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

>Osa12LNT0135200.1

GCACCCATCCTTTTTCAGAACAAAAAAGCAGCTATTACAAACATATATATTTGATTGCTGTTAGATTGGTACAAACAACCACGGAACAGAAACAACGGTACCAAACAAGATTTGCTACAAGGCCGACTTCCCAATTTTGAATGCAATCACTTCAATTCAGCAAAAAAATCGCTGAAACAAATGGCAGACAGAGGGGTGTTGTGTTGTACATCAACTGACAGATACTTCATTTCCTTTTGGTTTCGTATCGCTCGTGCATACAGTGTGTGCTGCTTAGGTTGTTGGTAACACTGATGAAGAAGATGTGCGGTGAAATTGGCACCACTTTGGAATTGGTTTCTGTTGGACAAAAGGATTTCCTCACGATCTGGTGGTCGATGGCTTCTCCACAACAAGTGTAAGTAACAAGAATGAGCCGAAAGAGATGATGAGCGCAATGGCCATCAAGATAAGCATGGCTTGTAGCGTGATATTTGGGCTCAGGAAGAAGATGACTGCGATGGCACCCGATTGCCAAACCCTCCACTGTGCAAAAGCTGCCTCCTTGACATCCTCGAACAGCAGCCCAAGTAATGCGCTTAACTGTGTATGTAAGACACCATCACCAACACCCCATAAAGCACCTATAAACAGTGGAACTGCCGCACCAAGCAATCCACCCATTGGACTGTAAAAAAGAAGTAACCAGAACAGGACTACAGCATGAAGAATAGCTCCAACCGAAACGATAGATGTAGCTGAATGAAGCCCAGAGGTCAAACGTCCAGCAACCAATGCACAAACAGCATCGGCTGCACCATATATTGCCATGGCTCCGCCAACTCCAGAGACGCCAAGAACAGGTGTTACAATATTTTTAGTGAATACAGCCCATACAAATGCCGCTTGTAATCCTGAATATACTATAAGAGGGATGATAAGAATCATCCTTCGGTCCTTGAGAGGGGCAACAATATACTTCATCATGGCCCCAAATGAGGAATGTGTTGGAGCAGTATTTCCTTTCTCATCCCTTTCCATCTCTCAGTAGTGCAAGAGAGATCAGATTTCCGATGACCTGTGTGCTAGCAAACATTCCCCAGAACTCTCCATTGAAGTTCCCCAAAGTTTGGCCTTCAGGCAAATTATTGTCTCTTGCATGACTGAGGGCAGCAGACGTGAGATATGTACCCTGCCCAACCCAGATGATCGATGCAGAAAAACCCAGATACAGGGAGGCTGGCACCATTGTGTACCATGTCGGGACGAGGTTAGCGAGGATGAAGATGACGTAGCCGCTGGTGCCGACGACGAGCGCGCGCTTGGAGCCGAGCCACGTGACCACGGGCGACGCGGTCACCGCGAAGAGCGTGAAGGAGGTGTACAGGATCCCCATGGACACCGTGCCCAGGTCGCCCTCGGTGTTGACCGAGCTCTGGAGGTTCTGCGCGGCGCAGTAGGCGGAGAAGATGAAGAGGAACGCGGCGGAGAGGACGTGCAGGTCGCCCGCGTGGCTCCAGCGGTGGCCCGAGTAACCCAACGGCGCGACGCCGGCGAGGAGCGGCGCCGTGGCACCCCCGTCGGCGCCGGCGCCGGCCGGCCGCCTCCTCATCGCCTTCGTCGTCGCGGTGGTGGCCTCCTCGCGCGTCCATGGCCCGCGGCGGCGGAGGCGGAAGCTTCTAGAAGCGATCGATCCGCGCGGCTTGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.714422
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0135200.1 12 23302326 A G
Osa12LNT0135200.1 12 23302618 C G
Osa12LNT0135200.1 12 23302737 C T
Osa12LNT0135200.1 12 23303071 G C
Osa12LNT0135200.1 12 23303678 A T
Osa12LNT0135200.1 12 23303784 G A
Osa12LNT0135200.1 12 23304577 A C
Osa12LNT0135200.1 12 23304956 T C
Osa12LNT0135200.1 12 23305370 G A
Osa12LNT0135200.1 12 23305582 A G
Osa12LNT0135200.1 12 23305659 C T
Osa12LNT0135200.1 12 23305743 A C
Osa12LNT0135200.1 12 23305842 A 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
Osa12LNT0135200.1 osa-miR5828 Cleavage 5.0 17.979 1 21
Osa12LNT0135200.1 osa-miR160a-5p Cleavage 5.0 14.028 1 21
Osa12LNT0135200.1 osa-miR160b-5p Cleavage 5.0 14.028 1 21
Osa12LNT0135200.1 osa-miR160c-5p Cleavage 5.0 14.028 1 21
Osa12LNT0135200.1 osa-miR160d-5p Cleavage 5.0 14.028 1 21
Osa12LNT0135200.1 osa-miR160e-5p Cleavage 5.0 14.028 1 21
Osa12LNT0135200.1 osa-miR171b Cleavage 5.0 20.139 1 21
Osa12LNT0135200.1 osa-miR171c-3p Cleavage 5.0 20.139 1 21
Osa12LNT0135200.1 osa-miR171d-3p Cleavage 5.0 20.139 1 21
Osa12LNT0135200.1 osa-miR171e-3p Cleavage 5.0 20.139 1 21
Osa12LNT0135200.1 osa-miR171f-3p Cleavage 5.0 20.139 1 21
Osa12LNT0135200.1 osa-miR166h-5p Translation 4.0 10.551 1 21
Osa12LNT0135200.1 osa-miR1440a Translation 4.5 21.481 1 20
Osa12LNT0135200.1 osa-miR2097-5p Translation 4.0 16.787 1 22
Osa12LNT0135200.1 osa-miR2099-5p Cleavage 4.0 10.1 1 22
Osa12LNT0135200.1 osa-miR2864.1 Translation 5.0 18.295 1 21
Osa12LNT0135200.1 osa-miR3982-5p Cleavage 4.5 22.137 1 21
Osa12LNT0135200.1 osa-miR5144-5p Cleavage 4.0 13.747 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0135200.1 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0135200.1 12 nan Morphological trait Seed RG543 RG81
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