

PCR data Exp. ID 32675
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 650	Approximate temperature 55°C

PCR data Exp. ID 32676
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Solanum pennellii LA716: 650	Approximate temperature 55°C

PCR data Exp. ID 32677
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 300+650	Approximate temperature 55°C

PCR data Exp. ID 32678
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 650	Approximate temperature 55°C

PCR data Exp. ID 32679
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 650	Approximate temperature 55°C

PCR data Exp. ID 9946
Forward primer (5'-3') TTGTGCCATGGGTTGTTGTTGATG	Digested band sizes (using HinfI) Solanum lycopersicum LA925: 500 Solanum pennellii LA716: 200+300	Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TGTAAGCTTTGCAAATGTAGCTTATG	Enzymes All possible enzymes for pennellii and and lycopersicum: RsaI, HinfI, DpnII, KpnI All possible enzymes for lycopersicum and pimpinellifolium: RsaI, HinfI, DpnII, KpnI
Accessions and product sizes Solanum lycopersicum LA925: 650 Solanum pennellii LA716: 650	Approximate temperature 53°C

Unigene blast matches for primers

SGN-U234980
SGN-U287893
SGN-U287894

Overgo hybridization and physical mapping

C2_At1g07080 was used as an overgo probe on plate 13 [well H1]

Plausible BAC Matches: None

Overgo Sequences

A sequence

TTGTGCCATGGGTTGTTGTTGATG

B sequence

GTGTAAAGCGGTTGTCCATCAACA

AB sequence

TTGTGCCATGGGTTGTTGTTGATGGACAAC

Marker sequence

NNNNNAATTTGNNNNNAATGAACACTTCCCTTTTATTCACTGTGTGGAAA
GTTTGATCTACCATAAGAATTATACACAATGGGAAACGTGTTTCGAAAAA
CTGAATTTGAGGAAAAAACTCGTTACTGATTGTGTTGGCAGTGACAGAGG
CAAAGAGNNNNNCTTGAACTACGCCACGCAGCTGAGACACCTCCGCATAA
ATTTGTGCCATGGGTTGTTGTTGATGGACAACCGCTTTACACTNNNNNGA
CTACAGGGAATTCATAAGCTACATTTGCAAAGCTTACAAAGGAACCGCGC
CTATCCCCGGTTGTAGCTCATCTGATTCTATAAGTTTCACTTCCAAGTTA
TCAACTATCAGTTCAACAATTACATCATTTGTTGCACAGAGAGTTAAGCT
TGCTGCATCTGCATAA

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_At1g07080

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