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

>Osa04LNT0258300.2

TAGAGGTGGGGTTCGAATAACATATAAGAACTGATTAACAGATTGACTGTAGAATGGTATAACAATATTTAAAGAACATATTCATAGGTCTGAGAAACTATCGAAGCCAAGTATACACGGGCAAAGCACATAGACGTATCAGTCATGCATATATATAGCAATATCATGTTATGATCCACACGTGCGCGCACAAAATGAGGCACATCACACGGTAAATATTCTAGTAGTTCAAGATGCACCCTGTGAAGAGAAAAGAAATAATTTAGCTGGGTCTGATATGAAGGTAAGTTGGATATAGACATAAGGGCAAGGGTAACCACTCATATGGATTAGCAGTAATGTTTAATTATATGACTAAACTGGAATATACTGATACATTGCTACGATGATATACATTGGAAGGAAAAGGTATTCCGACTGGAAAGCACATTTGTAAGTAACATTGAAGAAGGGTAATTAGATAGAATGGAGATCTACAAATTGATGTATAATAATGAATGTTGCATGAAAAAAAATACCATGGATGATCAGGAAAGAAGAAAACATATAGGCAAATGTAGGCCTTGTACAGTGCGATCACATATAGTGAAAATAGACGGGTTTTTTTTTGTAACTGTGGTTATGGACATTGAAAAGAACGGACGTTGTTAATTGATTAGTTCTCTAAGAATGCAAAATCATACATATCAATTCTCAGCACCATAGAGATAAATACAAATTTTAGGTATATCTGGATAAAAAATAACAGAGAAACTAATAGAACTTTTCTATGGATGGCAGTTGAAGAAAGACCAATAATTATATACCTAGTTCATGTGCACCTTTAATACTCACCTAGAGAGAAGGAAAGTGAATGATTGAGCCAAAACGCTGTTGTTTCCCAACGTCAAGAGGAAAGAAGGGTGTACTTCTATTGTTGTACACAAAACAGGGAAATCAGGCACATTTCATAGGTTGGACTGCATGGAGTCTGAATAAGCAGTGAATCAATAAAAGCATCATTAACTGAGGAAGAAAGTCATTCAGTAAACAGTGGGCAGTAGTTGTACATGAAACCAAAAGGGAAATGCTTGCAGTTAGTAGAAGCGGAGCTGGTATGGAAGAGCCCAATGCGCTGCATCAACTATAGCGGACAACCACTCACGATCATCACCTAGGAGACCAGGAGCCTGGCAAGCAGCCTGGAATGTTGGATACTGTTGGCCTTCAATTGTTCTGATCTCTGAGTACGACCTTGCCACCTTCACTATAGCAACATACGAAGATAGTAGGAATCCCCCTGGTTAGGGCCTACATTGGCTAGTCTTCCGACGTTACCAGTACCACGTCGATAATCCCAATACTTTCCATCAGCATGCCAAGTGAAGTGCTCTGGGAACTCTGCATATGTGTAGCACACAGCCTCAGGATAGGTCTTGTTAGCTTCAAACCAGGCAGTGAGCTTTGTAATTTGATTCCATGGGTTCTGCAATACTTGTTCTAGGCTGTCATCCTCATTGTATACTACACTGTTTCCGAGTGGTAGATGGACAGGAAGACGCTCAACAGAAGGGTTAGTGTGGTGAATTTCAAACTGGAGCAAGCGCCAAGCTGCATCATTGGGAGCTATACATCTGCACTCTAGGTAATCTTGGATCTCATTAACACCTTTGGTACAGGTAGATGATTCACCGGATGCTCTTTTACGTTGGAGACCAACCTTTGAACAATCAAAACCTTTGGTAAAATACTTGAATAAATATTTTTCCATCCCATCACGGCTAACTCTCTCTACATTTATGTGTGCTTGGTACTTCACACATAAATCCACATTATGCAGGAGAACAAATGCATTATCAACAGCAACACCATTCTTTTTGGTAGATATTCTATTCTTTGGTCGAGCATATCTAACATGTCCATTTTGTAAGATTGTTGTCTTCTCACAATATTCTTTTGGATAGTTCTTAGAGCATTCGCCGTTAACCATGCAAGCACATGATGGATGTCCCTCACCACAAGGACCATGAATCATAAATGCAGATACAGCATCAAAACCAATTGGATCGACAGAAGGATCAGGTAATTGTGCTGATATGAACTTATCAACCTCATCAGCAGTCAATGCACCAGTTTTTTTTAGCCATAAAATAATATGGACATGTGGAAGACCACGTTTCTAAAATTCGATAATGTATACAACTGCAGTAATTGGACCAAAAAATTCATTCTTTGTGATATCATCGATGAAGAGATGCAGCTTCATATGAAACACACGATCAACAATATCAGGCTTATATTCTCACAGAAATGAGCTGATTTAGCTCTATCCACCGCAGTTAGCAGACTATGCAAAGGCTCTGGAGGTGGCTTGTAGGAAGGCAAGATAACACTTCCTCCTTTGCAGCACTTGTTGTATAACGGTCTTGTTGTGTGACGCCGTCGGTCGATGCGCTCCTCATACCAAAATAATGCGCCACAATAACAACATGTGTGACTTGGTGGACCAAGGTTTAATGGTGAGAAAACAGAGCATCGAGACCAGCATCGAGATTGAACATTTACAATCGAGCAGTTTGATGAGCAGTCATGATCGAACAGTCGAGATAACATCATGATTGAGCATCACATACGAATCGTGGGAATGACCATTTGTAGGGATAGTGGTATGAGAAGACGATGCATCTTTATCATATATGGAAGATGATGAATGTGCCAACCGTTGTCGCAATACCCTAGAACGCTCTGACATATATGCTTTACGTTTTTTACGTGATTGAGCAGCCATGGCGGAATCTGGGCGAGGAAAATCTGTAAGTTGAGTATACGAACGGCGTCGAACAGGCCGGTTAGATCTGAAATTGAAGGCTGTGGGGAAGTCATTCGCGTGGCTTGATGGTGATCCATGTAACTCACCATCATTAGTCTCAGCAAGTTGAGTACACAAACGGCGTCGAACAGGCCGGTTAGATCTGAAATTGAAGGCTGTGGGGAAGTCATCGGCATCGTTTGATAGCGATTCATGTAGCTCACCATCATTAATCTCTAATATTGGTCGCTTACGCTTAAGGCGTGCACAAACCAGAGATTTTCCATCAGGCATAGACATAATCTGAAAGTTTTAGAGCTGAAATTAAGTGGGAACTAACAAAGAATCTATTGCATGTTGGCATGGGGTATAACACTGTGTAAGGTAACAAACTGGGTAGTAATGAGAACCAACGAACTGATAAAAGGAAATATAAATAATGAGAAGATAACTCAACATATGTAACCCTCTATACAAAGCTACTTTAAGAGCTAGAATATTACACGAGAATACAAAAACATATACATATAAGCTGAGAAAAGAATCACCCATGGTAATAATAGGAGCAAGCACGATCTACCATCAAGAGGTACATATTAATCAACGCAACAATAGGCAATGATATATGGTAACGATAAATCATCGATAAGCAAATTTGATACAAAACAACACAGGAGGTTGACATAAAAATTATAGACCATGACTGGCCTATATATAAATTAGACAATAGTATCTCCCCTGGTTGAACCTAATAGTATCTGAAGGCATTCTTAACAATAGCTTGCCGTGACCAAAGTAGAGAGAGAGAGAAAGAGCAGGAAAAGATTGCCAGGAAAGGCAAATATGCGCAATGGTCTATATATATGGAGTAAGTAAGCAACACTCTGTTGATTTTTCAAGAAGCGGGTGTGCACTCTAGGTGGAGCCGATAGCATTTTCAAGAAGCCAAGAACAACACTCTGTTGATTTTTCCCCAATTTAGTGAAAAGAGGCCCGATCTGTTCTGGTCGGTGAAAAAGAAATGAAAGGAAAGCGATAAACTATGAGCAAATATAATGGGTGAAGAAAAACAAATAATCGAGATGAAATGTTTAAGAATGCAAACACGATGTGACGCCGGAACTCAAGAAGAAAGGATGCAAAGCCGATCTGATGCTGGCAAACTGCTCATGTTGTTACATATAAGCCATCTTTAATTGAAGCTTTTAGCGATTCGACGCCCAAGAAAACCCTAGAGGGAGAGGGCAAGACGGGGTGCCGCGCGGGTGTGGGGAGACGGCGGCGGTCTCTAGGAAGAAGCGACGGCGGCCGCCGATGGCCTCGCCTGGAAGCGACGACGGCGAGCGATGCCAGCTACTTGCCCGAGGTCGAGATGAAAGGGGAACGGCGGCGCCGTCGGAGGCGACGACGCGGTGGAGAGAATGGGGAATCGGCTGGTTCACGGGTGCCCCTTTTTTTCTCTTCTGCCTGTCGTGAGCCTGGGTGGTGGGCTCAATTGACC

