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

>Osa04LNT0253100.1

CAATCATCACAATCCGTTTTGTCCGTCGTGGTGCGTCTTCTCGGTCTCGCGTGCATAACCCGCTGTTGACGCCAAAAATACACACTGGCCTGGGAGATCTGCTTAGCTCCAGTGCAGGTCCAAGACTTGATGAGATACGAGCGTGCCAATCAGTTTAATCCTGCAACTAGGCTTGCTGCTACTGGGGGACCTCAATATTGGGTTGTCTCTGGCCTTTATCTTGCTTGCTGCCGTTCACCCATCGCCAACTTCCGCCTTGCTGGCCACCCCGTGCTAGATCCATAGTTGCCATGGCCACCGTCGCCTGTGTTCTCCTCGTCTTCACCGTCGTCGTTGCGGTGTTCCCGGCATCGGTGCAGACAACAGGCACCGTGGGCGGCTAGCGCGAGGCGGGCAGAAGGTGAGGCAGTAGGCGCAAGCGACGAGGCACATGTTGGGGCAGTTGGAAGGGCAGGAGACGACGCAGGGGCGGCAGCCGGTGTTGGTGCAGGTGACCTGGTAGTCACGCTTGTGGTGGGGGCTAAAGGTGATGGTGGTCAGCTTCGTCTTCGGCGGGAGCTTCGGCTGCACGCGGGGCTTCGCATTCGGCGACACCAGCGGGCTCGACGCCGCCACGGAGACCAACGACGACGCCGTAGAGCTTGATGGAGAGGACACGCTCAGGATGGAGGATGGGAGGAGGAGTAGAGAAGACGGAAGCGGAGGCTGAGGAACGAGCCGGTGGCGACTCGCTTGGTCGGTGGAAGCGAGATTGGGATGGACGGGTGGTGCTCGGT

Coding Potentia
Explanation CPC Score
noncoding -1.06456
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0253100.1 4 9676413 T C
Osa04LNT0253100.1 4 9676452 T C
Osa04LNT0253100.1 4 9676917 T C
Osa04LNT0253100.1 4 9677465 A G
Osa04LNT0253100.1 4 9677509 G A
Osa04LNT0253100.1 4 9677554 T C
Osa04LNT0253100.1 4 9677722 A G
Osa04LNT0253100.1 4 9677822 T C
Osa04LNT0253100.1 4 9678517 T C
Osa04LNT0253100.1 4 9676679 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0253100.1 osa-miR160c-3p Cleavage 5.0 23.639 1 21
Osa04LNT0253100.1 osa-miR167a-5p Cleavage 5.0 23.683 1 21
Osa04LNT0253100.1 osa-miR167b Cleavage 5.0 23.683 1 21
Osa04LNT0253100.1 osa-miR167c-5p Cleavage 5.0 23.683 1 21
Osa04LNT0253100.1 osa-miR5504 Cleavage 5.0 24.334 1 21
Osa04LNT0253100.1 osa-miR5819 Cleavage 3.5 22.004 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0253100.1 4 qPEN-4 Morphological trait Panicle/flower RG190 RG908
Osa04LNT0253100.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0253100.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0253100.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0253100.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0253100.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0253100.1 4 qCER4-1 Morphological trait Shoot/Seedling RG190 RZ69
Osa04LNT0253100.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0253100.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0253100.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
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