Sol Genomics Network

SGN Marker C2_At1g61620

SGN-M3879
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	302818 (SGN) 125016 (CGN)	-	-	-
Capsicum annuum	Single	SGN-U197742	-	-	-
Lycopersicon Combined	Single	SGN-U216182	-	-	-
Solanum tuberosum	Single	SGN-U248230	-	-	-
Arabidopsis	Single	At1g61620 on TAIR	-	-	-

Mapped locations

Map: Tobacco N. tomentosiformis
Map version 91 (location: 46599)
Chromosome 2
Position 6.70 cM
Confidence F(LOD3)
Protocol CAPS

Tobacco N. tomentosiformis

Map: Tomato-EXPEN 2000
Map version 52 (location: 38222)
Chromosome 3
Position 106.00 cM
Confidence I
Protocol CAPS

Tomato-EXPEN 2000

PCR data Exp. ID 39494

Forward primer (5'-3')

ATGCATTCTAGAATGCCTTTTGTC

Accessions and product sizes

Solanum pennellii TA56

340

Solanum lycopersicum TA209

320

Approximate temperature

55°C

Reverse primer (5'-3')

TCCCTGGCTTTCTGCAGCATC

Digested band sizes (using amplicon difference)

Solanum lycopersicum TA209

320

Solanum pennellii TA56

340

Mg⁺² concentration

1.5mM

Enzymes

Map: Arabidopsis COSII
Map version 44 (location: 25335)
Chromosome 1
Position 22.74 MB
Confidence uncalculated
Protocol CAPS

Arabidopsis COSII

Other PCR data

PCR data Exp. ID 10319
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 3mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 340	Approximate temperature 55°C

PCR data Exp. ID 10320
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 3mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 320	Approximate temperature 55°C

PCR data Exp. ID 12754
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Solanum tuberosum TA3427: 1500	Approximate temperature 55°C

PCR data Exp. ID 12755
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Capsicum annuum TA3428: 1700	Approximate temperature 55°C

PCR data Exp. ID 12756
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1700	Approximate temperature 55°C

PCR data Exp. ID 12757
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1700	Approximate temperature 55°C

PCR data Exp. ID 12758
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1700	Approximate temperature 55°C

PCR data Exp. ID 12759
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Nicotiana plumbaginifolia TA3354: 1700	Approximate temperature 55°C

PCR data Exp. ID 12760
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Petunia x hybrida TA3311: 650	Approximate temperature 55°C

PCR data Exp. ID 32221
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 3mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1600	Approximate temperature 55°C

PCR data Exp. ID 32603
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Solanum lycopersicum LA925: 1500	Approximate temperature 55°C

PCR data Exp. ID 32817
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Solanum pimpinellifolium LA1589: 1500	Approximate temperature 55°C

PCR data Exp. ID 32818
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Solanum pennellii LA716: 1500	Approximate temperature 55°C

PCR data Exp. ID 32819
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Nicotiana sylvestris TA3346: 1700	Approximate temperature 55°C

PCR data Exp. ID 32820
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Nicotiana tomentosiformis TA3349: 1700	Approximate temperature 55°C

PCR data Exp. ID 32821
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC		Mg⁺² concentration 1.5mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes
Accessions and product sizes Nicotiana otophora TA3350: 1700	Approximate temperature 55°C

PCR data Exp. ID 10321
Forward primer (5'-3') ATGCATTCTAGAATGCCTTTTGTC	Digested band sizes (using amplicon difference) Solanum lycopersicum LA925: 320 Solanum pennellii LA716: 340	Mg⁺² concentration 3mM
Reverse primer (5'-3') TCCCTGGCTTTCTGCAGCATC	Enzymes All possible enzymes for pennellii and and lycopersicum: amplicon difference, HaeIII, DpnII
Accessions and product sizes Solanum pennellii LA716: 340 Solanum lycopersicum LA925: 320	Approximate temperature 55°C

Unigene blast matches for primers

SGN-U216182
SGN-U272294

Overgo hybridization and physical mapping

C2_At1g61620 was used as an overgo probe on plate 12 [well H2]

Plausible BAC Matches: P286H14, P024I16, P284H16, P096I05, P283O10, P256K09, P183L18, P126D19, P018N14, P187L20, P054D24

Non-Plausible BAC matches

P078P08, P059M17, P124N18, P156O06, P166G08

Overgo Sequences

A sequence

TGGAAAAGGGAGGAACAGGGTTTG

B sequence

TTATCTCCATGGGCAGCAAACCCT

AB sequence

TGGAAAAGGGAGGAACAGGGTTTGCTGCCC

Marker sequence

ATGCCGCAGAGACACTCGAAGAACAACAACGATCTTGCCTTCTTTACGTA
CGATGAGAAGAGAAAGTTAGGGTATGGAACACAAAAGGAGAGGCTGGGAA
AAGATTCAATCAAGCCATTCGATGCTTGTTCCCTTTGTTTAAAACCCTTC
ATCGATCCGTTGTGTTGCCAGAAAGGGCATGTCTTTTGCAAAGAATGCAT
TCTAGAATGCCTTTTGTCCCAGAAAAAGGATATCCAAAGANNNNNAAGTT
AGCTGCTCATACAGGTCAGCAGAAGCAAGAAAAAGAAGAGGAAGAGGAGA
GGTTGATGCTGCAGAAAGCCAGGGATCTTGATGCATTTGATCAACAAAAT
CATGGTCCAGTTCCGCAGTACAATGATAAGAACTACAACAGAGACAAAAA
TGGATTCCATGGAGCTAACAGTGTGAAAGCTACTTCTTATGAGGAGGAAG
CACTTAGAACCATGAAAGCATTTTGGCTGCCCTCTGCAACACCAGATGCA
CCTGCTAAGGTGGAAGCCCCATCCACTAGCACAACTTGTCCTGAAGGGAG
GGAAAAAATTAAGATGAAAAACCTTTTCCCTATACACTTCACTGAAGATA
CAAGTGCACAGAAGAAACACAAGTCTCTTGACAAGAGTTTCATATGTCCC
AGTTGCAAGGTCACACTAACCAATACTTTGTCACTTGTAGCACTTAATAC
TTGTGGACATGTCTTCTGCAAGAAATGTGCAGAAAAATTTGTGGCTGTTG
ACAAGGTTTGCGTGGTCTGTGACAAACCATGTAAAAATAGAAATCTGGTG
AATGTGGAAAAGGGAGGAACAGGGTTTGCTGCCCATGGAGATAATCTTGA
AGCAAAAGACTTCAAACACTTGGGGAGTGGAAGT

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_At1g61620

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