Nama : Usamah Jaisyurahman/A253150376

Oryza sativa isolate 52694 blast resistance protein Pi54 variant gene,
partial cds
GenBank: KR052929.1

LOCUS

KR052929 991 bp

DNA

linear PLN 24-NOV-2015

DEFINITION

Oryza sativa isolate 52694 blast resistance protein Pi54 variant gene, partial cds.

ACCESSION

KR052929

VERSION

KR052929.1 GI:953697188

KEYWORDS
SOURCE

Oryza sativa (rice)

ORGANISM Oryza sativa

Eukaryota;

Viridiplantae;

Streptophyta;

Embryophyta;

Tracheophyta;

Spermatophyta;

Magnoliophyta; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae;

Oryza.
REFERENCE 1 (bases 1 to 991)
AUTHORS

Vasudevan,K., Gruissem,W. and Bhullar,N.K.

TITLE

Identification of novel alleles of the rice blast resistance gene Pi54

JOURNAL

Sci Rep 5, 15678 (2015)

PUBMED

26498172

REMARK

Publication Status: Online-Only

REFERENCE 2 (bases 1 to 991)

AUTHORS

Vasudevan,K., Gruissem,W. and Bhullar,N.K.

TITLE

Direct Submission

JOURNAL

Submitted (01-APR-2015) Department of Biology, ETH, Universitaetsstrasse 2, Zurich

8092, Switzerland

COMMENT

##Assembly-Data-START##

Sequencing Technology :: Sanger dideoxy sequencing

##Assembly-Data-END##
FEATURES
source

Location/Qualifiers
1..991
/organism="Oryza sativa"
/mol_type="genomic DNA"
/isolate="52694"

/db_xref="taxon:4530"
mRNA

<1..>991
/product="blast resistance protein Pi54 variant"

CDS

<1..>991
/note="coiled-coil nucleotide-binding-site leucine
rich repeat protein"
/codon_start=1
/product="blast resistance protein Pi54 variant"
/protein_id="ALO78750.1"
/db_xref="GI:953697189"
/translation="MSELQSLPDLNRLSLVNLEKVSDTEDARMAKLQEKEKLETLMLR
WNMDAGNASRIDHEVLETLQPSQCLKTLEIVAYEGHVFPSWITSTEPYLTSLVEIRLV
NLRSCENALPPLGLLPCLKIVEISRVDNISCIDDNFYGHNGTFPSLEKLILSFMTSLE
VWEQSSRMNLFPRLAELVIIQCPKLRALHMEFPSIEKLILWMNNKMLYRSKEGLRGVE
KSLENLSISFCEELHASSGCEGLQALDRLKKLEICGCHELSCLPQGLQHLSSLTSLKI
DNCNKLEILPEWLENLPFLQIMCLSGCPILHSIPEGLTCSDIIVEDCPNFKEPS"

ORIGIN OF NUCLEOTIDE
1 atgtcagagc ttcaatcact gccagacctc aatagactat cactagtgaa ccttgaaaag
61 gtttcagaca ctgaagatgc aagaatggca aaacttcaag agaaagaaaa gctcgagaca
121 ttgatgttga ggtggaatat ggatgctgga aatgccagta gaatagatca tgaagtactt
181 gaaacccttc aacctagcca gtgcctgaaa actttggaga ttgttgcgta tgaaggacat
241 gtatttccat cttggataac aagcactgag ccatatctca catctctggt tgagataagg
301 ctggttaatc tgagatcatg tgaaaatgct ttacctccac ttgggctact gccatgtctg
361 aagattgtgg agataagccg agttgataat atcagttgta ttgacgataa tttctatggt
421 cacaacggta catttccttc actggagaag ctgattctct cattcatgac tagccttgaa
481 gtctgggaac agtcatctag gatgaatctg tttcctcgtc ttgcagaact tgtcatcatt
541 cagtgcccaa aattgagagc actgcatatg gagtttccat cgattgaaaa attgattttg
601 tggatgaata acaagatgtt gtacagatca aaggaaggtc tgagaggtgt agagaagagc
661 ctcgaaaatc tttcaatttc tttctgtgaa gagttgcatg cttcttcagg ctgtgagggt
721 ctacaggctc ttgatcgcct caagaagttg gagatatgtg gttgtcatga attgtcatgc
781 ctcccacagg gtttgcagca tctttcctct ctcaccagct tgaaaattga taactgcaac
841 aaattggaga ttttgccaga atggttggag aacctacctt ttctacagat aatgtgtttg
901 tctggctgtc caattctgca ctccattcct gaaggcctga catgtagcga cattattgtt
961 gaagattgcc ccaattttaa agaaccatca g

