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

>Osa06LNT0327200.2

GTCAGAACACGGGAAAAGTATCATATAACGCGAACAGCATACCAGGTACAGAACTTGGCTATCCAAATTAATCTCTTTATCCTAGTACTAGCAATTTGCATAGCTGTTTGCCTGCTTAACAGATTGTATTGTGTTGCGCACATGCTACCTAAGATACATTGGCCCAATTGAGTTTCAACAAATGCATTCTGTTGCGCACATGCTACCTAAGATACAATGGCCCAATCGAATTTTAACAAATGAAAGCTCATTCCTTCTTCTGAGTGTCCCTGGGAATGCAGCACTGGGGATAGCAAATATCTCTGGCTGTTATATTGCTGTTAACAAGAACAAATAGGGGTGGATGTCTTTCATGTGCCCTTTGGCATTCACCTCCACCTTGCACCTCCCAATCTGATTACCTCTTCAGTTCCAGAATCCCTGCGAGCTTTATCATCACCTGTATCATCCTTTGTGTTTGTCGCGTCACCATATAAATCCTTCAATTTTGCCAAGTTGGATGGCTCTGGTGGTCTACCAAATGGGCTAGAGCGGTGATTTTCACCTTCGGTTCTGCCACGGTTTGGACTCCTGCTCCTGCTCCTGCGGGCACTCGAACGTCCATGTCGATCAGAATCCCTGTCCCTCCTTTCACGGCCTTGTCTGTCAACATTCCTACTTGAATAGCTTGAACGACGGTAATCACGGTCTCTGTCCTCACGGGCATGGCGATCATGCTCCCTATCCTTGTGCCTACCACGGTCACGATCCGAACGATCACGCTCAGAATCATGATCACGTTCATGGCTCCGACTTCGTCGCCTCCTGGGTGAAGATCTTGCACACTCACCATCAGAACTCCTTTCTCTATCCCTTGCTGAAGGCAATGTCTTCCGGACAGGGGATGAGTCCCTTGTGGATGCACGGTGTGGAGCACGCTGACCAAAGGAGACCGACAGAGAAGCCTTTACTGAAGGAGGCCGTCGGGCAGTATCATCTGAACCAAGGCGACTAGAGTCCCCTGTTATTCCTGACTGCTTTGTTGGGAGCTTCATCTTCTCAAGATGGCCAGTGACCTGTCTCAAGATCGGAAGAGGCACTCGTGGAAGAAGACTGTCAAAGTAGTACTGCCCAAGTAGAAGATCTCGCACATAAACACCCATAGTAGTCATTTTACCATTAGATCCAGGAGAAAACTCCTCATCATCTTTAATGTAGGGTTCATACCAACTCCACAACGTCTTTGGTTCCGCAACATATCGCAGGTAAAGAAATCCAACAGCTCTGATGTAAGGCGAGTCAGGGTGCTTCAGCAGGCCGTGCATCTGCTTAACCGTGAGCTTCATGGTGAAGAACTTGTAGAGGAGGCAGAAGGCGCTGGAGGGCCCGCGGCAGTTGCCGGTCATCCATGGCTCTACGTGGTCAACCTGATTGTAGATCTCATCAATGACCTCGTGGTAAGTCTTCAGCCTGTAGAGCTCCTTGAAGTAGTCCGAGGAGAGGATGTTCACTGACAAAACCTTCTCCATGAGCACATCGATTGGCCTCCCTGATGACTGTATCTCCATTTCCCCTCCTCTCTTTTCTTCTCACCGGGATGCGAAGCGGCGGGCGGCGCACGGGGGAGGCCACGGCGAGCGGCGGCGCGGACGAGATTGGGGATTCGTTTTGGATTGGGGATTAGGGCGACGAGAAGAGGAGAGAGAGAGAGAGAGAGAGAGGTAACCGATGGAGGAGAGATGGAGTCGTGGCCGTGCGACCGTGGCAACGGGCGAGGTTACATCTTAC

Coding Potentia
Explanation CPC Score
noncoding -1.12176
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0327200.2 6 2286696 T C
Osa06LNT0327200.2 6 2287426 T A
Osa06LNT0327200.2 6 2288889 T C
Osa06LNT0327200.2 6 2289142 G C
Osa06LNT0327200.2 6 2285965 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0327200.2 osa-miR535-3p Translation 4.5 21.734 1 21
Osa06LNT0327200.2 osa-miR1428a-3p Translation 5.0 13.479 1 21
Osa06LNT0327200.2 osa-miR1861b Cleavage 3.5 16.97 1 22
Osa06LNT0327200.2 osa-miR1861d Cleavage 4.5 16.97 1 22
Osa06LNT0327200.2 osa-miR1861f Cleavage 3.5 16.97 1 22
Osa06LNT0327200.2 osa-miR1861h Cleavage 4.0 16.97 1 22
Osa06LNT0327200.2 osa-miR1861i Cleavage 3.5 16.97 1 22
Osa06LNT0327200.2 osa-miR1861j Cleavage 4.0 16.97 1 22
Osa06LNT0327200.2 osa-miR1861l Cleavage 3.5 16.97 1 22
Osa06LNT0327200.2 osa-miR2097-3p Cleavage 3.5 6.56 1 22
Osa06LNT0327200.2 osa-miR2919 Cleavage 4.0 20.201 1 19
Osa06LNT0327200.2 osa-miR3980a-5p Cleavage 5.0 18.842 1 21
Osa06LNT0327200.2 osa-miR3980b-5p Cleavage 5.0 18.842 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0327200.2 6 Hd3b Physiological trait Flowering nan nan
Osa06LNT0327200.2 6 qAC-6 Physiological trait Eating quality R2869 R1962
Osa06LNT0327200.2 6 alk6-1 Physiological trait Eating quality RM190 RM253
Osa06LNT0327200.2 6 hr6 Physiological trait Eating quality RM190 RM253
Osa06LNT0327200.2 6 ac6 Physiological trait Eating quality RM190 RM587
Osa06LNT0327200.2 6 qAC-6 Physiological trait Eating quality RM190 RM510
Osa06LNT0327200.2 6 qGC-6 Physiological trait Eating quality RM190 RM510
Osa06LNT0327200.2 6 nan Resistance or Tolerance Drought tolerance RM170 RM204
Osa06LNT0327200.2 6 nan Morphological trait Shoot/Seedling OSR19 RM225
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