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

>Osa06LNT0334600.2

CATGGATTTTTAGCCTCACCTGTGTATGTTGGGATTCATTCCAATCTGGTTATGATCTAGGTGCATATGGTGCGGTGTGTGAACTGCAAATGTCCTTTGCTGGTAGAGCCAAACTGACCGTAGTAATCTAGTGCAAATCACATATTCCCTTGGCATATCACTTGATTCATTGTGCAGCATGGTATATAAGCCACGTTTGCTTGTAAATCTTCATATTGGTAATGATATTTTATAACAATGGGGAGTCTTCGCTAACTCCCAATTGCGTAAGGATTTTCTTCTCCTGTTCAATATATTCCTGGTCAGGGTTCTCTGTAAAATTCGAGTGCAGAGCATTCCCAGCAGTATCTACTATTGCAGATGTTGTCATGGAGGATTCAATGCATAATATGGCAGCGATAGCATCAAGTTTCGTAACATCATTTCTGAACATTAGTCTTGCATGTGCTTGTGCTAGCCTTATCAAACTCTCAAGCATGCGCACAGTCGTCCTTGCTGCGTTCCGAGTTCCTGATTGTCGCTGACGCTGATAATAACTAGAGATAACTCTTTCAGCCTCCTTGGTCAGCACAGGTTTGAAATGCTGCTTCACATAGTGAATATACCTTCTCAACATGGACAGTGTCCACATTACTTCCGGATCACTTGTCTTGCCTTTCTTTTCTTCAGTGTTCTCAGCTAATATATGAGATGAAACTATTTTATCCCATTTTTTGTTTTTTGTATCCAAGAGAACAAGAACTATATCAAATCTACTCAACAGTGGTCCTGAAAGTGTTGTATTCACAGATAAGGATTCATTTGGATCGTATTGTCCTTTTGGGTTAGTGGCACCAAACACTGTAGTCCTTGTGTTGAGTGTTGTCACTAATCCAGCCTGTAATAAAGAAGAAATGACGCTTTGCAATGCTTATTGTTTGTTGCTCCATGGCTTCATGTATTGTTGTCCTGTCATGCTCTCGCATACTATCAAATTCATCTATGCAGCATAACCCTCCATCAGCAAGAACAAGAGCGCCAGCCTCAAGCATCCACTCCCCTCCATCCTTGACTGCTGTGACAGTTAAACCAGCACTGGTGCTTCCAAGACCAGTTGTGATCACTGAACGGTTGCTCAATTTAGCAGCAAATTTCAGAAACTGGGATTTGCCAGTGCCTGGATCACCGACAAGAAGCATATGTGGTTCTCCACGAACCTTTGTTCCTGAAGCATCAACATGCTGCACCCCGCCAATTAAGGTAAGAGCAACTGCAAGCTTCACTGTGAATAACCCATAAATTTGAGGACAAATGCCTTTCAAGATGGAATTTCTTCCTTTCAGTGGAGTAGCTCTGGAAGCTGCCCAGAATTCCTCAAACTTGTTGATAATTTCAACAGGTATGTCTAGATCAGACTTCAGTTCATTGGTTCTCCTGTTGAGTGCAGTACATAGACATTCATAATGCACAGAAGGCAAGACTAGCTGATATCTTTGAACTTGAAACCAAGGAACAGAAAAGGCGCTAAAATTAAAATACTAAAGTGCTAAAAATATGCCCAACTATGGTTGCATCCAACTACCTTGGCAGGCAATAAAATGAAAAATAAGAAAAACTACAACGCAATAAACTAGTAGAGTGAAAGTACAGTGTATGGGAAGCCTTTCCTTCATATGAGTAATGAGACCAGACAATACTACTCTGTTGTCATAAACTGCATGTTTCCTAAATGTCTTTTTTAGTTTTTCATCATTTAACTAATAAACACCAAAAGCCATTCCATGTACTTTCTGGATCGGCAATTATGTGCCAAAGCCATTGCTGGTATTATTACTGTGATAGATTTGGAGAAGCTTAAATGAGCCCCTGCAGGTTCGTTAAAACAACACTATGTAATGAAATACACTAAGAATGGCACATTATTGCTGGTATTACTGTGATAGATCTTCAGAAGTATAATGTGTCCCTTCAGGTTCGTAAGAAGAACACTATGCAATAAAATATGCTAAGAAGAGAAGAAACTATACCTGGTTCATTGCATACTCTAAATATGTTCAAAGAATCATAATTTGGAAGATTAAAATTAGAGAACTAATATTTGGAGAACACCCTCAGTATAAGTTATCAGTTACCTCACAAAATTGGCAATTAGCATAGGATCAAGGTTTGAACGTACATCCTTGATGTCAGGAGACCATTTTGCAGATAATCGACCCGTAACAACAACATCATCCCCAGCTTTAACAATATCAACAAGATCATCCATCAAAATTATAGGCATCGAACGGGGTATAGACCCAACACCTAGAAGCTGTATATTTTCTTGGATTTTTATTTCTTGGTAATCATGGCAGGTTATGCTATCTTCTATCAATTGGAAATTGGCACCTCCACAACCTTTTGCACTCTTGGATTTGCAAGATGCAGGAAGAGTTATACGATTCCCAGCCTCAAGCTCAGGATGAACCGTAAACCTGCACTTGCATTTCCTGCACTGATACTTCCTCTCGCCTTCGATCATCTTCACGCCACCGGACCTGATCACGGTCCCCTTCAAAGTGAGCAGAGTTCCCCTGTGCTTCACCCTCACCTTCCCAATGCTCGGGGACGCTTCAGGGCATTCGAGTGCCGACCCCGAGGTGTTGACGCGCACGTGCACGAACTTCTTCTCCATTGTCTCGTCGCCCGCCTTCCTCTTGTCAGCTCGTCGAGCGGCGGCATCGAATTTGTCGAGGGCGCGTTGCGCGGCGGCGTCGAACAGCTCGAGCACGTCCTTGGGGTAGTCGTAGAGTTGGTGGGCGACCTCGGGGTCGAACTCCAGGAGCTCCGCGAAGTCGATGACGAGGGGGAAATGGAGCTTGCCGTCCGGGAAGGGGAGGAGGATGCGGCGGAGGTCGTCGGCGTGGAAGCGGTTGAGGAAACTGTCTAGGCGACTCTCGAACTCGTCGAGGTCGTCGACGGCGAACTCCTCCGCCGGCGGCGGCATTTGGGCGGCGGTTTGGGCCGCGTATGGTGGCCGTACGGGCAGGAAAGGGCGGAGAAAAGCTGGCCGCGGAGAGGACACAAGGCGGTGACGACGGCTGACGGGACTGACTGACGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.853355
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0334600.2 6 6088952 G A
Osa06LNT0334600.2 6 6089126 G C
Osa06LNT0334600.2 6 6089384 T C
Osa06LNT0334600.2 6 6090560 G C
Osa06LNT0334600.2 6 6090605 A G
Osa06LNT0334600.2 6 6091117 T G
Osa06LNT0334600.2 6 6091470 C T
Osa06LNT0334600.2 6 6091589 C A
Osa06LNT0334600.2 6 6091624 A C
Osa06LNT0334600.2 6 6092351 G A
Osa06LNT0334600.2 6 6093294 A G
Osa06LNT0334600.2 6 6093491 C T
Osa06LNT0334600.2 6 6093859 C T
Osa06LNT0334600.2 6 6094521 A T
Osa06LNT0334600.2 6 6095083 C T
Osa06LNT0334600.2 6 6095291 A G
Osa06LNT0334600.2 6 6095974 A 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
Osa06LNT0334600.2 osa-miR5534b Cleavage 4.5 19.35 1 21
Osa06LNT0334600.2 osa-miR5811 Cleavage 5.0 23.45 1 24
Osa06LNT0334600.2 osa-miR5818 Cleavage 5.0 17.27 1 21
Osa06LNT0334600.2 osa-miR1320-5p Cleavage 4.0 19.012 1 21
Osa06LNT0334600.2 osa-miR1863b Translation 5.0 13.529 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0334600.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0334600.2 6 AsTol Resistance or Tolerance Other soil stress tolerance RZ516 RG213
Osa06LNT0334600.2 6 tns6 Morphological trait Seed RG138 RG64
Osa06LNT0334600.2 6 sd6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0334600.2 6 tns6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0334600.2 6 sd6 Morphological trait Seed RG138 RG64
Osa06LNT0334600.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0334600.2 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0334600.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0334600.2 6 qRCRJ-6 Physiological trait Source activity RM217 RM402
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