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

>Osa04LNT0260200.2

CCTTAATTCACAATGCAATTGCTATTGATTATAATGCTTGTAGAAATGTTAATGGAACACATTTCTTTAAATTCTAGGGAACCAAAAAGAGCCTTAGAAGAAAGTATGCCACAAAAAAAAAAAAACCTGAAGCTCTGTCAAGCTGGACTGATGCCGTACACTTGGGCCGATGACATAGCCATCATGCTAGATGAGATAATACCCTGAGCAACATATCCAGCAATTTGACCTGCTGTTCTGCCGTGATTTCATAAAGGAGCTCAAGCCATTCAAGATGTGGAAGCTACTTCAGTAGGCCATCCCTGTGATGTTTGGTCTAAGCTGCAGCCTGTAGGCTGCAGCATATCCACTGCAAACCCCTGAATTATTCATGATCACGCCAAGAGTTTCATCTTCAAGAGCTGACATCCTGCTGATTCTCCGTATTTGAGGGGTATAATGTGTTGAAGACGACCAGTGTAAAGACATTTCTTACTTCTGCAGGTGTACCATAAGATAGATCATGATAATCAATATTTCCATCTCTCTTCGGTTCATAGCCATGCTCCTTTTTCCCATGTTGAACACATTCAATTAATTTGAGAACCTTTAGGTAGGCTTGTAGTGGGATGAATACAAGATCTGAGGATGGTGCCTGAGGAATTTTTGCCATAGCATTTGCAACAAAATATTCATCAGTCATTTCAGTTAATGCCCGCCGCATTGAGACAGCTAGGCTTTGCACCTCGCCTACCAAATGCTTATCATCCCAGACTTGGGGTTCTAATAGCTCTGAAAATCCGGTATTATGTTGACGGTTGATTGATTTTCCAATATCTAGTGCCAATGACATATCACCTCCAAGGTATAGAGCTAGGGCAAAAGTAGCTACCACTAAAGGATCACGCGGTTGGCGTACTAATGCTTCATGAAGTGCTAAAATACTTATCCTGTAAAATGGAAGGAGAATAAAATGCCATTTTGCAGAATAATAGTGAATCCAAGTAATCTCAAATAAAAACATGTGCTTTTTCAAAAGAAGTTTGAAACATTTAGTTCTTGAGTAGCATTCATACTAGCTTCATAAATTCCATCTTTGTCAGTTTAAACAATCCAAACAGCTAGAAATAAAGCAATCAATGTATAAATTTTGGCCTCGGTTATAAATAGCAAGTTGAATAATGCATATCTCACCACAAACTATTATGGCATGGCCTGTTAGGAGCAAGAAAATTATCCAATTTAGAAAATAAGACCAGTAGCATGTTAGTTCCTTTATCCTTCCTCTTAAAACGAGTTGAAGAAAAATATGCTGCCTGAAAAGGCAGCAGGTGTTCAAGAAGACCGAATCTCCAAAGCAACCTTAAAGAAGCTTCAGCTGAACCATAAGCAAGCATATAGTTGATCTCCATGAGTATTCTTCCCTTATCAAGTCTTGCCACAGAGCAGGCAAGAGTTCGCACATAATAAGCAGTTTCTTTTGGAAAGTTGAACCCTAAACGAGCTGCAATTCTGATTGCACGTAGAATACGAGCACAGTCCTCCTGGAATGATGTGCCAGCTGGAATCACGGTACGAACCTTAGCTTTCTTAATATCCTCGATTCCTCCGAAGTAGTCGTAGATCTTTTCTGCATATGGATTGAACATTAACCCGTTTATAGTGAAGTCCCTCCCTTGGCAATTTTTCCATCGGATATAATCATTTTTGCTACAATGGGGGCTCTTGGACGTGTAAATTTGATTGCTAGTTGACCCTCGTGCATAAGTGTTAAAACTTGATACCTCAACAATTGAATTGTTCTCATATACATGACATATTGGGAACCGCCTTCCTACTATAACAGCTGATCCTGAGAAAGTGTCTTTCACCTGCCTAAGATCAGCTGTGGTTATTATGTCAAAATCTTTTGGGGTTTTCTTCATTATGAGATCTCGAACACAACCACCAACCAGGTAGACATCATATCCTCTGCTGCGGAGGCGGTGGAGGACGTTCCAGGCCTCGTCGGGGATCATGGAGTCCTTGATCCCGAACCGCTTCGCGCTCACCTTCTTCCACTCCGGCGCCTCCGCCGCCGCCGCCGCCCCACCGGCGTTCGCGGGGGCGGAGGAGGCGGGGTTGGAGTCGGAGTCGGAGGGCGCGGGGGAGGGCGACGGGGAGCGGCGCCTGCGCCGGCGCGGCGCCGCCAGCGCGGCGAGCG

Coding Potentia
Explanation CPC Score
noncoding -1.13125
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0260200.2 4 19499264 C T
Osa04LNT0260200.2 4 19500618 T A
Osa04LNT0260200.2 4 19501595 A G
Osa04LNT0260200.2 4 19502578 A G
Osa04LNT0260200.2 4 19503284 G C
Osa04LNT0260200.2 4 19503467 A T
Osa04LNT0260200.2 4 19503712 G A
Osa04LNT0260200.2 4 19498872 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
Osa04LNT0260200.2 osa-miR5531 Translation 5.0 13.349 1 22
Osa04LNT0260200.2 osa-miR5797 Cleavage 5.0 9.466 1 21
Osa04LNT0260200.2 osa-miR5815 Translation 3.5 16.58 1 24
Osa04LNT0260200.2 osa-miR6254 Translation 4.5 15.722 1 21
Osa04LNT0260200.2 osa-miR816 Cleavage 4.5 23.749 1 20
Osa04LNT0260200.2 osa-miR2095-3p Translation 5.0 17.11 1 20
Osa04LNT0260200.2 osa-miR2105 Translation 5.0 9.011 1 20
Osa04LNT0260200.2 osa-miR5499 Cleavage 4.5 15.834 1 21
Osa04LNT0260200.2 osa-miR5499 Cleavage 5.0 11.452 1 21
Osa04LNT0260200.2 osa-miR1319b Cleavage 5.0 19.447 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0260200.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0260200.2 4 qNOT4-2 Resistance or Tolerance Drought tolerance RG449 RG788
Osa04LNT0260200.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0260200.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0260200.2 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0260200.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0260200.2 4 qFRP4-1 Physiological trait Source activity RG449 RG788
Osa04LNT0260200.2 4 nan Morphological trait Root RG449 RG788
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