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

>Osa05LNT0313700.2

GGGGCTCACGTATTAGAAATATATTTTAGCTACAAATAGTTGGTGAAAATGGTATGTGTGAAGTGTGTTGTACAAACAAATGTACCATACATATTCACTCTCAAAATTTTGGTTTACACTTTACATGTATCTGGGATCTGGGTTACCAGAAGTTCATACATTTTCTGTGTTTCTGTGAGACCACAGGCCAGCGGCAAAGCTTTCTGCAGGCTTCTCGTTTTGGATGTGTTGTCCAGTATATGCCTCACCGTTGCATTGAGCATTGCAGTTGTTGCATCAGGTGCAAACACCCGGGAACAAGTTGAGCACTCAGTAGTCAGCACTCTCCTATTTGCTCCAACTCCAAAGCTCCGGAAGCATAATGCCCTTCATCTGCTGCTCCATTTCATTGAGCTCCATAACTGGCACGATGTGTACTGGAGACATTTGCAGTACATCACAGGCTCACAGATCGGCACAAACATACTGGACTTATCTATCATGGTTACAATTTTTGTCGCTATGTCCGCGCCAAAAAGTCATTAACTGCAAGTGAGGCATCACCATGTGCGACGGCATTCTCTGGCTCTGGCATGTAAAGTGTAGTAGTAGAAGCCTTCGTGTCTAATTGCAAGTCTCTGCTGTTGTCTATTGAAAGAATAGCACCATGAGCTTTTAACCACATTTCACACTCTTCTGATGCTTCACTATCAATTCTTGAGAATCCCAAAATTTGTGCAACATATCCCACTGGTATAGTCGGGCGATATGATTTAGACATGCATTTTACAGCCTCAAAACGCATTCGCTCCACATATAGATCCATGAGGCAAGAATTCAAGTTCGGTGCCTGCTTGTATAGTTTGAAAAATAGGACATAGTTTCCAGATGAAACAGCAGAATGAACTGCAAGGGCATGCTTGACAGCTTCATCTTGTTTGGCTTGTTTCGATAACCTTGCCAATGATGACAGCAAGTCTCGTTTATTATTAGAGTGCAACATGACACAGAGTAAATTGTACGCAGAGAATTCAAAGTAACAGCCCTTGATTCCCTCTGCATATAGCCTCTTCAGTTGTGACTGGCACTGGTTATATTCAGGTAGGTCACCTGCCTGCATTGCTAAACGTGCATGAGTTTCATAAACCTTGACAGTAAGTTCATTCTGGATTCTCTGAACTGTGAGATCTTGGCGAATAGACTTCAGTTGATCACATTTATAAAGATAATTCTTTTGAGATGTTTCAACCATGGAAAGGGCCTTCTCCAAGACATGCTCCGGTCTTACTGTGGCAGGATCAGGTGCTGATGTAAGCCGGAGATATCGTTTCTCAATTTCTTGGCATGTCCCCTTTACTGTCAATGCATCCCAATCCATATCCTCCACAGCCAAGGTAGTGCCATCTTCACAGCTTCTGGCAAGAAGAGCTGAAACAGCTCTTCGTGCATGTATATTAGCCATTACATCTTTACTTGCTGCAGAATTCCTCGATTTAGATGATGAATTCTGGTTCTTCTCAAAACGCTTTGACCTATGCTCCCTGCGCTTCTTCTCCTCAGGTGAATTTGCTAGTGCGGTTGCACTGGCATAATATTTGGTTAGATCCTGCTCCTTATCACTATCACTTGAAGCATTTCCATTTTGCATTTGATCTGAGTAACTGCTGATCTTTTGCTTCTTGGCAGGCCGCTGACTGACTTTGTTTGCAGTCGCATGATGAGACTGGAAAAATTTTCTGGAATCCCAGTTATTACTCATTCTGTTTTTGGCTTCCAAATTATTGTGGGTGGTACCATTCACCAACCCTTTTACCGGTTCCACCTTATCTGTAACCTTTTCCTCCACAACAGGCTCCCACCTACTTTTTTGGCGTCTCCTATTGGTAGATGTCGACAAGGAGGGACTTGAATTGTTTGCACTTGTTTCTGGAATGGTTGCAACATTTTGTACCAAAGGAAGCAGTGGCTCAGTGTCCCAATTCTTAGTAAGAAGGGTTCCATCAGCAATGGCGCTGTTTTTTATCTCTTCTATCATACTCTGGCAAGCAGCCTTCTGGGCCTCATCCTTGCAACAGTTGAGATTCCTCGTAGCATAATTATGTAATGAAAAAGGGAGTGATCTAGCATCATTCTTCACCATGGAAACACTAACATAAGCAGGCTTCTTTGACAAATCAGCACCTAAAATTTTCTTCTCGCTCTTTGGTATTACCATAGAAAAACCTGGAGCAATTCGAGGAACCTGCATTTTGTTTTCACTTGAATTTTCGGTTGCAATAAAAACAGTATTTTGTTGATCGCCATGATTGCTTTGCTGAACGGGGTTCAAATTCACAGTGCTCTGTGGGCAGGCTGGTGTCTGGCTGGCATAATGGTTTTGAGACCTTGGGTTACCTGCTACCTGGCCAGCATACTGGTTTTCCAACACCGGAGCGTGCGCCTGGTTGATATATTGATCTTGAGGCCCTGGACCACCTGAAGCCTGAATAGGAGGCGCAATAGAAGAACTTGAATTACTTTTCCATGATGTAGTTCCTGGAGGAGGTGGCTGGATACTGGGATAGGAGTAGCTAGAAGTAGTGTTAACAATTGAGTTACTGTTCCCGACTGGATCACCAGCAGGATTTGGCACGGTGTGATTGTAATAGTATGGCCATTGGTTGTACTGCTGTTGGTATGAGAAAGAATTGGTAGGCACTGAAATGGAATGCTGTACTGTGTTGGTATTGGATGACGGGTAGTTCTGATATGACTGAGCATAATTATTTTCAAAGCTTCCACCATTCCAGGTGCTGTTCTGATAATAGCTATTGCTAGTTCCATATCCTGGAGCAGTCTGAATGTTGATTTGTTCCTCCTTGCTGGACAGAAGAACCATTTGTAGTTTGTGGGTAACTATAATAATAGTTTGCATATTCTGCAGCAGTGTACCCATGTTGAAGTGAACTTGAGTAAGGCATGTGAGAATGAGTCGCATTTTCTGTGCCCATAGTTGGCTGAGCATTATGAGGTGCACTGCTTGCCACACTCTGATTGTCTCCCGAAACCGAAACATCCCTTTGTGGATCATAGTAAACTGTATCTTGGCTTTGATTGTTCACTGGATAGCTCCACGGGACTGTAGCTGCCCCAGTTGAAGAGGACCATGAATGATGCCCTAAAGCTAAAGGTGGATAAGTAGATGGATTTGTCTGCCCCACAATGCTGACCTCGGCAGGAGCGGCATCGGATCCAGCAGCCACCACCCCGGCGCCGTGGCTCGCCATCATTCCTCCCCCTCCCGGAGCTCCAACCCTAGCGAACCGGTCAACCGCCCGCCGCCACGCCAACGCAACGCAACGCACAACCGAACCGAGCTAGCGACCTCGATTCGTCGAGAGCGAGGCGAGAAGCCGATCGATCGGGGGGAGAGCAGCCGCACGCGAACGAATCGAAACCCTTAGGCAAAGGCGCGGTGGATTCAGGGAGGATTGGAATCGCGCGTGAGGTTTTTTTTTTTGTGTGTGTGTGTGTGGGAAGATGCGGGAAGCGAGAGGAGAGGCGGAGATGTTGCCAGCTACGGAAAGGAGGACGAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.879462
