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

>Osa12LNT0136200.1

CTTCACTGTTCAGTAACCAAGCTATCACTCAAGATCCTGGCCTTTGCTATCCATGGAAGTTTGTCAGTCAAGAGAACTACTCCTATCAGTATTGTGAGCTTGTGACTATCTATCGGAAGACAACATGGGTTTTTTTTGCTTCCTGGCTGATGAACTACCTACAGTCTACAGACAGCTCAAGGAACTGTACCAGTTTCAGACAACACCCCAGATTTCACCAAAAGAACAGAGAGTTTCAGACCACATCGAGCACCGGATTGGTTCACTGAAGATTGCTCGTGACACACCACAGCTGAGGTTCAGGCTTCACACCCACAGAAATGCAGCAGTCTCCATCAGTGAGAGCTGGAAGTGTGACATCAAACAAGATGGGGTCCAATCTAAGCTTCAGCTTTTGCACTTTCATAAGAACAGAACCAGCGTGGTCAGCAACCCCCCGTTGACGATTGCACTTCCGAACATAATGACGTCGCATGTGGCCTCCCAGTGCCTGCCCTGATCCAAATGACTTTCCGCAGGTATTGCAACGGTGGCTGTTGTCCTTCATAGCAGCAGCTGGAAGATCACCAAACTTCATCTCCTCATCTGAATTGTCGGTTCTTGGTTTCCTGAGAGCAGCATCTCTAACCAGCTCATGATCAAAATCATTTGGATCCATCTCCTCCTTGGGAACGATCAAACAGTTTTCCTTGTCACTTTGTCCATAGCAATCCTTGTAACCTGAGTTATTATCATTTATTGGCTCCTTGGAGCCAACAGATCGAACCGAACAACGATCCACGGCATTCATGTTAACCTCTGTCAGCACAATGGATCTCAAGCTACTGTCTTCTATATCTCCCAGATAGCAATCCTCATAAGCTGAAGTCTTGTCAAAGCACCCTGAAAGCAGTAGGAGAGCATCTGCAGCCTCTATCTCCTCCAAACTGAGTGCTGGTGTCTGCCTCTTTGATCGGAATGATCGCTTACGCTTCACTGAAGAAAACACCATTACATCTTGCATGCTATCAGCAATGCCCAGTGCTTCAATCAGCCCGGCAGCTTCTTCCTCAGCCTTGACCACCACCTTCTCCCCACCGTGCATCATCATGTGCTCCCTCAGCGATCCGGAGGTGGAGAACACCTTTGAGCACATCTGGCATTGTGTTTCAACACTCCTGTGGCAGGACATGTGGCCTCCAAGAGCATTCCCTGAACGGAAGCTCTTGTCGCACTTGTTGCAACAATGCTTCCAAGGCTTTCCTCTTGGTGCCATATCTGGATGCTTCTTGCTTCTTGTCTCGACGATCCGTGTGGAGAAGAGGAAGCAGAATAGGTGGGGCACTCCGGGTTGCTCAGGGAAAGATGACGACTCAATCGCTGGGTGCTTCCTGATTCTTGTCTCGCCGATCCGCGTGGAGAAGATGGAAGCAGAACAGGCGGGGGGCGCGTGCGTCCGGATTGCTCAGGGGAAGACGACGACGACTCGATCGCTCGATTCCCTCACAATATCCAGCTCCCGCGGAGGAATTAATCCGGAGGTGCCTCTCCTTCCCACCCTCTCTTGCTCCTCTCCTCTCCGCCGACGCCTACCGGTGGCCGTTTATCCTGCTTGCAACCGCAATCCTCGGAGAGAGAGAGAGCGTGCCCCGCGAGTGTACTTATAGGTCGGCGCGGCCTATGAATCTGGACGCGACACTGCGCCAGGTTCATCCTGCCTCGCCGGCTGCTGCTCGCCGCGCCGCTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.633754
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0136200.1 12 23952553 G A
Osa12LNT0136200.1 12 23952613 C T
Osa12LNT0136200.1 12 23952802 A G
Osa12LNT0136200.1 12 23953345 T C
Osa12LNT0136200.1 12 23953724 C T
Osa12LNT0136200.1 12 23953725 A G
Osa12LNT0136200.1 12 23953730 A T
Osa12LNT0136200.1 12 23953814 A G
Osa12LNT0136200.1 12 23953923 C T
Osa12LNT0136200.1 12 23954717 A G
Osa12LNT0136200.1 12 23955196 C 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
Osa12LNT0136200.1 osa-miR5791 Cleavage 5.0 13.908 1 21
Osa12LNT0136200.1 osa-miR166b-5p Translation 5.0 18.863 1 21
Osa12LNT0136200.1 osa-miR166b-5p Translation 5.0 20.912 1 21
Osa12LNT0136200.1 osa-miR166c-5p Translation 4.5 20.912 1 20
Osa12LNT0136200.1 osa-miR166l-5p Translation 3.0 20.912 1 21
Osa12LNT0136200.1 osa-miR2879 Cleavage 4.5 22.728 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0136200.1 12 nan Resistance or Tolerance Submergency tolerance R1709 RM235
Osa12LNT0136200.1 12 qSD12 Physiological trait Germination/dormancy RM3331 RM235
Osa12LNT0136200.1 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0136200.1 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
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