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

>Osa04LNT0255700.1

GGAGTTTAACCTTATATTCTTATAAATACGGACAGCACAAGTGCACAACATCACATCAGCATAGCACCTCGATAGATTGGCAAACAGAACAAATGGATGCTTGCCGGCTTCATCCAATTGGAACTGCTCGATTTAATTCTTGTCGTCTTCACCATTAGCTTCAGCATTGAAAGGTAGGCCTTCCGCCTATCTCAGACTCTCAGCTCAACCTTCATCAGAAGAAATCCTGGAGTCCCCGGCCGGCGAAGACGCGGTCGGAGAGCTCGGCGAGGAGCGCGTTGACGGAGAGCAGCGCGGCGGTGGAGCCCGCGATGACGCCGAGCACCACGCCGGTGGTGCCCACCACCTTCCCGGGCGCCGGCCACTCGATCTCCGACATCTCCTGCGCGGCGCCGGCCCACCACCCGCCGCCGCCGGCCGCGGCCTCCGCCTCCTTCCGCGCCCGCAGCACCTCCTTCAGCTCCGCCGCCACCGCCTCGGGGCTCTTCTCCCCTCCTCCTCCTCCTCCCGCCACCACCTCCCCGGCCTCCTCCGCGCCGTCCACCGCCGTGGCGGACGCCTCCTGCTGCTCCTGCTCCTGCCCCTTCTTGTCCTCCGCCGCGCCTGCGCCTGCGCCCTTGGACTTGGAGGCCGCGCGGGCGAGGCGGCCGCGGCAGCCGGCGGCGGAGCGGGAGAGGGATAGGGAGATCGCGGGAGGGCGGAGGGTGGAGAAGGAAGCGCGCGTGGCGGTGGGTGGCGGCGTGCGGCGGCGGCGTGAGGGGTGCGAGGAGGCGGGCGGCGGATGGGGTGGTGGTGGTGGTGGTGGTCGGCGTGGTCGCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.30345
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0255700.1 4 13818382 G C
Osa04LNT0255700.1 4 13818417 G A
Osa04LNT0255700.1 4 13818880 G A
Osa04LNT0255700.1 4 13819505 C A
Osa04LNT0255700.1 4 13818851 C A
Osa04LNT0255700.1 4 13819231 T 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
Osa04LNT0255700.1 osa-miR171b Translation 5.0 16.931 1 21
Osa04LNT0255700.1 osa-miR171c-3p Translation 5.0 16.931 1 21
Osa04LNT0255700.1 osa-miR171d-3p Translation 5.0 16.931 1 21
Osa04LNT0255700.1 osa-miR171e-3p Translation 5.0 16.931 1 21
Osa04LNT0255700.1 osa-miR171f-3p Translation 5.0 16.931 1 21
Osa04LNT0255700.1 osa-miR531a Translation 5.0 24.201 1 24
Osa04LNT0255700.1 osa-miR531b Translation 5.0 24.201 1 20
Osa04LNT0255700.1 osa-miR531c Translation 5.0 24.201 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0255700.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255700.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255700.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0255700.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0255700.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0255700.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255700.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255700.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
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