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

>Osa04LNT0283900.2

CAGGCTATCAGCTAGTAGAGATGGCATTCAACTACTGAAAGGAACACATCAAAAAATTCGGTTCCCTTTTCTCTCACTTCTACACATTCCACTTATTTCCTTGCTCAATATAATCTTAAACACCAGCATTATCGGGGTTAGAACACCCTCGCAACCAATTGTGTAAAACAGTGTAATGCTTCCAGCTTAATTGATCACATAAATCAGGTAATAAGATAAATTGAGCAAATAAAATTGACCTTCTTCCTTTGGGTGGTGGCTATTGAGAAAATTGCCAAAAACCCTCGGTCAACCGAATCCAAAGGTTATTGCATGCAAAAAAGTTGAATCTCATCCGACTTCGTGGCTGTCCAAATGACAGGCACTTTTTCTCTGGATGGAATTACATGGTGCGCTCTCTGATGACTATATTTTGTGGCTGATCAGAATAATGTCAGCCATATTTGTTCCAAATCAGACAGCAGTTGCTCTTTCACAAGCTTTGTAGTAAAGTGTCTTCTGCACATAGAAGAGCATGTATGCCTGAGAGGTTCTGACAGTATGCTCTTCAACTCTGGTTACCCAGGCATCATCACATTTGTACCAGTGATTGTTTAACCTGAGATATGTCACATAATGGCCAGCTTCTAGCTTACCACTATGCATGATCACCGCAAATATTTCAAATTCTGATGAAAATTCAGAAACTGAATCTGCATCACTAGCTTCTGATGGAAATATACGGTTCCCAAATCTGCTTCTGAGTATAGAGGACGATAGATATGGCGCCATGTCAAGAGAAAAAGGAAACTGTAAACAGTGATCAACCTTCCTTGACATTTTCTTAACTGATGAATGCTCAAACCTCTTAATATGAAAGCATGAAACCAATGGAAGCCTCCGAATGGACATTTGCTTCAGGGACTCTTGCCTCTCCTTGCAACGTTCACAGAAGAACTTCTGTTCAGCATCCAACCGCTCAGCCCTTGTAAACCGCTCCAAACATCTCATGAGTGTTGATACCTTGGTATTAGTGCCACCTGAGCTTCGCTCTCCATTCCGCACATGTACCTTTGGGTTTGCAACACCAAGAGAATTGTTATATCCAGCATCCAAGTCTAGAGAGATGTCCATACAGGGTTCAAAAGTTGTTGATGTGAACCCACAATGTGTGCAGGTGACATCTGATCTCAAGATGCCAGAAAATACCCTGTGTGCAATGCAACAATCTCCATGGCCTATTAGGGAAAAAAATACACATAATGGTTAGATCTATAACAGCTCATCTGCCTCAATATAAATCATAGTTCAGCCTATCAAAAGCAAGATAGAATATGTTCTCCACTACAACAAAAAAGAGAAAAAACACATTTGTCCAATTTGTTCCCCAATATCCAAATAGTACAGGACTACCATTTTCCACGACTTATCCTGTTTTCGTTTTTAGGGTGTAGAACCTACTGTAGAGTCATCCTCCAAAGAAGAGTAGGAGTGACAAATAATAAAAATAGTACAAAAGCAGCCACAAATGTTCACTATGCACCACACTACCAGCAACAGATGGATTTAGATATGCTTTTTGCTTCAACCAAAAATAAAAATAAAAATAAAAATAAAACTGGTATTGATTCATTCTTGGCTCAAGGGTGCACTGTTTTCACAATAAAAGGGTGGATAGAGTCATCCTCCAAAGAAGAGTAGGAGTGACAAATAATAAAAATAGTACAAAAGCAGCCACAAATGTTCACTATGCACCACACTACCAGCAACAGATGGATTTAGATATGCTTTTTGCTTCAACCAAAAATAAAAATAAAAATAAAACTGGTATTGATTCATTCTTGGCTCAAGGGTGCACTGTTTTCACAATAAAAGGGTGGATATTCTTCTTTTCTTTTCACATATCAGTTCAGTTGAATAGATGGAAAAGCTTTAATTTAAATAGTAGCAGGAGAGAAGCTAACTACCTTGGGCAAGTGATTTGTGTTGATCATCCTTTATATTTTCATGGATATGGTCAAGGATGGAGATAAAAAATTCATGTGCATCCTGTTGCTCGTAGCTCGCAAGATTTGATGCATGCTGCCACCAGCTAACAAACATAACGACAATAATCAGAAGAAAAACAATCACTTTAATTCATGAACCAGAATAAAGTAGTATGCCATGTTACTGTGCAAGTCCAAGTTCGTCAAACCAGATCAGCCGCAAAAAAAGACTTCACATATTTAAATTTCACATAGATATAAACTAAAGTTTAAAAATATTACTTCGGCTTTTTTTAGAACACCATTACTTTGGCTTGATAATTACCCTTTGTGTCACATAATGTCACACTATGATCACAACAGTTTGCTGAATACCCATAGGGCATAAACAAGAATATTACGATGAACGAATTGTAAAAACATATCCTGGTAAAGTATCAGCAGTGCTAGCAATAACTTATGTACCTGCCACATACTTGTACACTATCCTTCGCAGCAGCAAGATATGATGTCATTGCAGAAAATTTTAACTTAAATTATGCAATTCACTCATATGACTTGGCCCATATCCAATGATAGAGCAAATAGCTTCAAATGCACCTGATAAGAAGGTGCTCTGAAGAATTAAAAACTGGTCATGCATTTTGGAGTACTTGTACTTGATACATGAACATAGCTCAACAAATTCTAAGCATGCGAAATGTACTTAAGACCATATGACATTTTATCAATCAGGTCATGTGCATCCAAACGTGAAACCGTTACCCTTTCTAGCGAAACATATGGAACAGATCTCGCCCTTTTAGTAGCATATCTTGCTCACATCATCCCATTTCATGCTAACTGATAAGTAGTTCCAAATTGCAACCTATAGAGGAATTTGGCGGGGCTGTAGGGCGTGCGCTCCCCGGAAAAGGCGGCGGAGTAGATCTCGTCGAGATCGCACGCCAGGCACGCCGCCTTGTCGTTTGCCTCGGCGGAACGGCGCCTCATGGGCGTCTGGCGCGGGCAGAGGTAGCGGTTGTGCCGATCGCCGAGGAAGTAGTTCCGGAGCGGCGGCGCGTGTAGCAGAGCCTGGAGCACGGAGTTCATGAAGCACGTGTTGCCTAGGTTGTTGAGCCCGCGGAGCCCCGCGGGCGCGGCGGCGGATGCGGAGGTGGTGGGATCGGCGGAGCTGATGAGCGCGAATTCGGCCGGATCTGGTGCCCAGGCGCGGTACTCGACGCGGCGGCGCTTGCGGGGCGCGGCGGGGGAAGGGGAGGGGGAAGCGGATGCCGATGGGGGAGGAGGGAGGAGGACTTGGCGAGGACGACGGCGTGGTCGAAGTCCGGATCGTAGACCTGATCCCCGCACGCCCCGCAGAAGAGCTCGGCGCGGTCGACGTCGACGGCGATCTGGTGGCCGCCGGATGTTGAGGCGGAGGCGTTGGAGGCGGCGTTGGTGGGGCAGAAGACGGCGGCGCAGTGAGAGTGCAGGCGTAGAGTGCGGGACGAGGAGGAGGTGGGGGAGGAGCAGGGGGAGCAGCGGGGGAGCTCGCGAGTGCTCGCGGCGGATCTCGGGGCGTGCCGAGCGGGCTGTGACGCGGAGTGCAGCTGGCTGGAGTGAAGCGGAGTGGAGCGCGTGGTGTGGCGGTACGCGGCGAGGTGCGGGCACGGCGGCGGCGCGGACGGGGTGGTCATCGGGGCGGGGAATGTGGGGGATGAGGCGGTGGGCGCGGGAGTGGGAGGCGAGCGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.957536
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0283900.2 4 32934594 T G
Osa04LNT0283900.2 4 32935592 A C
Osa04LNT0283900.2 4 32933885 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0283900.2 osa-miR5537 Cleavage 4.5 12.062 1 22
Osa04LNT0283900.2 osa-miR5827 Cleavage 4.5 16.23 1 21
Osa04LNT0283900.2 osa-miR5827 Translation 5.0 19.433 1 21
Osa04LNT0283900.2 osa-miR5832 Cleavage 5.0 20.02 1 21
Osa04LNT0283900.2 osa-miR7695-3p Translation 4.5 12.51 1 21
Osa04LNT0283900.2 osa-miR169n Cleavage 5.0 14.968 1 21
Osa04LNT0283900.2 osa-miR169n Cleavage 5.0 18.58 1 21
Osa04LNT0283900.2 osa-miR169o Cleavage 5.0 14.968 1 21
Osa04LNT0283900.2 osa-miR169o Cleavage 5.0 18.58 1 21
Osa04LNT0283900.2 osa-miR816 Translation 5.0 20.665 1 20
Osa04LNT0283900.2 osa-miR1428a-5p Cleavage 5.0 18.473 1 21
Osa04LNT0283900.2 osa-miR1431 Translation 4.5 22.466 1 21
Osa04LNT0283900.2 osa-miR2097-3p Cleavage 4.0 12.506 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0283900.2 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0283900.2 4 nan Physiological trait Eating quality RZ590 RG214
Osa04LNT0283900.2 4 nan Physiological trait Eating quality RZ590 RG214
Osa04LNT0283900.2 4 nan Morphological trait Root RG214 C1016
Osa04LNT0283900.2 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0283900.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0283900.2 4 gpps4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0283900.2 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0283900.2 4 qSN-4b Resistance or Tolerance Drought tolerance RM255 RM349
Osa04LNT0283900.2 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
Osa04LNT0283900.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0283900.2 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0283900.2 4 nan Morphological trait Root RM3276 RM3335
Osa04LNT0283900.2 4 np4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0283900.2 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0283900.2 4 np4 Morphological trait Seed RG143 RG214
Osa04LNT0283900.2 4 QGwp4 Physiological trait Source activity RG143 RG214
Osa04LNT0283900.2 4 nan Morphological trait Panicle/flower RG143 RG214
Osa04LNT0283900.2 4 nan Physiological trait Source activity RG143 RG329
Osa04LNT0283900.2 4 QGn4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0283900.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0283900.2 4 nan Morphological trait Panicle/flower RG620 RG214
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