PRIMER
Input PCR template
KR052929.1 Oryza sativa isolate 52694 blast resistance protein Pi54 variant gene, partial cds
Range
1 - 991
Specificity of primers
Primer pairs are specific to input template as no other targets were found in selected database: Refseq mRNA (Organism limited to Oryza
sativa)
Parameter and details
Parameter name
Number of Blast hits analyzed
Entrez query
Min total mismatches
Min 3' end mismatches
Defined 3' end region length
Mismatch threshold to ignore targets
Max target size
Max number of Blast target sequences
Blast E value
Blast word size
Max candidate primer pairs
Min PCR product size
Max PCR product size
Min Primer size
Opt Primer size
Max Primer size
Min Tm

Parameter value
305032
2
2
5
6
4000
50000
30000
7
500
70
1000
15
20
25
57

Opt Tm
Max Tm
Max Tm difference
Repeat filter
Low complexity filter

60
63
3
AUTO
Yes

Detailed Primer Report

Primer
Pair
1

Sequence (5'->3')
Forward primer
Reverse primer
Internal oligo
Product length

TGCCATGTCTGAAGATTGTGG
TGTAGACCCTCACAGCCTGA

Forward primer
Reverse primer
Internal oligo
Product length

GCCATGTCTGAAGATTGTGGAG
TCGCTACATGTCAGGCCTTC

Forward primer
Reverse primer
Internal oligo
Product length

GCCATGTCTGAAGATTGTGGA
TGCAGAATTGGACAGCCAGA

Forward primer
Reverse primer
Internal oligo
Product length

ACTGCCATGTCTGAAGATTGTG
CCCTCACAGCCTGAAGAAGC

Forward primer
Reverse primer

AACCTAGCCAGTGCCTGAAA
ACTCGGCTTATCTCCACAATCT

Template
strand

Length

Start

Stop

Tm

GC%

Self
complementarity

Self 3'
complementarity

Plus
Minus
Plus

21
20

350
725

370
706

58.56
59.89

47.62
55

4
5

2
3

Plus
Minus
Plus

22
20

351
950

372
931

59.32
59.82

50
55

4
6

1
2

Plus
Minus
Plus

21
20

351
920

371
901

58.28
59.6

47.62
50

4
4

0
1

Plus
Minus
Plus

22
20

348
719

369
700

58.92
60.68

45.45
60

4
5

0
2

Plus
Minus

20
22

191
383

210
362

59.23
58.97

50
45.45

5
2

0
1

376

600

570

372

Internal oligo
Product length
6

10

Plus
193

Forward primer
Reverse primer
Internal oligo
Product length

TGGGCTACTGCCATGTCTGA
CACCTCTCAGACCTTCCTTTGAT

Forward primer
Reverse primer
Internal oligo
Product length

TGAAGATTGTGGAGATAAGCCGA
CAGCCTGAAGAAGCATGCAA

Forward primer
Reverse primer
Internal oligo
Product length

AACCTAGCCAGTGCCTGAAAA
ACTCGGCTTATCTCCACAATCTT

Forward primer
Reverse primer
Internal oligo
Product length

CCTAGCCAGTGCCTGAAAAC
TCGGCTTATCTCCACAATCTTCA

Forward primer
Reverse primer
Internal oligo
Product length

CCTAGCCAGTGCCTGAAAACT
AACTCGGCTTATCTCCACAATCT

Plus
Minus
Plus

20
23

342
649

361
627

60.91
59.74

55
47.83

4
5

3
2

Plus
Minus
Plus

23
20

359
713

381
694

59.55
59.11

43.48
50

2
6

0
2

Plus
Minus
Plus

21
23

191
383

211
361

59.86
59.55

47.62
43.48

5
2

0
2

Plus
Minus
Plus

20
23

193
381

212
359

58.83
59.55

55
43.48

5
2

0
1

Plus
Minus
Plus

21
23

193
384

213
362

60.27
59.55

52.38
43.48

5
2

1
1

308

355

193

189

192