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

>Osa02LNT0182800.1

CGTCAGGAAAGCACCATCTGAATATCTGATTATGCAGACTACCTTACGTAAAAGAAATGCCAACTACACCAATCGAATCCCAGTGACTTTAATTATCACCAAAATCAACATGAACTGATCAGTTCTTGTCCAGTACCGTTTGGACATGTATAGAACAACCAATTTGTCAGTAACAAGAAAAGGTCTACAAATTCACGGTTTAGAATTTTTTTTTCACCGCTGCATTCTTATCTACACCTATCTCTGCAGAACCTGCAGGCAATTTGTACATATGTACTTATTATAAATGGAACTCAAAATGGTTGAGTTCAACGTGCAAACAACGAATTTTTCATATCGCACTAACTAATGCACAGATCACCACGGAGATGTGCGATCGCCAACTAAAACGTCCCCAAGCAAGCGTCGCTGTACACGGCCACTCCATTTGCCACCAAAGCAAGAACAATCATGAACACCGCGAGATACTTGTCGCCCTTCGTCGCTATGCCGTGGCGATCCCTCAGTGCCATTCCAGCAGGGAAAATGTAGGCAATGGCGACGGCGGCAGTGGCGCCAGTGAACTGGAACGCGTCCCAAATGTTGGGGACGAAGTTGGCGGCGAGGAAGATGACCGTGAGGAGCGCCGCCGTGATCGCGCCGAACCTCCGGTTGTCGGAAGAGAGGGGCCTCGCCGAGGGGAAGAGGAGGCCGTCCATGTTGAACCGCAGCGCGTGGAACACAATGGGGAAGACGAGCATGAGGTGGAGCACGTAGCTGACCCTGACGGCGTCGTCGAGCACCAAGCTGTAGGGGATGCCGAGGTCGGAGTCGAAGTTTGCGAGCACGTCGTCCAGCGTTGCCTCGCCGAAGAGGAGGAAGCCGAAGAAGCTGGTGGTGGTGTACACGGCCAAGCAGAGCAGCAGCGACGCCCGCACTATTGGCCTGATCTGGGAGTGGTCCTTGAGCTCGTTGTGAATTGGGTGCACGTTGTAATGGCAAATGTAGGCGGTCACAAGAACTGGAGCTGCAGTGAAAAGTCTCCAGGTGGAGCTCCAGTCATGAACATCAGGGAACAGTTTAGGCATCGGAATCTGCCCTCTCATCAGCTTGATGGTGGTGATTCCGGCAGTGATCACCACGAACACGACGGCCAGAGCAACCGATAAGGCCGACGTGTATTTCAGTGAATCGACTCGCTTGAAGCATGTCAGTGGAGTGAACACACCGAGCGTGACGATGACGAGGATGGAGAAGCGGCCGTTCCACCGGTTTGGACCGAACCATCCTTCTATCACGCCGTGATGGTGCACGCCGCCGCTGGATGACTTCCCAGAGAGCACATCGCCGATGATGATCATGTAGACGACCATCACGCCGACGTTGTTGACGACGACGCAGAGCTGGAGGAGCCCCCTGCCGAAAGCACCGAAGGCGTCGCCCATGGCCTCGCCGTACGAGGTGGCGCCCACGGCGCGGCTGAACCGGACGAGGAGCTCGATGGAGGCGTCCGTGAGCACCGCGGCGAGCATCACCAGGATGAGGCCCGGCACGAGGCCGAGCACCTTCATGGTGGCCGGGAGCGCCATGATGCCGGCGCCGACGATGGTGGTGGACAGGTTGAACACCGCGCCGGAGAAGGACGCGCCGTCGAAGTGGTCGTGCGACGAGGCGGCGCCGTCGTCACCGCCGTCCCTCTGCTTCCTCGGGAGAAGTGGCTCGCTGCCCTCCGTCGGCATTGGCATCACCATCCTCGCTGATCCACGCGTGGATTTGCGCGGACGGAATTCCAGTTTTTTTAAATCGCGTTTTGATCTCTTACTGAGTAGAAGCTGAAAATTCTTCACGCAGACATGGATCGAAGAGTCCAAAATGCACAATCAAGACAGGCAGATTTGATGAGGTGATGGGTTCCCTTCCTTCTTCAGTTCTTCCCCTTTAACCTCGCGACCGGAAAACGCCGAGGCAGGCTATCGATGGCGAGAAAATAAGGGGAGGGACAAGCATGGTGGCGCTTTGGCCGGACGAGACGAGGCATCTTATAATTAGACGACTCCTGATTTAGCAACTAACACCACTCGCTAAAAGCCTAAATCAGCTGAAGTTCAAGCGAGCCACCGGCCACACCGCCCGCTTTTACATGGCATGCCTAAATCACCTGAAGTTGTAGCGCCACCAAGCCACGGCGGAACCCGTGCCGGCTCCGGCGCCGCGCACGGACGTGTCGGCAACGGCCACCGCTGCTGGCGCGAGCGGAAGGACGACGATGGTAGGAGGGTTTTGGGTTGTGAATTGGCCCATAAAAAAGTGGGCCTGTAGTGGGCCGTATGGATAGACGGGAAGAATTTAGCTGTGAAAAAGTTCACTTGAGTTCCCTGAACTGGAATACCAATGTCACTTGATTATCAGGTTCCTTTCGTTCTTAAACTGTTAAACATTTCCATCGATCTGCTTCTAAAATTTTAGTATAAGTACAATGGGACTGATCAAATACCAAGTATCTTTTGAAGTTGCAGTCTAGATTCAACTGTAGATCAACAGATTGTATTCAACTGTAGATCAAATCGTATGTATCTAGTTAACTTCTTAGCAAAAGGTGATGTAATTCAATGATCGAACCCATTTGAAAATCCATTTTGCCACAAACAATAGGACTACACACCATCAGGTGAATTACCTAGCAAAGAGAAATTAGACCTTTTTGATAAACTAAAGAAATATGCAACCTTTGATGCATATGGAACTATGGAAGCAATAGGGAGGAGGATCCACACAACACAGATAGTTCATACGCGAATGCTTCATAAGATACTCAAGTATAGGAATACTACCTTTGTGAAGGGATGCATAATAAGAAATAAAATAGAGAATATAAAAAGCTCCTAAATATAAAATAGGTTAACAATCACATACCTGTGCACTATTGCACTGTTCACTCTTCCTTTGTTCTTGATCAATTCAGTTGATGTCATTGCACCATTAGAATAAAAAGAATTGATGGTTAAAAACTGGGCAAAATAGAGTAAGGACAACATAATTCTCATTAGTCACAAACAAATGAAGTAGGAAAATTAAGAATCAGGTATAATAATCTTCATTGCCATGAGGGAAAAGATGTGCTGGATAATTGATTGAAAGAAAAAAGGGAGGCTGATCTTTCTTGATTCACCAGGGATGTAGAAGGTCGCTTCAAGCGTTGACGAAAAATTAAACCTCCGTAGACTATTTGTCATCTGTTTCTGGATCGAGACGATAAAGGAACTTCTGTTCAAAGGCTAGCACCTATTGACGTGATTTGACGATGAAGCTGCCAAAATTTCCAACATATTCAGCAGTCGTTGAGGTGGGGAGTTGTCAATTTCAACCAAAGATCCAACAAAAAAAGTCGATCGCAAACAGCCCAACTGCAAGGCACCATCGAGGAAGCTCTAAACAGTTATGGTGTTGATTAAAAAGCATGATGGTCTTTCTCAAAAAGAAAAAAAGCATGATGATGGGTTTGATTGCTGCTATTAAGGTGGCCTATCTTTTCAGCTCCGGTGCTTGCTTCGGCTTGTTTTTGTAGCATGCAAACACCGAGCATGTCAACAGTCAAGAACCTGGGAAGCCGCTTTAATTTTTCGGCTTTCCCAGTCCCGGCGGAGCGTGGAGCCACGAAGAGACTGAGAGGAAGCAGGGAGCGGAAACGACATAGGTGTTAGTAGGTGCCGGCGGTGGTGGTTTCGCTTCTCTCGGATGTGGATTCGGAACGACGCGGGAGAAGGAGAGTCAGCCATTGCTAGGGGCGGAGTGGGTTGCAGGGGGCAGACGAGCACGATGCGGCGCGGCGCCGCAGCGTCTGTCCCCACGGCGTGCAGCGAGATGCGGTACGGGAGACGGATGGTGCAGTTGGGAGCGAGCGTGAGCGTGATGCAGGGAGGCAGACGAGCGCGATGCAGCGTGGCGCCGCAGCGCCTGTCCCCACGGCGTGCAGCGAGAGGGATGCGGTGGGGGAAGCGGAGCGAGATGCGGGAGAGGAAGCCGATGCGGGCGCTCGCGCAAGAGAGGAGCGATGCGGTGGGGCGTGGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.37048
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0182800.1 2 30259614 G A
Osa02LNT0182800.1 2 30259734 A C
Osa02LNT0182800.1 2 30259756 G A
Osa02LNT0182800.1 2 30261438 C T
Osa02LNT0182800.1 2 30261453 A G
Osa02LNT0182800.1 2 30261529 A G
Osa02LNT0182800.1 2 30262508 C A
Osa02LNT0182800.1 2 30262654 A T
Osa02LNT0182800.1 2 30264719 G A
Osa02LNT0182800.1 2 30264786 T A
Osa02LNT0182800.1 2 30265289 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa02LNT0182800.1 DTM_#DNAt_MULE_japo_Os0709 Chr2 - 30260137 30261396 1259
