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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa05LNT0319400.1

GCAGCATATTCATCCATTCATAGCCACAAAATAAGTCTGCTAGTGTAGACAAGATGCAAAATAAATAGAACAGTAAAAACAGCTGTTAAGGGTAGATTAGTTGAGCTTTTATACAAACTCGGAAGAAAGAATAGTAACTGATGGCAGCTACATGAAAGAATCATAAAAACCGGTGGCGGCTACATGCCCGGCCTTAAACGTAGATCCATCTTCTGGGTGCTTAATCTCTTCGCTACATCCATAGCAGTGCTTGCCATCTATAGGCGGATTTTGGAGATCCAGACACACCACATACTCGTCATTAATAAAGGAGCGTCCCCCAATTCTCCTTTTCTCCTCAAGAGATACAATGCAGGTCGGCACCATATCATAGTTCTTGGGATCCCAACAAACTTCGGCGAAAAATAGCTCTTCCTTTGAATCTAAAGATGCTATGAAGTTGACATGTCCATATTTCTCACCCTTCTCTCTAATTGTACTGCTTTTTAAGGCTTTGATTAAGCTGTATTGAATCTTATTGTTTTCATCCTTGTTATAGTAATCCAAAGCACTACTTGCATACTCATTAGACTGACGTTGTGCAGCTGCAACAAGATCAATATTGCCATACAACTGTTTTGGTTGAGCTTTAGTTGCAGTCATAAAGCTATCAACCAAATAGTTAAAATATGGATCACAATCATCGTCTGAAGAATCCACCACTTCATCTTCCTTATCTGATCCATGTGTATCAGATAATTTCTCAGAATGCCTCTGGAGATCAGAGAGAGGCAGAGATGATAGCAGCATCAGAGATGATACTAAATATTGTCTTTTGCTCTGGAGATTAGAGAGAGGTAGTACTCCTGAGCTTCCTGGGACAGCTGGGATATCTTCTGTTGGTGGTGGCGGCACAGACCTGTTGGGATTACGCCAGTCCCACACCCAATCCAAGCCGAAGCCGGCACCACTACCGCCACTCCTCCCACCCATCGGAATGCCGCCCTCCTGGTCAGCGCCGGCACCACCACTGCCCCTCCTCCCACCCATCGGAACGCCGTGCTCCTTGTTAGTGCCGGCATCGCCACTGCCCCTACTCCCACCCATCGGAACGCCGCCCTCCTGGTCAGCGCCAGCGCCACCACTGCCCCTCCTCATACCCATCGGAACGTCGCCCAGTGGCACCAGAGATGGTAGTAAAGATTGTCTTTCGCTGAAATAACCATTGCATATACTTTGTAATTATCATAAGTCTGAACTAGGGGCAAAAGGTAGCTTCAGTTCGCAAAAAAAAAAAAACAGGGACAAAATCACAAAGTAAGAAAAAGGAGGACATAATCATGATTGAGCACCAAATTAAGTTGGGTAAAAACATCATCGCCCCATTCTTATTCTATATATCCTAGTTAATGAGATGAACCAGTGCAGATAGAGATAGGTACACCATTTCCCCATTCTTACTCTATATATTGTCTAGAGTAAAATTGTTGAATCTGTGCAGATTTCGGTAACTAGAAGATGTACAGATGTCGATAGAGATAACTAGAAGTAGAGATGAGTGACATATACTTCTCGAAATCAGAGAGAAGCGAGAGAAGCAGTGCTCGCGAGCTTCCTGGAACAGCTAGGATATCTTCTGTTGGAACGCCACCCTTCTGGCCGACGCCGGCGTCACCAGTTCACCACCGCCCCTCCTCCCACCCATCGGAACGCCGCCCTCCTGGCCGGCATCGGAGACAACAGATTGTACCCATCGGAACGCCACCCTCCTGCTGTCCGGCGCCTCCACCCTCCTGCTGTCCGGCGCCTCCACCCTAATCGCAAGCGACGCCACGGCCAACCTCCTCGCCGGCGCTCCTCTCCATCGGCGGAACTAGGGCTTGTTTGCTTTCCCCTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.918596
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0319400.1 5 26996345 T C
Osa05LNT0319400.1 5 26996090 A T
Osa05LNT0319400.1 5 26997901 A C
Osa05LNT0319400.1 5 26998042 C T
Osa05LNT0319400.1 5 26998043 G A
Osa05LNT0319400.1 5 26998292 T C
Osa05LNT0319400.1 5 26998492 C A
Osa05LNT0319400.1 5 26998461 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa05LNT0319400.1 osa-miR1437b-5p Cleavage 5.0 22.573 1 21
Osa05LNT0319400.1 osa-miR167e-3p Cleavage 3.5 15.687 1 21
Osa05LNT0319400.1 osa-miR167i-3p Cleavage 3.5 15.687 1 21
Osa05LNT0319400.1 osa-miR166i-5p Cleavage 3.5 16.119 1 21
Osa05LNT0319400.1 osa-miR5511 Cleavage 3.0 22.965 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0319400.1 5 qml5-4 Morphological trait Shoot/Seedling C246 RM274
Osa05LNT0319400.1 5 qGT5-1 Physiological trait Eating quality RM538 RM480
Osa05LNT0319400.1 5 qRGR-5 Physiological trait Germination/dormancy RM421 RM480
Osa05LNT0319400.1 5 qRFC-5 Physiological trait Eating quality RG470 RG474
Osa05LNT0319400.1 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0319400.1 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0319400.1 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0319400.1 5 nan Physiological trait Eating quality RM163 RM31
Osa05LNT0319400.1 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0319400.1 5 QFla5 Morphological trait Culm/leaf RG470 RG346
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus