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

>Osa02LNT0182900.1

AGGTACAAGGGAGGAAAAAAGCATAAACAAAATGTTACATCTTGAAAAATATTGCTCTGCAAACTTATTCTACCAATAGTTACAGAATCTGTAAAAGTAGAAATATCCTATGCCTAGGAAGTGCTCTTCTTTTAATCTTTGTACAGCTGATCTGATACCTGCTTCGATTTGTGATTTTGCATTGGCATGCAGTTGCTTGCTTTAAATTTTTTTTTTTGGCTATTTTTCCATTGTACAGTGGTGTCTCTTGCTGTACAGATCCTGCTGCAAACAACTAATGATGGTTTGCCTTCCACTATTTGTTATCGTGTCATCTCGGCCCAGAGAGCTCGACTGCCTGGACCAGCAATGACGAGTCATCCGTCAGGTCAGAGTAGCAGCGACCGAAGGTGAACTCAGGCACTTTGAACTTGTGTGAGTCAGCGCGCTGGGATGCTTCCCACCGCTCTGCCAGTCCATCTCCCTCCAGCATCCTGACCACCTCTGACATCCTGGGCCTGTGACCAGGGAGATATTGGGTGCACAGCAGTGCCACCTGCACCATCTCCTCCAGCTCGACACGGTCGTAGTTGCTTCTCAGGCCCTTGTCGACAAGCACGTCGAGCTTCTTCTCCTGGTGCATCTTCTTCACCCAGTCCAGCATGGCTCCCTTCTGATTTGATGACTTCCCAAATTCAAGTGCAGTTTGACCAGTGATCAATTCAAGCAGCAGAATTCCAAAACCAAAGACGTCGGTCTTCTCAGATGACTGGCCGGTGGAGAGGTATTCCGGGGCAATGTGCCCAACGGTACCCCTGACAGCTGTGGTGACATGTGAGTCACGATGATCTAGGAGCTTGGCAAGCCCAAAATCTCCAACAATGGCTTCACAGTAGTCATCAAGCAATATGTTGGCTGCCTTTACGTCCCTATGAATAATCTTGGGGTCACACTGCTCGTGCAGGTACAGTAGGCCTCTTGCTGCACCGAGTGCTATCCTCTGTCTGGTGATCCAGTCCAATGGTGGCTTCCCTTTCAGACGCAATGCGACACTCCCATTTGACATGTATGGATATACCAGAAGCCTCTCAGTAGCAGTCATGCAGAACCCATAAAGCCTGAGGAGGTTCCGGTGAAGCGCCAAGCTGATCATCTCAACTTCAGTCTGAAACTGTGCCTGCCCGCCTGCAGCATTACCATCTTTCAGCCTCTTGACAGCTACAACAGTTCCATCTGGTAGCTTTCCCCGGTAAACGTTTCCAAAGCCGCCTTTTCCTAAGATGTTCTTATTGCTGAAGTTCTCTGTTGCAACCTGAAGCTCTCTGAACTGAAACCTCTTCACATTTCCTAGGTTGACATTCTCTGTGTGTTGCTCATCAACATCAAAAAGAATTTGATGGTTTCGCCTATGCCTCCACCAGAACAGCAATCCCATAACAGGGATAAGGAAGCTGATGCAGCCAATTGTAGAACCAAATGCAATTGCAACCTTGTGGCTTTTAGATTTTGCTGGCATCAGAGTACCCTGTGTATTATTCAGGCTGTAGGACATCGGCATTGGTAAAGTTCCATAACAATCATGTTCCGTACCCGCAGCACAGATCAACGGATTCCCCACTATATTGAACGTTCTTGCCAAAGAACCAGGTACTGGACCACTCAGATTATTATACGAAAGGTCCAGGAAAACAAGCTGTGATAAATTAGCTGATGATGAAGGGTATGCACCAGACAGGGTGTTGTTGTTGAGCCTCAAGTACTGGAGGCTTTCGAGGTGGCCTACTGAGTTTGGGATTCCACCAGAGAAGTGGTTACTGGAGAGATCAAGTGTTTTGAGTTTTGTTAGCCTGCCAATCTCTTCTGGAATTGGACCATTGATGTTGTTGTTCTGCAGAAGAACTATCTCAAGATTGGTCAAGTTGCCTATGCTTGCGGAGAGCAGGCCAGAAAGATTCTGGCTTGGAGCCTCCAGGCCAGTGACAAGGTTCTCAGGTGAGCAAGTGACCATGGTCCAGCTGCAAGGATCCACGGAGTCTTGGTCCCAGTTCTTGAGCACACCGTGAGGATCCTTGAGGGAAGTCTTGATCATCATGAGAGCTTGCACTTCATAGTTTACACCCTTGGGAGAGAGGAGGGCACTTGCAAGCCTGCAAGGGAAGGAGAAGGAGGCAAGCAACACCAGTGAGTAAACCGCAAGAGCCACCTCCATTGCCATGGAAGGGCGGAAGCAGGAGAGGAAGGGCTAATCGCTTGTGGTGGTGTGTTCAAACATGGAGGAAGGGTGAGGCCAAGGAAAAGAAGCATGCAGCCTTCTCTTCTCACAATT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.8382
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0182900.1 2 30318215 C T
Osa02LNT0182900.1 2 30319002 G T
Osa02LNT0182900.1 2 30319182 C A
Osa02LNT0182900.1 2 30319206 A G
Osa02LNT0182900.1 2 30319540 T A
Osa02LNT0182900.1 2 30319566 T G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0182900.1 osa-miR5792 Translation 4.0 13.716 1 24
Osa02LNT0182900.1 osa-miR5792 Cleavage 5.0 22.291 1 24
Osa02LNT0182900.1 osa-miR5831 Cleavage 5.0 16.767 1 24
Osa02LNT0182900.1 osa-miR3979-5p Cleavage 5.0 20.46 1 20
Osa02LNT0182900.1 osa-miR5160 Cleavage 5.0 21.32 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0182900.1 2 nan Morphological trait Panicle/flower RG139 CDO686
Osa02LNT0182900.1 2 Hd7 Physiological trait Flowering R3393 R2511
Osa02LNT0182900.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0182900.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0182900.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0182900.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0182900.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0182900.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0182900.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0182900.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0182900.1 2 AsS Resistance or Tolerance Other soil stress tolerance RM318 RM450
Osa02LNT0182900.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0182900.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0182900.1 2 qER-2a Physiological trait Eating quality nan nan
Osa02LNT0182900.1 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
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