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

>Osa06LNT0338300.1

GGTAGAAGTATATAGGCATGATGGCCTTTCACATGCTGACAGAATATATAATTCACACAATTTGGACAGGATGTCACAAAAGATCTCAGCTCACAAAGACAATACTTGTCGCACTGACTTAAGTTGACAAACATAAGTTCATAAAATGCCAATAGGGGCATCACATACACATGTCACAACAGGAACTACTCATCATCGCTATCTACCTCAACTGGGGCAACTTCACCTTCACTCCAATATTCCACAGCCGTGTCGTCCTCTATCTCATCACCAGACGATTCACCATCTTCAGCAGGTCGATTTTGCTTCATAAGTCGAGCAACTTCAGAAGCATCAACAACCTGGCGAGCTTCATCATCTCGGTTCAAAGGCAGGTCAGATAAATTCTCATCTACCTCTGGTCTTCTCCCATCTTCCTCAATGCACTGTGTCTGTTGATACGGAGATGCACTAGGTGCATTTTGTTCATCAACATTGTATAAATGCCGATGCTTAAACATTTGGACAAGCTGCCAATTTTCGCCATGCTTATTATCTGGCAGGTAGAAAATCTGTTTAGCTTGAGTCGCTAGTATGAAACAATCTTTCTTGTACCAAAAGCTTCCAGTATTGACGCTTCTAAAAAAACCATCATCTTTTAGTGCAGTCTTCTTGCCATCTAGCTTGTACCATTCACATCTAAAAAGAACCACCGTTCTTGTATTCCCATCATCCTTGCTGTTGTACTGCAACTCAATAATATCTGTCAACTTTCCAAAGTAATCAATTACCCGACCATTATGTATTCCAGCACACGCCACTCCAGAGTTTTGAGTCTTCTTATTTATGTCACGCTCAGCAGTACAGAACCGGACACCATTGACAACACATGAAGAGTAAGATCTTACTCTCAGGTCAGGGCCACATGCTAAGGCAAACAGGTCATCATCTACAATATCTGAATTGTTCAACCTCCACATATGGTTCCTGAACCAAGTAGCAAATCCAAGCCTAGTCCTTCTATCAATATCAGCTGCTTGCACCCCTGCTTCCTGTAATTCGCCTTGAAACATTTTTATATAATCCTGGGCCTGATCGCAATTATATAGGATATACCAAACCATTTGATCAAAATCTTCAGAGTAACCATAGTCACATGCACCAATCAGATTAACACCGTGCCCAAAAACATCAATATTGAAGGCCGATGGATCTGAGAATCCTGGATTTCTCGGTGCTCGGTTAAACCTAGTCTCCACATCCTCCATATACCTAGAGCAGAATGTGAGGGCTTCATCTGCAACATAAGCCTCAGCAATCGAGCCTTCCGGTCGTGCCTTATTCCTAACCGACCTCTTCAAAGTGTACAATCGTCGCTCAACAGGATACATCCACCCAAATTGCACTGGCCCTCGAAGCATTGCCTCGTCAGGCAAATGGACAGCAAGGTGAACCATTACATCAAAAAAAGCGGGTGGAAATAGTTTTTCAAGCTTGCATAGTATAGCTGGTATTTCTGTCTTCATTCGAACCAAGATATCTTTGTTGAGTGTTTGGCTGCACAATTCCCTAAAAAATTTCCCAAGCTCGGCAATCACTAAACATATATCATCATCCAAAATACCTCTCATACCAGCAGGTAATATCCTTTGCAACAGAATGTGGCAGTCATGAGTTTTAAGCCCATGCAAGCTGGTTCCCTCTGCAGTTATGCATCTTTCGATATTTGCAGCATAGCTATCTGGGAACTTTGTTTCTTTCAAAAATTTACAGAATTTAATCTTTTTTTCCCTAGACAATGTGTATCTAGCTTCAGGCATGTGATAATCATCTCCATTTGGCTGCAACTGCAATTCTGGTTTAATATTCAAATCAGCAAGATCAAGCCTTGCATTAACATTGTCTTTTGACTTCCCATGTATGCCAAGAAGGGTACCAAGGAGGTTTTCACAAATATTCTTTTCAATGTGCATCACATCTAGATTGTGTCTAAGCTTCAAAGATGGCCAATATGGTAAATCCCACAAACTAACCCTCCTACCCCAAATTGGCACATGTCCCTCTGAACGCTTCCTTTTTTGACCTGGTCTAACATCATTTACCTTGGCCAATTCTTCTAACAGCTCTTCAGTTGTGAATGTACCTGGCTTCTCTTTGCTTTCATGTAGAGAGGCATATTCATTATTCGTGCGCAGACGATGACGCCTAGGAAGGAACCGACAGTGACCAATATAACAAAGCTTGTTCCTTATGGAATATGATAGAGGATTTTTGTCACAATGGAGACAAGCAAAGAAACCTTGTGTGGTCCGACCAGACAAAGTACTAAGTGCTGGATAGTCATGAATGCACCACAACACGGCAGCACGAAGCTTGAAATCTTTTCCTGTCAGAGCATCAACTGTATCAACACCAGACCAAAGACTAAGTAACTCCTCTATAAGAGGCTGGAGAAAAACATCAAAGTGCTTCTTCCCAGGCGATCTAGGACCAGGAATCAACAAAGCCATCATGAAGTTTGATTCTTGCATACATGACCAAGGTGGAAAGTTGTATGGAATCACAAAAATAGGCCACATACTATAAGATGATCTCATATTGCCAAACGGATTGAAACCGTCTGTAGCCAGGCCAAGCCTAAGGTTCCTTGCATCTTCAGCAAAATCTGGCCAGCATTTGTCAAAATCTTTCCATGCCTCTCCATCTGCAGGATGGGACATTTCCTTCTCTTTGGGTTCCCTATTCAACTTATGCCATTGTGCTTCCTCTGCTGTTTTCTTGGTAGCAAATATTCGTTGAAGCCTAGGTATCAACGGAAAATGCCGCAATACTTTTTCTGGAACCTTCTTATTCACAGGATCTTTCCATCTTGATGCTTGACAAACTGGACAAGTATCAAGTTCTGCATACTCCTTTCTAAATAGCACGCAATTGTTTGGGCAAACATGTATTGACACATAACCCAGTCCTAAAGTACGCAGCATTTTCTTTGCTTCTTCATATGAATTGGGAAGACAATTGTTCTCTGGGAACGCTTTGCGCAAGACTTTCAACTGTGCAGAAAATGCTGAGTTGCTGATCCTGTAGTATGACTTCAAATGGAGCATCTTGACTACAAATGAAAACCTTGAAAATTGAGTGCAACCAGGATATAGCTCATGCTTTGCCTCTTCCATCAGAGTTTTGAAAACAGACTCATGGTTACTAGATGGGTTGCCATCTCCATTTGCTGCATTATTACAAGGTACTTGAGCCCCCATGAGGTCTGTTAAGATATCTTCAACTCTATCTGCAGCATTGTTTTCATGTTCTATAGGATTAGAATGTGGATCCACATCTACTGGTTCCTCCAAAACATGAACATCATTGGCCTCTCCATGATGAATCCATCTTGTATATGTACTAGACATCCCATTGAGCAATATGTGCCTCTCCACATCTCTTTGAGCCATGGATTTCTGGTTAATACACCGACTACATGGACACAAAATTGCAGCATCCCCAGGAAATCGCTCTTCAACAAATTTCATGAAATTTCGAACACCATCAATATAATCTGGTGTGAAAAGTGCACCATGTATCCATCGTCTATCCATCAGGCCAATCAGTGGAGCTCTTCAATGGTTGAACTCCAAGGGAAGCCAATGGAGCTCGTCGATAGGCGAGCCACGCCGGAGGCAGGCAGACTGTAGATCTCGACGGCAGAGTACCAGGACAAACCACTGCTACCGCACCCC

