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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 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0136200.1 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0136200.1 12 nan Resistance or Tolerance Submergency tolerance R1709 RM235
Osa12LNT0136200.1 12 qSD12 Physiological trait Germination/dormancy RM3331 RM235
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