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

>Osa09LNT0441000.1

AGTACTGAAATGGGGCACATACATTAGAATCTATTAAGTGTCACAAAACCAATCATGCTCCACTACAATCACCGATAAATTAATTACAAGTTCTTTCCATAAGACAGGAGGAATATGAGTCTGAAATATGTTTCCATAGTTCAGACCAATTTGTAACCACTGGTGAGAACCTTTCCCTCTGTCTTAATGAAAAGACGCAAATATTTTGCGCATTCTTGGAAAAATGAAAGACGAGGAAAAAGAGATACAAGAGGCACCCACATTTCACGCTCATCAGCTACACCTAGCGTCGGCCCCGAGGTTTTGACCGCACTTTAGATGTACCACCAAAGCTGGATCCTGAAGCTGTAGCTCCACCTCCGAACGGCGTAGAAAACAGTGAGGTTCCACCTAAAGCGGGCGTTGAAGCAAAAGATGGAGTTGTATTCCCAAATCCAGATGGAGCCGGCGTTGATCCAAGCGTTGGAGTAGAGACTGTCCCAAATGGTGTGGACAGCTGGGCTGATCCAGATGTACCAAAAAGGTTGCTGGATAGAGTTGGAGTTGTTGGAGTTGAAAAGAGACTTGAAGAAGATGGAGCGGAAGCTGGAGTGCTGAATGATGGAAAAGCACTTGAAGAAGTCGCTCCAGAAGGAATCAATGATTGCTGTGGTTGACTCGTCACTGTTCCAGCAATTTGAGTTGTGGGCTGTACAGGAGCAGGCAAATGCAATGTTGGATGTACCCTTCTGGCAGCTGCTTCTTGTTTAGCCGCTTCTCGTCTATTTGCCTCTAAAAATGGATCATTGGCATTACCCAATCGCCGCTGCTCATGTAGATATTCAGTTTTCAATGACTCAACATATTGATGAAGATTTTCCACCTTAGAAGCAACATAGATGAAATAATCATGCACATTCGACATAACCTTCGGTAGAGATTCTAATGAGGCTGATTGCCTTTTATTGTTCTCCATTTGAACAAGCTGCTCTAGCTCCGCGATCCACTTGCAGCATTCTCCAAGATATTTCTCAAACCTGTTGATAGTCTGTTGCATAAAATGGGAAGGCCGCTTTGGGATACCACTATAGAAATCAATGGTTGGAGCCAATGCTACTGGCTGATTGGACTGAGCTCCAGCAGGACCAGAAGGATTTGAGCCACCACCATTTGCTCCAGCACCTGGACGGATAAATCTTGGTCTCAGCATCATATATGACCTAATAGCAAATTCTGTGTTTCGCATCATTTCATTCACAACAGTCATTAACTCTTGAACGGAAGCCTTCTCTCTTTCCATCATGGTGGTTGTCCCTCCAAGTTCCTGAGCAATTTCACTTGCATCATTCTCAAAATTGACAGTTGAGATTGAAGAGTCATGAAGGCGAGAACACTGATCCAACCTCTCGCTCTCGTCCCTGTACTCCCTTATTTTATCCCCTAAAACCCATGTATTGACCACATCAATGCAAAATGAGGCAGTAGCTTAAGTAATCCGTAGCAAATGGCATAGATCATAGAGCACAAAACGTGTTTCCCCTTCCCCTGAAACCCAAGTAAACAATGATCTGCTAAACCATCAGAAACAGTAGCCCTCCATAGTATATATTGCTAGAAGAACATATTTGTTTAAAGCAAACTGATCTCTGAGAGACTGTAAAGGCACAAGCTTATCGCATAAAGCGTTA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.465061
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0441000.1 9 17009403 G A
Osa09LNT0441000.1 9 17009467 A G
Osa09LNT0441000.1 9 17010086 C T
Osa09LNT0441000.1 9 17010692 C T
Osa09LNT0441000.1 9 17010998 A C
Osa09LNT0441000.1 9 17012010 A T
Osa09LNT0441000.1 9 17013562 A T
Osa09LNT0441000.1 9 17012337 A G
Osa09LNT0441000.1 9 17012795 G A
Osa09LNT0441000.1 9 17012875 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa09LNT0441000.1 DTM_#DNAt_MULE_japo_Os3366 Chr9 - 17012098 17013215 1117
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0441000.1 osa-miR1861e Cleavage 3.0 22.1 1 22
Osa09LNT0441000.1 osa-miR1861g Cleavage 3.0 22.1 1 22
Osa09LNT0441000.1 osa-miR1861k Cleavage 3.0 22.1 1 22
Osa09LNT0441000.1 osa-miR1861m Cleavage 3.0 22.1 1 22
Osa09LNT0441000.1 osa-miR2105 Translation 5.0 18.185 1 20
Osa09LNT0441000.1 osa-miR5150-3p Cleavage 5.0 23.549 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0441000.1 9 rdw9 Resistance or Tolerance Drought tolerance R79 R2638
Osa09LNT0441000.1 9 qSB-9 Resistance or Tolerance Sheath blight resistance C472 R2638
Osa09LNT0441000.1 9 nan Morphological trait Panicle/flower RM257 RM566
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