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

>Osa05LNT0311700.2

GTGTTTTAAGTATTGTTAGTTTGAATATGATTATTCTATGCATGAGAAATAGTTAAACTATACACAACATAGAGTACACATTAAAATATAAGAGAAAAATAAATAAAGTTGCTAGAGTTGGAAAATATTTTTAGGTCCTCAGGAAATTGGACCAGCCCCCATTCCCAATTCAGCCTGACCTTTTCATTTTAGGGTTATGGACTTTTAAAACGAGAGGCTGTTGTCTGAGTTGCTATTATGAAACACATCGATAGTCTCCATTCCATCTGTGCTTGTTTTCGTTGAAAAAAAATAGGTGGACAAAGAGAAGTATGAACTAGAAATTTCAATGTTTTTCAATGGACCGTATACATGGATAATCCGAAGAAAAAATATCTTACTTTTCAAACTGATCACAACGCTGTGATCAGAGTATGCTGTACAAACAGGGTAAAAAACACGGTAAAAACACAACAATGTGAAAAGGAACGCACAGACTTGATATATAGTTTCCTCAGGAGTCCTCTGCGAGATTATACATTTGACGAAAAATAAAAATCACATTAACGGTAGGCCAGTTCTAATCTCTCTAAACCATGGCCACATGATCATCGGCAAAAGCTTCTCAAATATAAACGAGATAAAGAGAGCATCACATATTACGAATTTTTACATAAATACCAGGGAGGACGATCCACAGATGGACTCATCTCAAGCAAACATGAAAATGGTAACAAGAATGCCCTCAGAGCTCATACAAATATCCATCGATGGTGCGGGAGACAGCCTCAAATTGTGTGAAGGATCTGTGATGCTAAACCACTTCCTGGGATGATGGTAAAGTACACAGCCTTATATTTGAGGGCACAGGTTGGTAGCATATTTGAGAGAGAGAGAGAGAGAGAGACGCACAGAGCGAGAGAGAGAGAGAGATGGGTACAGCACTTCCCAGAAAGCCAAACACCATCTCTGTATATCAAGTTTCATCATTGGGCTTCAAATCAAAGCATGGCACCTACGTAGTGCTAAACCTTGGTGAAACTGCCAATATCAATCAAATAAAACAATGATCCAATTCAGAATCGCAAATACTGGCCAAGCAACAACACAAAGGTACTAGAGAGTAGAAACACAATATGATATTGAACAGTTAATAAAAACAAACCTACACAAGCGACAACAAAAATGTACTAAAAGAAATGAAGCACTCATTATGTGATATTATAACAGAAAAGAATGCAAATGATGAGTCTCTCGTCAAGCCAACATACCCAAACCTGCTGGAAACAAAAAATAGAAAGTGTCCATTTTGATTAACCCCTTAACACTTGTCCAAGTCCAGGAATCGCTAACTCAACAAACCGTGGCCATTCAACATTACCCACATAAATAGTTTCTTTGCTGCCTAGGTGGAGGGGCCATACCAAAACTTATAATTATGTGCTAAGCAGTGCTGACTCATCAACATGTTCACTTGTACACATTTCACCAGCATGGTTTTGGGCAATGGGGAGTTTGTAATGATTTTGATAGATCAAAGATGTTAAACATGCGATATTTGTAGTTTTGGGTTGCCGCGAATGTTCAGGTAAAATGGCCAATAGTACAATAAAAAGAACATTGACAAAAAAACTTACAACTTGTGCATGTGCAGGGAAACTTTATTGATGGCAAGTCTCTCTGATGCATTTCATTGATGGCATATATGGTCAGTGATTTGCCCGCTAAAACTTATGCAGTACCTGCATTCCAAACAGATCCTTCGATGACAAATTCCCTACTCGTGCATGGATTTTGAGGGAGGAGAGAAGACCAAGTGCCATCTATGCATATTAAGTTTTTATTATTAGGCAATGCATTTAGATATGCTACTACCAAGCAAAGCAACATTGTAAAAATATGGAAATATGAACCTGCTGGTAATCAAGACCATGGCTATCGCAGGCTCTTGATTCATCGTATTATACAGGAGGTAATAAAAAAAGGTGGTAAACTAGATGAGAGAAGGAATATCGACAAGATATGTTAACACAAAAAAGAGATAAACAATGTAGTGGCATAAGTTGAGGTATTTTGAATCTACGAGGAATAGACAAGGTGGAGATATTTGAATTGTTCTGAACATCAATCACTACATCTGCAGCCATGATACATTAAGTGTGTACTTGTTTGCACGGCAATGGACCAACTCCGTCAGATAGTAAATTTCTGGGAGTTACATCAGGCTATTAAGGAGACACAGAGTCTGAGAGGCAAGCAACAAAACTAAAAGATCCAAACAAAAAGATTGAAAGGTCGATATTACCAAATGGCCCTCTGATTTCACAACTTTGTTTTTCATCTTAGGCTGGCTAATGCGGCAGCCCTCAATGCTGGCACTGAAGCATGTCTCAAGGGAACGGCAGAACTGGATGATGATGATCGATGACGACGACAACGACGACAACTGCCACAGCAGTGGCAGGAGCGGAGGAGGACGAAGAAGAAGAAGAGAAAAAGAAAGAAAGAGAGCTACTTTTCCAAAGCAGAAGCAGCAGCAGAAACCATGGTCCTGCCAATTGCGCGGACCGACATGTCAGTGTTTCTCCAACCCCTGAGCATGCTTCAGCGCCCAGATCATTGAGGAGCCAACGCCACACTAGCCATTTTCAGCTCAACCCATTGCAGATGCAAAGGGCAACCCCATTAGAGCTCAAGTCCGAGCCGATCTATCTATCCATCCATCCATCAACCAATCGATTTATCGATTCACGAGGGTCTTAGTCACAATCATCATTGGGCCAATGGCGAATCCAGGCAAAAACGAGAGAGATCAGAGGCACCATGCCACAGTGAAAACGAAACAAGCGAAATGCATAAGAGACAGGTGCACCAGAAAAAGGACCATCCATGGATGGACTCATCTCAAACGAACTGGCAAACGTGCCATAAGAAAAATAATGCCCTCAGAACTCACATACACAGTATCCATTGATGGTGCAGGAGACAGCCTCAAATTGTGAGCAAGGAAATGTGAGGCTGAATGAATTCCTGGAATGATGATGGAAGGTTAAGCTAGCTAGCTACACATGCACAATCATTGGAATGAACCATTCCAAATGATGACATGTACGAGAGAGAGAGAGAGAGAGAGAGAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGACGGATGGATGGATACAGATCATACAGCACTTCCAGGAAGCAAAACACCATCTCTGTAAATCATGTTTCATCACTGGGCATTTAAATCAACTAAATCAAAGCATGGTACCTGTTATTCTACTGCAGAAGGTACTAAATTTAGGTGAAATTGCTAGTCTGAATCAAATAAAACATTGGTCCAATTCAGAATCAAATCCAGATGCTCTGCAAAGGTGGGGAAACATATATGACTACGTGGTCTTGAACAAGGAAAACTTCAACCAAGAGAAAAGGAGGGGAAATCGTGCAAGTGAGAATTTTCCTTTTTTAAAAAGGAAAGTCATAAAAAAGAGGGGAAGTCACGTTCTTGATTGATTGTATGAAGGGGATTAAGAAAGGAAGCAAATGAGTTATTTCTCAAAATATCATGGCTCATAAGTGGATAGTGATTTGGTTTTATGATATGGACGACTGTCATGAAGTCCAAAAGGTACCACTTCAATACACTCTGGTTTCTTGAACAAAATAAATAACATGGCAATGAAAAAAATAACAAATGAACTTATCACAGTGTAAATAAAGTAATAAACTAGTCAATCTGCAGAATGAAAACCCTCAGAAGCTCTAGCCTAGAAAAGGTGTCGAACTTATCACTTGGAGCACAAACACAAGCTGACTTAGAATAAGTCAATAAGAGTATCTAGGAACCGTCATCTGGGAAGAGTTAAAGAGTCAGCTCTGCTGGGTGTCTATCAGTTAAAAATGAGACGAAAATACTGGCCGAGCAACAAACAGAAAGGTTAGAGTAGAAACACAATAAACAGTTTAACAGAACAAACCTACACAAACCACAGCAAAAATGTACTGAAGGAAGTGCAAATGAAAAGCCTCTCATCAAGCCAACATATTCAAACTTGCAGGGAACAAAATTTTGAAAGTACTAAGTCCATTTTGATTAACCCCCTCAACTCTTGCTCAAGTCCGCAAGTTAAAAAACAGTGACCATTCAATATTTGTACCCACGTAAATAGTTTCTTTGCTGCCTAGGTGTGTTTTGAGTATGATGTGAGGAGCCATGCAAATTTTTATTGTGCTAATTGAGCATTTCACCGGGTCCACTACGTCCATTTGTACGCATTTCACCGGATTGGTTTCAGCAATGGGATGAGTTGCAATAACTTTGATAGTTCTTGAACATGTAGTTTGGGGTTGACCAGGAAGTTGAGGTGGTAAAATGGGCAATAGTAGACTAAAAATATCGAAAAAACATACAGCTTGTGCATTTGCAAGGAATGTTATGCCCTCAAGACTCACTTATGCATTTCATTTATGGCAACATATATGGTATCTGATTTTCCCGCTAAAACTTAGCGGTACCTGTATTCCAGACAAATCCTTTTGATGGCAATTCCCAACTGCTGCTGCTGCTGCTGTCACATGAGGGGGGAGATAGAGGGGGGAGGAGGAGCCGAGGAGGAGGAGGAAACCATGTGCCATCTCTGCATAGTAAGTTTTCATCATTGGGCAATGCATCATCATGCTACTACCAACCAAAGCAACATGGTAAGAAAAAAAATAATATGAACCAGATGGTAGTCAAGATCATGCCTATTGCAGGCTCTTGATTCATCACATTATACGGGAGATGATAAAAAATAATAAGGAATACAAAATGAGACAAGGATGAACCAGAACGTATGTAACAGTATGATCCTAATGCCCTCTGGCTTAAGACATAAATGCACCTCTGCATTTCAAGATGACACAAGAGACGGGCATCCAATTTGTAAATCAAAATTAGAACTCGACGAGGCATGTTAACACAAAAAACAGAAACAATGTAGTAGCATAAGTTGAGATATTTTTGCAATTGCTAGCAATAGACAAGTGGAGAGATGTGAACCGTTCTGAAGATCAATCACTCAGACATCTCCAACCATGATACATTACGTGCGTGCTGTTTACACGGCAATGGACCAATTTCGTGCATTACATCAGGCTATTAAGTAGACACAGAGAGTCAGAGAGGCAAGCAACAAAACCGAAAGATCCAAACGAGAAGACAGAAAGGTCTGTATTACCAATTGGCCCTCAGATTTCACAACTTCGTTTTCCATCTTAGGCTAATGCGGCGGCCCTCGACGCTGGCACTGGAGCATGTCTCAAGGGTACGGCAGAAGAGGACGATGATGATGATGCACGACGACGACGACGACCCGCCGCAGCGGTGGCAAGAGAGGAGGAGGAGGAGGAGGAAGAGGAGAAAAAAGAAAGAAAAAGAGCAGGTTTTATAGTATAGCAGAAGCAGCAGTAAACCATGTTCCTGCCGCGTGGGCGGGCCCACATGTCAGTGCCTCTCCGACCCCCCCAGCATGTTTCAGCGCCCAGATCATCGAGGAGCCAACGCCGTACTAGCCATTCTCGGGACCTCAACCCGCTTGCAGATGCAAAGGGCGAGCCTCAAATCCGAGCCGATCTATCTATCCATCCATCAACCAACCAACCAATCGATCGATTCGCGAGGGTCTAAATCGCAATCATCATCGGGCCAACGGCAAAATCCAAGCAAAACGAGAGAGATCAGAGGCATCAAGCCACGGCGAAATCGAAGCGAGCGGAAATGCAAAGACGAGACGGTAGGGGAAGCGGATACGAGTAAACCTCCCGCCGAAGCGGGGCCGGAGGCCGGAACCCCGGTTGATCGGATCGGCGAGCTCCCCGTGGCCGGCGGGGGCTCCGGAGGATCGGAGAGCACGAGGGATTGCGGCCTCTCCGCCTCCGCGAGACAACCCGAAACCCTAGTTTTGCCCGTGCTCTCGCGTTCTCTCCCATCTCTCTTCCCTCTTCCCGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.971941
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0311700.2 5 21451315 A C
Osa05LNT0311700.2 5 21451340 T A
Osa05LNT0311700.2 5 21452163 A T
Osa05LNT0311700.2 5 21452290 A C
Osa05LNT0311700.2 5 21453418 A C
Osa05LNT0311700.2 5 21454102 A C
Osa05LNT0311700.2 5 21454464 G T
Osa05LNT0311700.2 5 21454598 T A
Osa05LNT0311700.2 5 21454735 A G
Osa05LNT0311700.2 5 21455291 T C
Osa05LNT0311700.2 5 21456849 C T
Osa05LNT0311700.2 5 21451348 G A
Osa05LNT0311700.2 5 21457097 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa05LNT0311700.2 osa-miR5179 Cleavage 4.0 14.038 1 21
Osa05LNT0311700.2 osa-miR5834 Translation 4.0 15.887 1 21
Osa05LNT0311700.2 osa-miR5079b Translation 3.0 12.505 1 22
Osa05LNT0311700.2 osa-miR5079b Cleavage 4.5 12.949 1 22
Osa05LNT0311700.2 osa-miR156b-3p Cleavage 4.5 12.062 1 21
Osa05LNT0311700.2 osa-miR156c-3p Cleavage 4.0 6.299 1 22
Osa05LNT0311700.2 osa-miR156c-3p Cleavage 4.0 17.91 1 22
Osa05LNT0311700.2 osa-miR156g-3p Cleavage 4.0 6.299 1 22
Osa05LNT0311700.2 osa-miR156g-3p Cleavage 4.0 17.91 1 22
Osa05LNT0311700.2 osa-miR166c-5p Translation 4.0 21.264 1 20
Osa05LNT0311700.2 osa-miR166d-5p Translation 5.0 14.713 1 21
Osa05LNT0311700.2 osa-miR166l-5p Cleavage 4.5 20.537 1 21
Osa05LNT0311700.2 osa-miR166g-5p Cleavage 4.5 20.22 1 21
Osa05LNT0311700.2 osa-miR529a Cleavage 4.0 18.815 1 20
Osa05LNT0311700.2 osa-miR1428a-5p Translation 5.0 10.408 1 21
Osa05LNT0311700.2 osa-miR1854-5p Translation 4.5 14.244 1 21
Osa05LNT0311700.2 osa-miR2101-5p Cleavage 5.0 15.263 1 22
Osa05LNT0311700.2 osa-miR3979-5p Translation 4.0 13.553 1 20
Osa05LNT0311700.2 osa-miR3979-5p Translation 4.5 13.608 1 20
Osa05LNT0311700.2 osa-miR2873b Cleavage 4.0 17.641 1 21
Osa05LNT0311700.2 osa-miR3982-5p Translation 4.5 16.272 1 21
Osa05LNT0311700.2 osa-miR5079a Translation 3.0 12.505 1 22
Osa05LNT0311700.2 osa-miR5079a Cleavage 4.5 12.949 1 22
Osa05LNT0311700.2 osa-miR5151 Cleavage 4.0 10.032 1 22
Osa05LNT0311700.2 osa-miR5500 Cleavage 4.5 16.916 1 22
Osa05LNT0311700.2 osa-miR5831 Translation 4.5 12.549 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0311700.2 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0311700.2 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0311700.2 5 nan Morphological trait Seed RG13 RG573
Osa05LNT0311700.2 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0311700.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0311700.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0311700.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0311700.2 5 nan Physiological trait Eating quality RM163 RM31
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