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

>Osa04LNT0260500.3

AAAATTTAGTCTCCCATAAAACTGATGGATAATACTGTCAAATCTATTATTTTAACTTTTATGGGCCAGCTTCCCACTATGTAGTCTCTGACTGGCTCAACACACCAAAATACAAGATAGGGTTAAGAAAATCTCGCATGAAAATAACCGCAAGTCCCTGATGAAAAACTCACATGAATGTTCAACAGTACGCGCTCTACTCCATTTCATTTTACCACCAAAAGCGTAGCTGTACTGAGAATCCCACTAGAGCTACTGCACTTGCAGCATTTCAGGGTCAGGGCACTGTCAAGTGTCAACTAGCACCATTGCGACCTCGTAAGTTATAAACCCTGGATCATGGAATGGAGAAGAAAAGCTCAAAAGCTAACAGTTCTAAGGCTTAACCGATTTTGTAAACCTATGTATAACTACAACAGAAGGGTCAGGATTGCAGGATAGCCAGAGAGGAAGATGGTAAGCATGACTCGACTAAATCCATGGAGATATCCATGTACTTGCAGAAGGACATCACCCAATATAACGCCTTTGGTGCCTCAGAGGAATGAGCAGATCCCTTGTTTGTAACAGGTGTGGGATTAAATGCTGCTTCTGCCATCCGTATATATTGAATCATAAACTCAATATACTGGGTTATATGGGAAGGACCAAACTGCTGCAGAAGTGTACCAAGCCCTATGACCAGAGCAGAGAAATCAGCTACAGATTTCTTTAGTGGATTGGTCAAATTGCCCAAGTGAATGTCAAGAACATATTTTGGTAACTGCGATATGGAAAAGATGCACAGCAATCTGGTCAAGAACATTGGAGGCTCTTCAGAAATATAGATAGCCTGAAGAGGTGAAAGTAAGCCGCAAAAGTTCTGCTGATCCTTTATATTGTTAAGGAAGAGTCTGACATTGTGATCCTCGGCCCCTGTCTCAAACCTCCCATTCTGCAAACAAACTGAAGATGACAAAATGTCCACAGCCGAGCTTATAGTGTTTGCTCTGACCTTGCATGCTGATCTCAATTTAAAGGACACGAGATTTCGAACCAATTGCAGCTGTCCGATTGTTGCTAATTTCTCAACCAGTGGTCCCCATGATGAATGCAACATCTTCACCATTTCCTTATATGATGACCAACCCATCAGAGGAATGGACATGGGAGGCCCCAGTAGATCATCCAGCTTATTCAATTCCTCTCGACATTTAACATCAACCAATGTATGTAAATCTTTCATTGCATGCTCCACACTCTGCTTTACTAGTACATGTATTAAGGAATCCAAGCAAGCTAATCCAACTTGTCCCACACATGATTCCAGCAAATGAAAGAAGCGCATACCAAGCAATTCATTTCCTCCTGCATCAAACCAACCCATCATAGCCTCTATAAACATGGAGCGCGATGGATCCGTTAAATGAACTATATATTGCAGCAGGTGACCAAAAAAAGTGCCCGGATTGGACATATGATTCGATGGTTTCACCATATTAGTGGATGGTTGCATGCATCCCATAAACTCTAAGACCTCCCTTTTAGCACATTCTTCTAGCACAGCAGTCAATGTTTCTTCCCAGATTGAACACCCGTCAATGTGCAGTATGTGCTGTAGGAATTCCATTCTCTGCATCTGTGAAAGCATATAATTTGACAATGACATGAGATTGCCTTCTATATCACCATAAATGAGCAATGATAAGGCTTTCAGCTTGCCTTGTAGTTGGCTTACTAACTCCTTTTTTATCATTTGCTTAAGCCATCCACCAGATCTATAAGGCCATCAAAGTTCTTTGACATGTTCAAAAGGCCCTCTGAAACAATGCATAGTTTGGCAGCCTGCTGTGCTTGGCATAGTTGTTGATCCAACTGCATGAGATCTTCCAATGTTTCCTTGTTGATGCGATTTATTAGATGAGTGGACTGTTCAGCATTGATGTAATCCACATCAATAGAAATTTTAAGCAATATAGCCGGGATAATATCTAGAACTGCAAATATTTTAGCTGCATACTTTGAAGCATAGTAGGTTGAGACATACTGAAGATCTGGACTTTCATACTGCTTGATCCTCTGCAGCGGTGCATCCAACCATGATTGAAATTTAAGAAACATCGTATGCAAAAATAAAGACTCTGATGGATCTTGACTGATCTTCTTCTTAAGAAGTTCCTCAAAATAAGTAAGATAACCCCATGCATACTTACCATCAGTAATCTGAGAGAGAGAAGCATATGGTTATTGTTGACGGCTAAGCTTAAAAGGACAGCAATTTTGTAATATCCCAACATTCCAATTTTGGAGAAGTAACTCACCAATGCACTGAGAAAACACTTATGGACTCTTGGTTTAGGTTTAGAACTTTTATCATATCATGAAGATTCTTCTGTATTTTGGAGAAGCCATGCTTTATCTGTATATTCTCTTTGATTTGGTGAAGTAGCTCAATATCTTTTAGCGTAGATAGCACACGATGAATTATCCTGCCGGAGTTTCCAATTGTGGCATAATCCAGGGAGCTAACCTCTGATGACAGGTGCTCCAACCAGTCTTTGATGCTCTTGTTTTTTAATTTGCATGACGCAGCCCAAGTCCCAAGATAGTTCTGAGACAGGTCCTTCATACATTCCAAAGCATCATGCCTCTTCTCATACCACATACTTTTTCTGGTTTTCAATAGTTCAGCATGCAGTTCCTTCACCTCAAACTCAAGTTTAGCAGTCTTCATCAGGAGCTGTAACAGCTTCCCTTCGTCAGCATGTTGTGATGACCCTAAACAGATCACTAGGTCCCTTGCCTTCTTATCATTTGTCATGCGGTGAAGCAAAAGCCAACGCAGTGTGCAATTGCACTCTCTGATGATAGAAAGAAGATTCAGAGAATTATCCAGAACATATTCCTTGTTTACCGCATGCATATGACTATCCAGGTCAGCTAGAAGAGAAGATACCTTTGTATAGTGGTATAGACTGCGATCACGTACGAAGGTGGGAGAAAGGCAAGAAACTAATGATGATTTCGCTTCTTTGAATGCATCCCATGAGACAAGTAAATCTACCGAGAAATGCAAGAAGATGGGAACCACCCAGTTGTCCTTAAAGAAGCGATCAACAATCTCCCGCATAGCCAAACCGTTGTGTAGAAGGTCACGAGAATAAAATAACAACACATACATGTGTCCACCTTGCAATGAGAGAGCGGTTGTCCGGTGCTGCGGATCAGGGTAGAACCGGACATTGTTGTAAACATCACCATTTCTCAAGCAAGTTATGACAGCATCCACAATGAGCTCAGGAAACTGAAACCTCCTAAGCAGATCCTCAGGCTTCTGTACAGAGATGATTTCCACAGTATGCAACGATGAACCGGAGGCACCAGGCGAAGGAGGTGTAGTCACGTGCCGACGACAGAGCTTGCATATGCGCTCCACATTAGGGAAGCTGAAGCAACGCTCGTGCCGCAGATACGCCACCAGAAGTCTCTCACGCAGCAATCCGCTAATCCTGTGCTCCATTAGCAAAGCCATACACCCAAACAAAGTCATCGATTCTGTAAGCAATTGGCAAGCCCAGTTACTCTCCAGTACACCATCCAATGTGCAATGCACATACAGCCCTTCCTGCAGGTCGTTGAGGTAGCTGCACAGCTCGTCGTGGTAAGCGACGGCGGCATCCAGCAAGGCGAAGAACCTCCGCATGTAGGAGCCGCAGGACTCGCGGAGCTCGTCTTCCAGGGCCTCCAGCTCCATGTTCCCCTCGATCCTCGCCTCGAATTCGCCCGGGGAGTCGAAGTATCGGAAGTCGAAGAGGACGGGGTGGAAGCGGCGGTCGGCGAACTGCGACGGGGCGCGGTCGGAGAGGAGGAGGAGCTCGGCGATGAGGGCCTCCGCGCGGGCGCAGAAGGCGAGGAGCTCCGGGAAGTCGCCGGCGGCGACGGCGGCGGCGGCGGCCGGCCGGCTGGGCCCCGCCTCCGCCATGTTTGGGTGATTGGGTCAGTTCGGTACTTCGGTCGGTTGGGGAGGAGAAGCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.754368
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0260500.3 4 19697206 T C
Osa04LNT0260500.3 4 19704410 C T
Osa04LNT0260500.3 4 19696175 A G
Osa04LNT0260500.3 4 19696203 C T
Osa04LNT0260500.3 4 19697574 C T
Osa04LNT0260500.3 4 19698137 G A
Osa04LNT0260500.3 4 19699296 T C
Osa04LNT0260500.3 4 19700398 C G
Osa04LNT0260500.3 4 19700428 C T
Osa04LNT0260500.3 4 19701662 A C
Osa04LNT0260500.3 4 19703948 T C
Osa04LNT0260500.3 4 19704201 T C
