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

>Osa04LNT0254300.2

AACATTGTCCTAAATGACTTCCTTTATGAGTATGGAGGGAGTATTGATCAGTGGTTAATTGGGTTAGCTTGTTAACATGAAATCAACAATAAAATGATATGATTGGGCCAGCCTTACTATTGAAACCAAGAATAAAATGATATGATGGGTGAAATGGTCTATTTCCTATGACATTTCTCAATAATACTAATCTACAATTTGGCTGTCATTCTATGAAAGATTGGAAGTGAGAAAGCACCTGGAAAGAGAAAAACCAAATCATGCGAACTCTTAGTTCCAAAAATGCATGGTTGTACCTTCCTGATAGTGTTTTTATTTTCTGGCAGGGCTCTTAATAGGATTTGAACAATTGAAAATGGCCATGCGTGTGCAACAGGAAATGTAAATTCAGTATGAACCCCACAATAGATACAAAGGAAGAATCTGTATAGCAACACTTCTGAACATTTTTGAAGATACAAACGAAAATATAAATTCAGTATGAACCCAGTAATAGATCATAGGTTAGCTCTTGCAAAGTACAAGTACAAAGAAAATCAGAGGAACAAAGATCCCTCTTGGAATTCAGAAGATCTACTCCAATATTCAGAATGACCAATAATAATTCAAACAGTAGATCTCAGAATCAACTTTTTGTACAATACATAATATCATTAGGTTTCAATAATAAATTATGAGAATAACATTTTTTTTCAAACTAAACAGTAGACCACCATATTTTTATCCTAACTGAACAGTAGACCACAATATTTCCATTTCATCTTTCCCCGGGACAGCATATGCTTTCTCTGATACGGCATGAAAAGAAGAGGACTAATGGTTGAAAAATCTAAAATTTGCACTGGAAAATAGAAGTGAATTTGACAATTGGCATCACACGGAAACACTTTATTCAATCATCCAGATCCATTTCACCCCAAATCCAATCATTTTACTTTTCTATCAACCAACAAAACGGTCACAGTGCACGGCTTCATATGGCACAACTACATTATCTAGAAACGTCATAACTCAAGGAAACATCTATCACCTTGAGAAGAGGTTGACGGTGCTGCATAAATGAAAATATACATGTCACATTTCAGTTAAAAAAAAGTGTTCTTTCAGTCCAAGTTGCATAAACACAAAGTCAGGAATTGTAGGATTTTGTAGGTACAGTTTAATGTTTCTTAAAGATGAACTGACATTCATTTACTCAAATCGTAGGTAAAATCTGACCCCGACGCAAGCACAATTCACATGCTATCTTGCGTGCAAAATGGAAACCTTGACATGGTAGTGCTCACATGCTGTTGACATCAATAGGAGGAATAGAGAGCAGGAGATAGAGTAGGCAGTGTTTTACCTGTTTAGTAAATAGTCTTAGGGAGGTGAGTGCGCCATGGACGAGGTTGCCGGTGGTGTAGTCTGTGCCACGTGAAGGATTATCCCGTGCCAGGGCAAGGCACAGAGTATCTTGGCAACAGATGCAGTTTCAGAGTCTTGACGGCAAATGCAGTTACAGATCGCGGATCAACAGATGCAGTTTATATAGTCACCTTGATATGCCTTAGGAGATCTTTCTTCAAAGCCTAAATCCCAGTGACGCACTAATCATCAATCTGATGAGCTGCTGCTCCTCATGAACATCCCGCGCTTACGAGACGAAGCCCTCCTCGCCTACCAGGGAACCCCACCTCCAGATCGATCGGCAGGGCGTCCAGACGTCTGTCGCTAGCGGCACGCACCCTTCGTCCCTGGAAGCACACCTCCACCGATCCGCCTCGCCCATGCATCAATCGATCAGCCTCGCCCTTCGATTCGACTCGAACTGAGACGGAGGGCAGAGGCGGGAGGGGCGGAGGCCGGGCACCGCGTCGCGCCCTCCAAGCCTGCTCGTCGCTGGCCGTGCGTGGGCGCGCGTGACGCGAGGAGGCCGCGCAGAAGGGAGGAGGAGGAGGAGTCCGTCGAACACCTCGCCCGCGAAGGGAGAAGGGATTTGGGCCGCCTCGCCGGCGACGAGCGCGAGGGGAGGAGGCCGGAAGGGGAGGGGAGCCGGAGGGGGAGGAGGAGGGGAGGGCGGTGACGGAGGAGGCGAGGGGGAGGGAGCCGGAGAGGAGGGGAGGGTGCGGCGGAGGAGACGAGGGGCGAAGCGAGGAAGAGTGGAGGTGCGGCCTGGCGGTGATCTGACGACGGGAGGAGCGAGAATGGGCGGCGCGGCTTCGGCGGCGGTGGCGACCTGGCGACGGGAGGAGCGAGAATGGC

Coding Potentia
Explanation CPC Score
noncoding -1.32454
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0254300.2 4 11427640 A G
Osa04LNT0254300.2 4 11427658 C T
Osa04LNT0254300.2 4 11428132 T C
Osa04LNT0254300.2 4 11428145 T C
Osa04LNT0254300.2 4 11428396 A C
Osa04LNT0254300.2 4 11429134 A C
Osa04LNT0254300.2 4 11429233 G A
Osa04LNT0254300.2 4 11429338 A G
Osa04LNT0254300.2 4 11429342 A G
Osa04LNT0254300.2 4 11429618 T C
Osa04LNT0254300.2 4 11429754 A G
Osa04LNT0254300.2 4 11427605 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
Osa04LNT0254300.2 osa-miR5818 Cleavage 5.0 20.818 1 21
Osa04LNT0254300.2 osa-miR5827 Cleavage 5.0 10.589 1 21
Osa04LNT0254300.2 osa-miR156j-3p Cleavage 4.5 22.779 1 22
Osa04LNT0254300.2 osa-miR156j-3p Cleavage 5.0 24.56 1 22
Osa04LNT0254300.2 osa-miR156j-3p Cleavage 5.0 10.078 1 22
Osa04LNT0254300.2 osa-miR529a Translation 4.5 10.454 1 20
Osa04LNT0254300.2 osa-miR529a Translation 4.0 17.489 1 20
Osa04LNT0254300.2 osa-miR1879 Translation 5.0 7.621 1 24
Osa04LNT0254300.2 osa-miR2101-5p Cleavage 4.5 12.727 1 22
Osa04LNT0254300.2 osa-miR2931 Cleavage 4.0 13.913 1 20
Osa04LNT0254300.2 osa-miR2931 Cleavage 4.5 9.94 1 20
Osa04LNT0254300.2 osa-miR2931 Cleavage 5.0 12.839 1 20
Osa04LNT0254300.2 osa-miR2873b Cleavage 5.0 18.761 1 21
Osa04LNT0254300.2 osa-miR5075 Cleavage 2.0 10.919 1 21
Osa04LNT0254300.2 osa-miR5161 Cleavage 4.5 16.13 1 20
Osa04LNT0254300.2 osa-miR395w Cleavage 4.5 22.274 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0254300.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0254300.2 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0254300.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0254300.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0254300.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0254300.2 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0254300.2 4 qPEN-4 Morphological trait Panicle/flower RG190 RG908
Osa04LNT0254300.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0254300.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0254300.2 4 nan Morphological trait Root RZ69 RG449
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