Coding Potentia
Explanation CPC Score
noncoding -1.14677
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
Osa06LNT0338300.1 osa-miR5525 Cleavage 4.5 12.354 1 22
Osa06LNT0338300.1 osa-miR5807 Cleavage 4.0 15.426 1 24
Osa06LNT0338300.1 osa-miR6247 Translation 5.0 16.336 1 21
Osa06LNT0338300.1 osa-miR6251 Cleavage 5.0 19.403 1 21
Osa06LNT0338300.1 osa-miR164a Cleavage 4.0 16.2 1 21
Osa06LNT0338300.1 osa-miR164b Cleavage 4.0 16.2 1 21
Osa06LNT0338300.1 osa-miR164c Translation 4.5 17.66 1 21
Osa06LNT0338300.1 osa-miR164c Cleavage 4.0 16.2 1 21
Osa06LNT0338300.1 osa-miR164d Cleavage 4.0 16.2 1 21
Osa06LNT0338300.1 osa-miR408-5p Cleavage 4.5 16.996 1 21
Osa06LNT0338300.1 osa-miR164f Cleavage 4.0 16.2 1 21
Osa06LNT0338300.1 osa-miR395o Cleavage 4.0 8.782 1 21
Osa06LNT0338300.1 osa-miR820a Cleavage 4.5 13.99 1 21
Osa06LNT0338300.1 osa-miR820b Cleavage 4.5 13.99 1 21
Osa06LNT0338300.1 osa-miR820c Cleavage 4.5 13.99 1 21
Osa06LNT0338300.1 osa-miR1856 Cleavage 5.0 17.482 1 21
Osa06LNT0338300.1 osa-miR2098-3p Translation 5.0 18.218 1 20
Osa06LNT0338300.1 osa-miR5489 Translation 5.0 16.237 1 21
Osa06LNT0338300.1 osa-miR2275d Cleavage 5.0 15.764 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0338300.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0338300.1 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0338300.1 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0338300.1 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
Osa06LNT0338300.1 6 nan Physiological trait Flowering R2171 R2123
Osa06LNT0338300.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0338300.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0338300.1 6 sd6 Morphological trait Seed RG138 RG64
Osa06LNT0338300.1 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0338300.1 6 sd6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0338300.1 6 tns6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0338300.1 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0338300.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0338300.1 6 tns6 Morphological trait Seed RG138 RG64
Osa06LNT0338300.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0338300.1 6 nan Physiological trait Eating quality RG64 R2171
Osa06LNT0338300.1 6 S5 Physiological trait Sterility RG213 C235
Osa06LNT0338300.1 6 qNFGP-6 Physiological trait Source activity RM136 RG456
Osa06LNT0338300.1 6 qSF-6 Physiological trait Source activity RM136 RG456
Osa06LNT0338300.1 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0338300.1 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0338300.1 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0338300.1 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0338300.1 6 nan Resistance or Tolerance Blast resistance R2171 RG64
Osa06LNT0338300.1 6 nan Resistance or Tolerance Blast resistance R2171 RG64
Osa06LNT0338300.1 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0338300.1 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0338300.1 6 qTL6-1 Morphological trait Culm/leaf 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