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

>Osa04LNT0280100.2

ATCAAAATTTTTACTCAAAAACTCAAAACGAGTACCTTGTCTAGTACATGGCAAAAGAATCTCTTCCTCACACAGGAATACACATGTTAGCTCACCACACTCTGATGTGTTTGCTACACAACATTTGCTTGCAGATACATTTCGCAATTGTACAAAAATTACAGGAGACGTGGATTCCTAAAACAGATGTTATCCCTTCCTGAATAATGCTAGAGGTGCAACTATACTCTTCTTCTCTTTGCAATGCCATTCTTCTCTAGTTAGTGTTATCTCTACTTGATAGCAACGAACAAAACAAAAGGGTGTCGGAAAGGGTACCATTCGGCAATCAAACATAAGAGGTCAAGCGCACCTGCATCACATTTGTGTGTGGAATGCTCATCGACATCATCGCCCTGCGGCAGTTGTTCCTCAAGAATGCGAAGAAGTAGTTTATGATCAGCTTCTTGAAGAACCAGGAATTCTTCCTGGCTTTGACGATGGGGTTGTCAATGAGATAGACGGCTCCAGATTGCTTGGCCTGCCTGATGAATGCGAGCTCCAGCTCAAGGTTCTGTGTGTAATCCACCACAGGATCGTGCTGAGGCGTTGAGCAACTGGCCTCAGGAATAACTTCTGCCGAAGGCACAAAGTCTGCCAGGAGAGGGACGTCAAGCGAGTAGAGGCTACCATTTGGCGCTACGATTGTCCTAGATGGGGTTGGAGGCTCCTCGTCAGAGTCGATGTCGTCTCCACTTTGTAGGGATAGCTCTACTGCCTCCCGCTGTATGAACTTCTCGAGGCCTTCAATCAGAAGGCGCTCAAATGTGCTTTGGCTCTCCTGGTTCTTATCTTTGTAGCCGTACCTTGCAATACAGCGGAACATGTGATAACCCCTTGTACAAACACGTTGGAAAAGAAACCTTTCAGTCTGGGGAACCACGGGCACTGGTACATTCCTGATGCATACAAAAACGATTATCGAGTGGATTGCAGGAAGGGCAATCAGAAAATGACCAAAAATTGCCGGAACTCCTTTCACTATCTCACTGTAGACCAAGCCTAATCCAGGAGCTCTAATAGTACCAAGGTTGGGCCCCAATTTTCTCATCAAATCCTTTGAAAGCTTCTTTTTAACTTCACTGTCATACTTCAGTTTGCTTCCATAATTCCAGATGAACATAACCATTAGAATACCAGATGCAAAAATTATCAGAGCCCAACCTCCATCTCCAACACTACTTAGAGACGATGAGAAGAAAACCAACTCTAAGGAGAGGAATGTGATGACAAATGACAACACTTTCACAATACTGGTTTCCCAAATTAGAAGCATTATGATTGTAACATAGACTGTGGCCATTATCATCACCCCAAGCTCAGCTATGGCTGTTCAATATGGAACAGGGTAAGCGCATGTAGAACACTGAGCATTACAACTTATTAAAAAGCAGATAAATAGACAGATTTGCACTAAAAAGTATAACCATATAATTAAGTTATTACTAGATGAATACCCTGCCACATTGCTGAGGGAAATTAAGTTGCATAATATGCACAAATAAGATTAAATACGAATATTAAAACTAAAACAAATTGATACTTATGAATTTTGAGGCCTAAAAAATTGAGATTACTTGGTGTTATGAGAGAAGAAAGAAGAGACAATTTGAACCATAGATCTATCATCCAATGGCTAGAAATAATTAAGGTGATGTGGCTTAATGATAGAAGAGAGATAACATTAACTACACTTAGTGGGGATGAACTATACAAGTATATAGGATTACCATATGCATTGCCAACATCATATATGCTTCTGAACAGCAGAATAAAGCCCAAGCAGGAAAACAATAAAAACCAGTTCACGACAGGAATGTATATCTTAGCCATAAATTTCCGAGACGTATGAATGATCTTGAGTCGAGGAAAGCAACCAAGAGCTATTGACTGCTTTAGGCATTGGAATATAGCTGTCGTCATTGTTCTACTAGCAATCAATGCGGCTAAATTGGCTATTAAGAAAACAGGCCAGAAAACTCCACTTGGGATGGATGAGAAGAAGATCTGCTCAGATGAATTTTGGTTTGCAATAAGAAAAGCGCCTTGTCCTAAATAGGCCAAGACAAGGCAAGGAAGAACAAGAAGCGCAAACATTGACTGAACATATCTTACAGGAAAGTAGGAAAGATTTGCAAAGATTGCCTCGGACCCTGTTGCACATAAAAGACAGCCAGCAAGGGACAGCCAAGCCTGAAAGGGATTCCTCCCAAAATAATAAATAATGTAGAGAGGATTAAATGCTTTAAAAGCTGCTGGGCCATATGTACTGAGATTGTATATACCAATTCCTCCGAGACAGCAAAACCATATAAGTAAAGAAGGGCCAAGTGCAAACCCCATTTTGCTAGTGGCATACCTCTGTACACTATACAAGATTACAAGAAGTACAACTGAAATCATCACCACAAGGCCTTGTGAGGCATTTGGTATCCCAACTTTCAAGCCACTGACAGCAGACAGCACTGACATAGCTGGTGTGATAACTCCATTTGATATGAACATTGCAGTCCCAAATAGCACTAGACCTAGAAGCAACTTCTTCAATAGCAATGAAGATTCAAGCTTCTCCTTTACTTTTATGGATCTCTCAAGCTCTGGCGTTGGAAGCTTGAGTCGGAAACTCGACATCCTCTTCTCAGAGTGTACTTGGTTTGGAATGAGACTCACTTTTGCATTTCTGCAAATCAAAGAGTACAACGCAAATATACCACCTGTAGAGTCATGGAATCACTTCACCATCATCATTAGCCCAAAGGACGACTAAGACATACTTCACTAGTGGCATCGAAATTAGAGTATAAAGGACAAGTGACAGTGCTCCAAGAACATCCTCCTCTCCAAGAATGGGATACTTGCTGAACATGACATCAAATGTATACAATGGACTTATTCCAATATCTCCAAACACCACAGCAAGAGTCTGAAGGGCAAGAAACATTGTCCTCGCTGTCCTCGATGTGCTGCGCGACGGAGACCTCGTAGCCCTCGACGTCGAACCAGTCGACGGACGGCACGGTGCGGATCAGCTTCTGCTTCTCCCCATCCTCGCCCTCCCCCTCCCCCTCGCCGCCGCCGCCGCCGTCCTCCTCGTCCTCCTCCTCCTCGGACCCGAAGCTCCCGCCCCTGCCCACGGCCCCGACGGCCGCGGCCGCCGCCTCCACCGTGTCCCCGTCCTCCTCCCCCTCGTCGTCCTCCTCCGTGGATACCCACCGCCACTCCATCGACGGCGCCTTCCGCATCCCCCCGCCGCCCATCGCCGACGCCGACGCCGACGACGACGACGACGCGGCCATAGTATCCCGATCGGATCGAGAGGCGAGGCGAGGCGAGGCGAGAAGGGACCAGGAGAAAAATTCGTCTCCGTGTGTTGCGTGTGGAGATGTGGAGGCGCGGATGGAGGAGGAGGAGGAGGAGAGATCAGGAGAGAGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.795929
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0280100.2 4 30953411 G A
Osa04LNT0280100.2 4 30954186 T C
Osa04LNT0280100.2 4 30956519 A G
Osa04LNT0280100.2 4 30956617 T A
Osa04LNT0280100.2 4 30956810 G A
Osa04LNT0280100.2 4 30957324 T C
Osa04LNT0280100.2 4 30956244 C T
Osa04LNT0280100.2 4 30954714 A 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
Osa04LNT0280100.2 osa-miR5534b Cleavage 3.5 18.607 1 21
Osa04LNT0280100.2 osa-miR5143b Cleavage 4.5 14.599 1 24
Osa04LNT0280100.2 osa-miR5143b Cleavage 4.5 17.298 1 24
Osa04LNT0280100.2 osa-miR5819 Cleavage 1.5 20.266 1 21
Osa04LNT0280100.2 osa-miR6254 Cleavage 5.0 17.491 1 21
Osa04LNT0280100.2 osa-miR5079b Translation 4.0 9.873 1 22
Osa04LNT0280100.2 osa-miR810b.2 Cleavage 5.0 14.179 1 21
Osa04LNT0280100.2 osa-miR2104 Cleavage 5.0 14.638 1 22
Osa04LNT0280100.2 osa-miR5079a Translation 4.0 9.873 1 22
Osa04LNT0280100.2 osa-miR5143a Cleavage 4.5 14.599 1 24
Osa04LNT0280100.2 osa-miR5143a Cleavage 4.5 17.298 1 24
Osa04LNT0280100.2 osa-miR5145 Translation 4.5 15.83 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0280100.2 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0280100.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0280100.2 4 nan Morphological trait Root RZ23 RM255
Osa04LNT0280100.2 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0280100.2 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0280100.2 4 qPN-4b Resistance or Tolerance Drought tolerance RM317 RM255
Osa04LNT0280100.2 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
Osa04LNT0280100.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0280100.2 4 gpp4 Morphological trait Seed RZ569 RZ565
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