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0313700.2 5 22725637 T C
Osa05LNT0313700.2 5 22725683 G C
Osa05LNT0313700.2 5 22725849 G A
Osa05LNT0313700.2 5 22728055 A G
Osa05LNT0313700.2 5 22728117 C T
Osa05LNT0313700.2 5 22729683 T C
Osa05LNT0313700.2 5 22730023 A T
Osa05LNT0313700.2 5 22731805 T C
Osa05LNT0313700.2 5 22731974 G C
Osa05LNT0313700.2 5 22732275 T C
Osa05LNT0313700.2 5 22733220 T C
Osa05LNT0313700.2 5 22731623 A C
Osa05LNT0313700.2 5 22733845 A C
Osa05LNT0313700.2 5 22728919 G A
Osa05LNT0313700.2 5 22730382 C T
Osa05LNT0313700.2 5 22728338 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
Osa05LNT0313700.2 osa-miR5528 Cleavage 4.0 15.789 1 21
Osa05LNT0313700.2 osa-miR5543 Cleavage 4.0 18.062 1 21
Osa05LNT0313700.2 osa-miR5793 Cleavage 5.0 18.554 1 21
Osa05LNT0313700.2 osa-miR1437b-3p Cleavage 4.0 20.786 1 24
Osa05LNT0313700.2 osa-miR167a-5p Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR167b Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR167c-5p Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR156k Cleavage 4.5 15.48 1 21
Osa05LNT0313700.2 osa-miR159a.2 Translation 4.0 24.678 1 21
Osa05LNT0313700.2 osa-miR166k-5p Cleavage 5.0 12.961 1 21
Osa05LNT0313700.2 osa-miR167d-5p Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR167e-5p Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR167f Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR167g Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR167h-5p Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR167h-3p Cleavage 4.0 19.243 1 21
Osa05LNT0313700.2 osa-miR167i-5p Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR167j Translation 4.5 23.343 1 21
Osa05LNT0313700.2 osa-miR528-5p Cleavage 5.0 14.295 1 21
Osa05LNT0313700.2 osa-miR529b Translation 3.0 17.269 1 21
Osa05LNT0313700.2 osa-miR1860-3p Cleavage 3.5 13.974 1 22
Osa05LNT0313700.2 osa-miR1865-3p Translation 4.5 21.287 1 24
Osa05LNT0313700.2 osa-miR2874 Cleavage 5.0 23.37 1 24
Osa05LNT0313700.2 osa-miR5157a-3p Cleavage 5.0 18.371 1 24
Osa05LNT0313700.2 osa-miR5157b-3p Cleavage 5.0 18.371 1 24
Osa05LNT0313700.2 osa-miR2275c Translation 4.5 15.268 1 23
Osa05LNT0313700.2 osa-miR5523 Cleavage 3.5 17.505 1 22
Osa05LNT0313700.2 osa-miR5803 Cleavage 5.0 20.752 1 24
Osa05LNT0313700.2 osa-miR5512b Translation 4.5 21.843 1 21
Osa05LNT0313700.2 osa-miR5512a Translation 4.5 21.843 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0313700.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0313700.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0313700.2 5 nan Physiological trait Eating quality RM163 RM31
Osa05LNT0313700.2 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0313700.2 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0313700.2 5 nan Resistance or Tolerance Drought tolerance C43 RZ70
Osa05LNT0313700.2 5 nan Resistance or Tolerance Drought tolerance C43 RZ70
Osa05LNT0313700.2 5 APAGE1 Physiological trait Eating quality nan nan
Osa05LNT0313700.2 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0313700.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
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