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

>Osa08LNT0406300.2

CAGGCTGAATCAATGATTATGTAAGGAAAAAACCCACGAATACATTTGCAGGGGATGCTGTTGATGAGTAATTTTGCATACATCGTTGTACAGATTCTACTGAGAACAAAACTCTTACACATTACAATCTAAAGATGAAGCACCAATGCATATAAAAAATGAAAATAAAGTTTTACATAATGATCGGAGTAATGTGTCCATGGTGATGGTACAACTATATTTGATCATACAAATCTACCAGTCAAAAGAAGACATTGTGGCAATAACATTCTCCGCTGAAAGGTTCACATCTGGAGTACTAATTGCAATGGACCTTTCATCGCTTGAGTTGCCTGAAGCTGAAAGCCATTCAAGATCCAGAAAGTTTGAATCACCAGAATGAATGCAACTTTCAGTTTCAACACCTAGAACATGATGTATCTGAGGTACCATGGGAGTATACCTTAAGTTTGATACCTCACTTTCAGAGGTCAATGAAATTTCATTGCCATGTACTGAATTAGATTCCAACACTGGAAATTGTGACCCACTTTTAACATCAAGCAATACTACATTCAACAGCTCCTTGTCTCCATTATGGCAACCACTACATCCAGATATGGATGTGTTGCTTTCACAAAGAATGTTGCCATATGATCTCACTCTTTTTACTGTATTGTGGAATTAAAGAAAACAGTATAAGAACCCCTTACTGTTTTACAATGTGCATATTTCAATAAGGATTATTTTTGTTTTCTTCGAACGTAATCAGCAGGGAAGCTACAAAAGGTAATACATGGCTAAAAGCTCTAGTTTTAATAGGAACAAACATCCTGCTACAGTTCAAACACGTTTTGGAATAGCAAATCAACATAACATGCAACTCCTAACTATGTTTTCACTACTGCGTACCATTGACTCCTGTACCATGATTTTTTTTTGCTACTTACTGTTTTTTAACAATGCTTCAGATGACCTCTCTTTGCAGAGAATATTTTCAGAAAAAGATCACGGTACAGATAAATTAGACGAATGTCCATCTAAAATGAGAAATATAACACCATATGAAGTCAAGCAAAAGGGCAAATATATTCTCTACTGAAGTTAAGTAATAGAATAGCAGTGCAGAATCCACCAATGTCCTTCAATGAGATGCCTTACTGCAGCGTATCATTGTCCAACTGAAGCTAAGCAGGTTTGTCAATATAAATGTTGATTTCATAATAAAGAAAATCATGCAAGGAAAGTTCTTTTATGGGTGTTAAATAATTCATAGTGGAAGTCTAAAAGATAAGAAAAAGGAAGCACTTTAGTGAGCCCAAACGCTACCTAAGCTATTAAAGCTTAAAATCAAATGTTGTAATTCCCTTCCAGGCAGCCATGACAACCAACGAATATCACTTCTCCGTGAATAACCCAATTAAACCATTGTTCCTACTTTAATCCACGATCGCCACATGGGAGCACCAACCGTTTATCCTGCCTATTCAACTGTGGGTTGTTCTTAATGATTTTGACATTTATTGAAGATATCACCTGGACTGCAGAGAAATTAGGAGAAGTTTGAACAAAGAGCCACATATGTTCTAAAGATCACTTTGGAGTAATTGATCATCTTGATTCTATCACTCACTGGCAGTGGCAAGGTTGCAATTTAAAAGAATTTCAATAGTTCTCGCTTTTATTTGAATCGGTCATTCATTAACTTAAGGAAATGCATCGGTAGGTGGTGATTGTTCAATTGATGTAGCAACATAGATGCTAAAAATGGATTCATCTAGTCTTAAGGGCATTGCAAACAATTATTTGCTCGTGGAAAGGTTTAGAAAACCATTTTGGTTTATGAGAAAAGCTTCCAAAATAATTAGGAATCAGAATCATTCAAGACCAACACAGAAAGTGAAGCAGCCATACCTCGTCATAGGGAATGATGATAGAGGAACGGAGGAAAACATCCTACAGGTAAACATACATCATATACATCAGAAGGACAAACGGTATAACCACCAAGCAAATGTGTAATTTTCAATGCATATATGCAAATCAAATATATATCTTTTTGGTAGATTTTTTTTATAAAAAAAAACATTAACTCGAATAAAAACCTCTTAGCTTCAACCTCCTAATTTGATTCGCACTGTAATCCAAACATACCATCTAGCATCCTTATAACTAAATCCAAATAACCACCATCTAGCATCATTTCGACCAAATCCAATTTTGCTTTAAAAGGTTAAATTTCAACATACAATACAAGATATGCCACCAGCTGTAGAGTAAATAACAAAAAAAAAAAACAGGGGGAAGATTTCAGTGCATCCATGTAATAGTATAGACTGATAGCCATAATTGTTGCAAACTCACAACACAAATAATAGCACGGTTGGGGAAAGTTTTAAGACACAGACCATTCTTCTGATAAGTGCTTGACTGCCCGGACTTGTAGTGAGAGTGGAAGAAGCACACAACCTGCATCAATCATCACCAGGAAAAATCCATCATTAGCACAACTGCACAAGTCGCAATTGGCAGACTCTTAAGAGAACTTCCCTTGAACAGTGCATCGAACAGGGACTCACTGAGAAGTAACAATTGGCTGATGGCACCCAGAGGTTGGAGCTGCCAATGTCGAAGATGGCGGTGAACTTTTTATATTAGAAAATGCCATATTCAAAAGGGAAAAAAATAATTGCCAGGTTGAAATTTTAAGTATTTCACAATATTTATGTAGGGTTTATTTTGGTCTTACAGATAAATTACTCTCTTGGTGTGACTGTGACATCTAACAACCTTCCAATTGCAAGGATACACATCTTGTTCACGCCAGTTGAGGAATATCCCATCAGAAGTTGTAACTGCCTTCTTGAAGGCAAGAAGTGCTTCATCATCTGAACTTAGTGCACTTGCTTCACGAGCACCAAGGTGCAGAATTAACAAAATTAAGAGGAAACTGGGCTGTTTTCTCAGAAAAGAGCCCATTGGTCACCAGTTGGTGAAGCATATAAAGATCACCTCAGCTTATTACAGAGTTCATGTGTGAGGTATACTATGTGGATCCTCTTTTATGGGAGATGAACTCCACATGTAGATGTGGCCCTGATGAGGGAGGCAAATTGCTGGCACTTGACGCAAAGGACGCCGTCGATCTGGATGGAGACGTTGTCCTTGGTGATGGCGGACTGGTCAGGGATGGGGATGGCCTCCTCCTTGAGCGAGTGGACGTAGGCGATGTGGTCGACGAGGGGGGCGAGCACGTCGATCCCGGAGCCGAGCGTCTTGACATACTTGTCGAACAGCTCCACCACGAACGCCTTCTTCTCCAGCACGATGCTCACCCCCCCCCCAACCTCCCCCAACAGTTCACCGCCGTGCTCAGCACCACGTACCTCGAGACGTCGTCGCGGGAGAAGGAGCATCGAGGGAGGGGGTGGGACGAGAGGGAGCGGGCGGCAGCGGCTAGGGTTTCGGGGGCCCGCGATGGTGGCGGGGGCGGTCGACGGCGACGGGGAAGCCGGAGGCGGCGACGTCTGTGGCGGCGCGAGGCGACGGCGACAACGGCGCGAGGCGGAGGTGGCGGCGCGAGGCGGAGGTGGCGGCGCGAGACGGCGGCGGCGGGAGAGGGAGAGAGTGGGGGACGAGGGGGAGCGAGCGGCGGCGGCAGCAAGGGTTTGAGGGGCGATCGACGGCGACGGCGACGCGAGGCGACGGGGAAGCCGGAGGCGGCGGCGGCGGGAGAGGGAGAGAAAGAGGGGAGGAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.883109
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa08LNT0406300.2 osa-miR5541 Translation 5.0 17.386 1 21
Osa08LNT0406300.2 osa-miR5788 Translation 4.5 15.399 1 21
Osa08LNT0406300.2 osa-miR5815 Translation 5.0 16.066 1 24
Osa08LNT0406300.2 osa-miR395f Cleavage 5.0 18.801 1 21
Osa08LNT0406300.2 osa-miR395f Translation 5.0 20.911 1 21
Osa08LNT0406300.2 osa-miR396a-5p Translation 5.0 11.601 1 21
Osa08LNT0406300.2 osa-miR396a-5p Translation 5.0 19.335 1 21
Osa08LNT0406300.2 osa-miR396b-5p Translation 5.0 11.601 1 21
Osa08LNT0406300.2 osa-miR396b-5p Translation 5.0 19.335 1 21
Osa08LNT0406300.2 osa-miR444d.3 Cleavage 4.0 15.986 1 21
Osa08LNT0406300.2 osa-miR2093-5p Cleavage 5.0 18.668 1 20
Osa08LNT0406300.2 osa-miR2874 Translation 4.0 14.334 1 24
Osa08LNT0406300.2 osa-miR2876-3p Cleavage 5.0 13.476 1 21
Osa08LNT0406300.2 osa-miR5075 Cleavage 5.0 16.818 1 21
Osa08LNT0406300.2 osa-miR5075 Cleavage 4.5 17.166 1 21
Osa08LNT0406300.2 osa-miR2863c Cleavage 5.0 13.534 1 24
Osa08LNT0406300.2 osa-miR5496 Cleavage 5.0 6.877 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa08LNT0406300.2 8 nan Resistance or Tolerance Drought tolerance RM72 RM331
Osa08LNT0406300.2 8 qDSR 8 Resistance or Tolerance Other soil stress tolerance RM3572 RM404
Osa08LNT0406300.2 8 hd8 Physiological trait Flowering RZ562 RG978
Osa08LNT0406300.2 8 qALRR-8 Resistance or Tolerance Other soil stress tolerance RG978 C1121
Osa08LNT0406300.2 8 dth8 Physiological trait Flowering RG333 RZ66
Osa08LNT0406300.2 8 hsa2(t) Physiological trait Sterility nan nan
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