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

>Osa06LNT0345500.1

GAACGACCAAATACTCCAATCGACAATTTGAGAAGAGAATAAGAATATCTCCAATGGAGCACATAACTGGACCTTCTGTCGAATACACAAATGCGTAACATTGAAATTGTTATGCTATTTTCTCTTGCGCTGCTGGCTAAAGAAAAACAACCTAACATTGAAATTGCTAATGAATTGATTATGCTTCAGAGATACATCTCTTTCACCATGTTTACAAACGCGCAATAACTCTGTGGTAGAAAGTGAAGACATGCGGCATACCAACCTTGTTTTTTATATAAGCTAACACTTGTGGCATCGGGCATCTACTGCTTGTAATCCCAGACGACACTGAAGGAAATTACTTAAGAAGAGGCATTGACTGCTTGTAATCCCAGACAGCACTGAAACTCTGGAAGAAATTACCTAGAAGAGACTATGTACTTGAATTCTTTCCTATTAAGAAGATAGGAAAATCAACTCCATTCTTTTGGCAAAGACAAATTACCCTTTGTACTCTAATATATTTTTGCTGCGTCTGCAAACAACAAATTACGGAGTATCAATTAATGCACAGTGCACAGCTTTTGTATTCTTTTTGTGGTTAACATCTTATTAATTGTATCACACATAAACCTTTCTTAGCATCACCACATCAGTACCAGGACTTATGAACTAAAAAAGAACATGGGTACTACTAATGGCTTTAGATGTTAGGCCACAGTTACCTGCAGAAGATCTGGTGTTGGCCCTTTAGATGCATTTAGCTGTGAACTAAATCATATGCACATTTGACATAGGATAATTTAGATGCGAGAGTACAAAGATAATGAAGGACGGTGGAAGAAACAACTGCCCAGAATCTATTTCATCTCAAAGAAGTTGTTTGGAAGGAAATGCCCAGATTTGGTGGTTTTCAACATTGCATACACCTGAAATTTTAAACTGGAACTAAATTTCTGAACATTTAAATACATATATAGTTTATTAAATAGCATTTCAAATTATGCAGGCCTAGTAGTCTAATCTCTTGAAAGCCTGAAAATCAAATAACCAATAGAGAGTAGTTTTTTATCTCTTTTTTGATTATCTGGTTTTGACTGACCATCATAGGAAAACAATTGAAATATATGCTTACAACGAATATAACGGTCCCAGACATTGTTTAAGCAATACTAACTATTCACTATGCATATACAGTAGCTAGTACCAGATTAGTTGGAGTAATTGATATATGGAAAATAATGTCATTGAGAAAGCTTTCAATTAACATTTCTAAGATGAAAGTGTTGGGTCTTGAGACATGGTCAACCACTTTCAAGTCTTTTAACTCTGCAAGGCTGTAATTTGTTTCTAGCTTAATAATGTCTTCCATCTTTGGTTCTTGATTTTCTAAGCACATTTGAACATCATGAAAATTTGAAGGTGAACATAACAATAAAAGATGCAGATTGGAAGTTCTAACCTGAAACATGGCTCCATTATGTGTATCTATACTATTGTAATAGTATCAACCAACCACTTAGGAAAAGGGGAAAAAACACCAAGTTAAACGATGTCGACAAAATAAAATAGTTAAATGTGAAAGCCTAACAGAAGATAGTAGTATTATGGATTACTTTCATAAGCATATGCCACACTACATAATATTAAAAGATGTGGATTGGAAGCTGTAACCTGAAGCATGGCTACATTATATTTATTTTGCAACATTGAATATGTTGTGGACATAACCAGAAGCAAACTGGCATAACTGGAGACCATAATCTAAATATCGCAGCCCTGATTAAGAGAGGAGAAAGCTCGATAACTTGTTCAGTATGACGGTAGATGCGCAGAATGAAAGTCGTCCTCTCTGTAATCTGCGACTTACACCTCATCCTAGCCCATCAATTTCTCCACAGAACCATGTGGATTTTGTGCTAAATGTATGCAGAAGGGTATCAAAACGATTCACCGGCGAGGAGACCAATGGCCGAGACCATCGATTCCGATGACCCCCGAACCGGATCTGTAGCTCACCGAGGATAGGGAGAGGAAGAGGGAGGCGGTGGGTGGCCTGGAGATGAGAGGAGAGAAGAGGGGAGAAGGTGGCCTGGTGTGCCGAGCGAGGGGAGCGGCACGGCGGCAGGCGAGCAGCCGCGGCGGCGGCGGCGGCGGCGGCAGGCGAGCGGCAGGCGAGCGGCGGCGGGCAAGCGGCGGCGGGCGAGCGGCGGCGGCGGCAGGTGAGGTCATGCGCGCGCGAGCCTAGTAGTGCGGCTAGGGCGAGGATGGCTGGAGGAGGGCGAGGATGCAGCGGCGACGGCGCGCGCAGAGGAAGAAGGGCGAGGCGGCGGCGAGAGGCGACGGCGTGGCGGCGTAGAAGGGAGAGGCGACGCCGCGCGTGCACC

Coding Potentia
Explanation CPC Score
noncoding -1.10171
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0345500.1 osa-miR6246 Cleavage 4.0 16.933 1 23
Osa06LNT0345500.1 osa-miR169i-5p.2 Translation 4.5 12.85 1 22
Osa06LNT0345500.1 osa-miR529a Translation 4.5 24.356 1 20
Osa06LNT0345500.1 osa-miR1859 Translation 4.0 15.392 1 22
Osa06LNT0345500.1 osa-miR1862d Cleavage 3.5 14.941 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0345500.1 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0345500.1 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0345500.1 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0345500.1 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0345500.1 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0345500.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0345500.1 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0345500.1 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0345500.1 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
Osa06LNT0345500.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0345500.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0345500.1 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0345500.1 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0345500.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0345500.1 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0345500.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0345500.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0345500.1 6 gw-6 Morphological trait Seed C235 G294
Osa06LNT0345500.1 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0345500.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0345500.1 6 gp6 Morphological trait Panicle/flower RZ667 RG424
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