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0182800.1 osa-miR5534b Translation 4.5 16.555 1 21
Osa02LNT0182800.1 osa-miR5535 Translation 5.0 18.978 1 22
Osa02LNT0182800.1 osa-miR5800 Translation 4.5 21.419 1 21
Osa02LNT0182800.1 osa-miR5821 Cleavage 4.5 16.158 1 21
Osa02LNT0182800.1 osa-miR5837.1 Cleavage 5.0 24.539 1 21
Osa02LNT0182800.1 osa-miR419 Cleavage 5.0 18.555 1 21
Osa02LNT0182800.1 osa-miR1425-3p Cleavage 4.5 18.792 1 21
Osa02LNT0182800.1 osa-miR810b.2 Translation 4.5 14.909 1 21
Osa02LNT0182800.1 osa-miR1440a Translation 4.5 19.255 1 20
Osa02LNT0182800.1 osa-miR1442 Translation 5.0 17.592 1 20
Osa02LNT0182800.1 osa-miR1850.2 Cleavage 4.5 14.192 1 21
Osa02LNT0182800.1 osa-miR1861e Translation 4.5 17.013 1 22
Osa02LNT0182800.1 osa-miR1861h Translation 5.0 17.013 1 22
Osa02LNT0182800.1 osa-miR1861j Translation 5.0 17.013 1 22
Osa02LNT0182800.1 osa-miR1861k Translation 4.5 17.013 1 22
Osa02LNT0182800.1 osa-miR1861m Translation 4.5 17.013 1 22
Osa02LNT0182800.1 osa-miR2095-3p Cleavage 1.5 20.282 1 20
Osa02LNT0182800.1 osa-miR2105 Cleavage 4.5 14.463 1 20
Osa02LNT0182800.1 osa-miR2875 Translation 4.0 15.904 1 24
Osa02LNT0182800.1 osa-miR5146 Translation 5.0 17.338 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0182800.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0182800.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0182800.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0182800.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0182800.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0182800.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0182800.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0182800.1 2 AsS Resistance or Tolerance Other soil stress tolerance RM318 RM450
Osa02LNT0182800.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0182800.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0182800.1 2 qER-2a Physiological trait Eating quality nan nan
Osa02LNT0182800.1 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0182800.1 2 Hd7 Physiological trait Flowering R3393 R2511
Osa02LNT0182800.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0182800.1 2 nan Morphological trait Panicle/flower RG139 CDO686
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