Osa04LNT0260500.3 4 19705140 G C
Osa04LNT0260500.3 4 19705958 C A
Osa04LNT0260500.3 4 19706709 A G
Osa04LNT0260500.3 4 19706792 T C
Osa04LNT0260500.3 4 19706793 A G
Osa04LNT0260500.3 4 19707362 G A
Osa04LNT0260500.3 4 19708312 C G
Osa04LNT0260500.3 4 19704335 A T
Osa04LNT0260500.3 4 19709070 T C
Osa04LNT0260500.3 4 19697719 G A
Osa04LNT0260500.3 4 19700455 C G
Osa04LNT0260500.3 4 19700751 G A
Osa04LNT0260500.3 4 19702549 A G
Osa04LNT0260500.3 4 19702662 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa04LNT0260500.3 DTM_#DNAt_MULE_japo_Os0098 Chr4 - 19702305 19702675 370
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0260500.3 osa-miR5535 Cleavage 5.0 20.811 1 22
Osa04LNT0260500.3 osa-miR5794 Translation 4.5 14.982 1 21
Osa04LNT0260500.3 osa-miR5797 Translation 5.0 14.516 1 21
Osa04LNT0260500.3 osa-miR5811 Cleavage 5.0 14.574 1 24
Osa04LNT0260500.3 osa-miR1437b-5p Cleavage 4.5 12.921 1 21
Osa04LNT0260500.3 osa-miR319a-5p Cleavage 4.0 21.37 1 21
Osa04LNT0260500.3 osa-miR530-5p Translation 4.5 17.647 1 20
Osa04LNT0260500.3 osa-miR1426 Translation 5.0 12.574 1 21
Osa04LNT0260500.3 osa-miR1438 Translation 5.0 18.97 1 22
Osa04LNT0260500.3 osa-miR1865-3p Translation 4.5 14.409 1 24
Osa04LNT0260500.3 osa-miR2868 Cleavage 4.0 16.279 1 20
Osa04LNT0260500.3 osa-miR5149 Cleavage 5.0 9.856 1 22
Osa04LNT0260500.3 osa-miR5161 Cleavage 4.0 14.234 1 20
Osa04LNT0260500.3 osa-miR5337a Cleavage 4.5 13.084 1 21
Osa04LNT0260500.3 osa-miR5339 Translation 4.5 21.242 1 21
Osa04LNT0260500.3 osa-miR5485 Cleavage 5.0 17.617 1 21
Osa04LNT0260500.3 osa-miR5510 Cleavage 5.0 19.948 1 21
Osa04LNT0260500.3 osa-miR5519 Cleavage 4.5 15.863 1 21
Osa04LNT0260500.3 osa-miR5519 Translation 5.0 11.044 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0260500.3 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0260500.3 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0260500.3 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0260500.3 4 qNOT4-2 Resistance or Tolerance Drought tolerance RG449 RG788
Osa04LNT0260500.3 4 qFRP4-1 Physiological trait Source activity RG449 RG788
Osa04LNT0260500.3 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0260500.3 4 nan Morphological trait Root RG449 RG788
Osa04LNT0260500.3 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