Coding Potentia
Explanation CPC Score
noncoding -1.30176
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0258300.2 4 16870214 T A
Osa04LNT0258300.2 4 16870426 C T
Osa04LNT0258300.2 4 16872286 G A
Osa04LNT0258300.2 4 16864912 T G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0258300.2 osa-miR5532 Translation 4.0 12.528 1 22
Osa04LNT0258300.2 osa-miR5828 Translation 5.0 16.891 1 21
Osa04LNT0258300.2 osa-miR7693-5p Cleavage 5.0 13.404 1 24
Osa04LNT0258300.2 osa-miR160e-3p Cleavage 5.0 13.105 1 21
Osa04LNT0258300.2 osa-miR535-3p Cleavage 4.5 9.697 1 21
Osa04LNT0258300.2 osa-miR2094-5p Translation 5.0 18.738 1 21
Osa04LNT0258300.2 osa-miR2095-3p Cleavage 2.5 21.276 1 20
Osa04LNT0258300.2 osa-miR2863b Cleavage 5.0 19.252 1 21
Osa04LNT0258300.2 osa-miR2863b Cleavage 4.5 14.78 1 21
Osa04LNT0258300.2 osa-miR2871a-3p Cleavage 5.0 9.014 1 21
Osa04LNT0258300.2 osa-miR2871b Cleavage 5.0 9.014 1 21
Osa04LNT0258300.2 osa-miR2929 Cleavage 4.5 15.768 1 21
Osa04LNT0258300.2 osa-miR2931 Translation 3.5 13.107 1 20
Osa04LNT0258300.2 osa-miR5083 Cleavage 5.0 16.234 1 20
Osa04LNT0258300.2 osa-miR5489 Translation 5.0 18.004 1 21
Osa04LNT0258300.2 osa-miR5515 Translation 4.5 17.5 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0258300.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0258300.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0258300.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0258300.2 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0258300.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0258300.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0258300.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0258300.2 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