Citrus CAPS Marker Database

Locus name: Tf0328

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 62
Main product (bp): 1200
Comment on PCR:
F-primer: CCGCTTGTAAACGAGTCTT
R-primer: ACTTTCAGCTGGCTTGTTACC

EST info

EST Accession number 1: CK938765
EST Accession number 2:

sequence-tagged site (STS seq)

STS:

GCCGGTGATGCCGGTCTTCGAATGGGGAATATGGGTCATGGGTTCGGGGAAAGTTCGGCT
CTCAGAGATGGGTCGATGGGGGAATCAACAGTGACTGAGCAGAGTGGTGGTGGGTGTGGC
AGAAAGAGAAGGGATTTGAGCTCTGAAGATGAATCTTCTAAGATTGTTTCTACTACTAGT
AGTGCCAATGACTTGGTACGTATAATTTTATTTTCCATTAACTTTTTAGTAAATTTATGG
GGTGTTTGAATTTGTCTGGTGGTTAATTGAAAAAATAAAAGTAAGACAAAACATTAAAAA
A

STS source:
STS Forward / Reverse: Foward read

STS:

TTTTTTTGACGCTCAATTGACGGGAGGATTTCCTTTCTTTCAAAGTTACCAGATATTTAG
ATTTTTAAGATTTGAGATTCTGGTTATTGTTCCTTTCTTCCTATTTGATTTATTAGTAAA
TGATTGAAATTAAAATAAAAGAAAGAAAAATTTGATTTAATATTGTTTAGCCTTTTTTTG
TGTGTGTGTGGGTGGTGGGGGTAGAATAAGATGAATCAGAAATGGAAAGAAACAGTTATT
AGGTTGACTCTCAGAATGTGGGTTTTTATGTTGGTGGAGCTCAGGTACATTGGCCATGAT
AATGATGGTTGATCTGTGTTCTGACTTTAGT

STS source:
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Experiments: CAPS pattern of hybrid cultivar

Experiments: CAPS pattern of Citrus collection

Experiments: Segregation pattern

Target on C. clementina (v1.0)

Transcript ID: Ciclev10021606m
Scaffold: scaffold_3
Start: 2530708
End: 2533942

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00509:mRNA_27.1
Scaffold: C_unshiu_00509
Start: 178211
End: 181426
Gene function: Transcription factor bHLH79

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

Km/O41 map info (Nakano et al. 2003)

Km/O41 LG:
Km/O41 cM:

Rp/Sa map info (Ohta et al. 2011)

Rp/Sa LG:
Rp/Sa cM:

CAPS genotyping (Hybrid cv/Citrus collection)

CAPS genotyping:

Cultivar identification (M: Cultivar identification manual / T: Ninomiya et al. 2015/ K: Nonaka et al. 2017)

Cultivar identification M/T/K:

SNP typing by Illumina GoldenGate assay (Fujii et al. 2013)

SNP1: SI039
DNA sequence around SNP1:

GAATGGGGAATATGGGTCATGGGTTCGGGGAAAGTTCGGCTCTCAGAGATGGGTCGATGG
[A/G]GGAATCAACAGTGACTGAGCAGAGTGGTGGTGGGTGTGGCAGAAAGAGAAGGGAT
TTGAG

SNP2: SI180
DNA sequence around SNP2:

TTTTTTTGACGCTCAATTGACGGG[A/G]GGATTTCCTTTCTTTCAAAGTTACCAGATAT
TTAGATTTTTAAGATTTGAGATTCTGGTT

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: