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

>Osa06LNT0339200.2

CTTCAAACTTGTTGTTTAAGTGGCAGTGTGTTTACTCTTGAAGGATGTTCATGATGCTTCTCATAGGAATTCTTACTTATCTTCCTTGATCTCAGACATTTCGCGATGCTACTTGCTAAAATGGTCACCAACAGAAGGTATATTGTGACACCGATTACTAGACCATAGACATAAACTGAGGTCCTGAATTTCCTGCAGCTTCCCGCAGCGAAAGCCGTCATGAGAGCCAGCAAATCTAGTATCATGATCAAGTGCAATACCCCAAGTGGTACATTCTTCTCCCTGACAGATTTGCTCAGCAGAAGCATGATCACAACAATGGATGACATGAAGGAGAATGCATTGAAGCAGAAGAATGCTTTGTAGCGATGGGGATGAATATTATGAAGGACTGGGTCGCCAGCCTTGTGTTTTGGGGGATCTGAACTGTCATCCGACCAGAAGCCACCAGGTGGGTTCAGACCAGCTTGGTATGTGATGGAGGCCGCCAAAATTGAAAGCAACATCAGATACTTGTGTCTTTTTCTTTCACTTTTGTCACCAGGATCTGGACTTCCTTGGATCTCAGAACCAATATCTTGCCTAACCTCCTTAGTCTGAAAAATCCACTCAAGCAAACTTTCCATACACTTGCACAATGGCTTTCCTAGTTTATCATATGTTGAAGACATAATGAAGACTTGAATCATAAGGGAGATCAGAACTGCAACAGCAACGATGATGAGATAAATAGATTGTTTTGCTTTCCTGCAGCTTCCTGCAGCATAAGCAATCAAGAGGCCAACCAATCCTGCTGCCAAACACACTCGCAATGCATAGAACTTCATACCATGCTCACAGGATCCCTTGTTCACGAGTAGTATTGTGATGACAACAGATGACACGAATGAGACTGAATTTGAGTAGTAGAACACATTATAGCGTCTTAAATTGTTCTCCTGAAGGACTGGGTTGCCTGTAAGGGTGCGGTTGATATCCTTGTCATCAGACCATACACTTCCTGGAGGGTTCATGCCAGCTTGGTATGTGACAGTCGCAGCGAGAATAGAAAGAATCAATAGTAGATTGCGCCTTCGCTCCCAATCCTTCTCATTGCCATGCCCTGTCTGGTTGCTGCCATGGAGAGGCGACCACAAATGTCTGCACGAGAGGCGGTTTAGCTTTTCTGCCACCTGCCTTTTCCAACCTTCTGGGATTACATGAATTGCTATCAAAACATGAATACCAACATAAGCAAGCACGAGGAGTACCATCACTGAGATATAAACTGAATTCTTTGTCTTCCTACAGCTTCCCATAACATAAGCCCCTGTTAAGGACAGGAGGATCACTATCATTGCTATCTGCAGTGCACGCCGTTTTATAACCTTGTTGGCCATTCTTCTGTTCAGGAGCATAATGATCATGACAACGGATGCAACAAAGGCAATTGCATTTAGATAGAAGAATGCAATATAGCGAGGGTGGTGAGTGTCCTCAAGGATGTGATCACCAGATGAATGATAATCCTCGTGTCTTGTCCAGAAGCCGCCTGGTGGATTCAGACCTGATTGGTATGTCAGAGATACTGCAAGAATCGCAAGGAGGAGTAGATATGTGCGGCACTTCTTCAGATGCTTAGCAGTTTGATTTCTATTGCCATCTTCATTGGGAGATCTTTCATTCTTGTCAATATAGCCATTCTCAACATGTGGAGCAATTTTATTATCTTCAGCAATTTCAATCTCACTATGTCCCACAGGCACATTAGGAGATACTTTCTCTTCTGGTGTAACAACAGTCCCAGGTTCATCAGTCGACGAAGATTGTTCCATTTTATTTATAACATGCTGGCTGTCTGTAGATCGATTGTCAGGGTCAGGCATACTGCCTTCAGTATCTGTAGTCTTTAAGTCGTTAGTCATTGTGGATTGTTCCTTCATATCTGTAACTTGATGGCTATCTGCAGATTGAGGCTCAGGGTCAGAAATACCATCCTTAAGTGTCTTGAAATCATCGATTGATGAAGAATTTTCCTTTGTATTTGCATCTTGCTGATTGTCTGCAGATTGATGCATACCGTCCTTATAGTTTGTAGCATGTTGACTTTTTTCAGATGGGTGCTGTGTGTTGGATATAGATTCCTCTGCGGTTGGTTGGGCTTGGTCGTCTATAGACTGACCCTGCAGGTTGTACACAACATCTGTGCTACACATAGATTGCTGATAACCGGCCGATGGATGGTCAGAGTCAGGCTCAGCCTCCTCGGAATTTGCAGATTGACATTCGCCAGAAGGCTGATTCTTCGCATGTGACTCTCCCTCTTCAATATCTGTACTTTGCAGAGCATTTTCTTTTACTTGTGCATCTGGTTCAAGCTCCGTTTGCAGATGATTTGCTTGAGAATTTTCTTGTTCTCTATCAATTGATCTGTTTCTCTTAAAATCCAATGAAAAAACCCGGCCAATTGTACCAATGCATGTCAGAGTGTCTGGTTTGATCTTTTGTAGCCAATCTGCGACAGGTTTGTAAACCAAGATTCCAGCCAAAACCACAAAGCAGGTCAAGACTATGATGGAAACAGACATAACATAGAAAGAAACTGCTATATCTCTACAGCTTCCTGCAGCATACGCACCTATCAGGCCCAATAGGTCAGCTACCACACACACAATAACTGCTTTAGATCTTATTCCATGCATGCTCAATTCTGGGCTAAGAAGCAACATGATTGTGACCAAAGATGCCACAAATGAAGTTGCATTGCAACTCATGAAAAAATTATACCGAAGAAGATAGTTACTCCGAAGAATAGGGGTTGCTGGATGACTGCTGCCTTCAGTCCAAAAACCACCTGGTGGACTTAATCCTGCTTGGTAAGTGATAGTTGCAGAAAAAGTTGCAAGTGTCAAAATGAACTTGCGAGCCTCCTCAATGTTTCTTTTTTGATCGTTGCTCCTGTTCTCCTCATGTACACCCCACTTTGCTTGAATTTTCTGTAGCAGCATTTGTACTCTCTCTTTCAACCATTTTGGAAATATCCTTGTGCATAACAAAATGTGAATTCCAACATATATGAAAACAGCAACAACTAGGACCCATATATAAATGGAAGACTTTACTGCCCTGCAGCTTCCAGCAGCATAGGCTCCCATCAAGCTGAATAGGTCTAATATCATGGTAAATTGCATTGAACGGAGCCACAAATTCTGCCTCGTCACACTCTTACTTAGAAGCAATATGATTAAGACAAGAGATGCAGCAAAGGCTGTTGCATTGCAGTAAAAGAATACCTCATACCGTGGGAAGAAGTAAACACGAAGGAGAGGTTCACCAGCATCACGTCCATTAGTCGTGTTTTTTGTCCGAAATCCACCCGGTGGGGTTAATCCAGCATTATATGTCACACTGACTGCTAAGATTGCAAGCATTACAAGGTACTTCCGCAGTCTCCACAAGAGCTCAAAATCAACTGTGATGCTGGGTGCATGGCTACTGGCCAATAAAAACCTACTGGACAAACCATTCATGGAGTCTTGCCTGTCGCTGCCAGTTTCCATGCCATACTCTGCCCTATCCCCATTGGTGTTGTTTTCTTCACTCTGTCCATTGACTGGTATTAGGACATCTGTGGTATTGGTCAGAGCAATGGTGAGCTTGGGTTGCCTTCCATTTTCCATGTGGTTCCTCAATATCTGAGATTGCGAGTCTGAGGAGCAGTAGGTAAGACTTCCCTTGATGATATAATATACGTTTATAAGATACAATAGAAGATAGCTTGCTTGCTTGACCCCACAATGATAACCGCCATATGAATTATTAGCTCTATGTGTATAGAGTTGTATTAACTTGCTCTATGTGTATAGAGTTGTATGAACTTGCTCCCATCCAATTATGAGTGCATAATAGGTTCCTGACATGGAAATGCACTCTGTGCTAACATAATCACATTGAGAGGCCAACCCCATCGGCCATATGCTCATTTCCTAGCTGATATTGCATGTTTGCAGTCAGAACATGGATGACTCTGCTGCTCAAACTGGTAAGCAATTGTAAGGATAGTCCAGTTGTTGAAGCCCTAATGGCAGTGTGAACGCACATGTTTCCAAAGGACAGCAGCAGAAAAAGGGCGGGGCCATCTTGCAATAACCACGCACATAAATAACACTACCAGCTCGTGCTCAATAACTCGCTAAGAAATCGAGTGCAGCTGAAACAGCCAATATGTTGAAAAGATGCATCTAATCGAATCAGACATAATCGGCGTACATGTTATTTTACAAGGAATATGGCCACCTTGCAGTTAGAACATCCAAACAACTAAAAGATAGTAGTGGTGGGGATTCCCGACTTTTAATATGACAACGAGATGGATTGTATCTTCTGCACTCAGATGCCACTGCTAGCTGCTGACAATGATTGACTTTGGAACACGCAGGTAAGCAAAGCAATGCCAGTAACAAAATTAAGTACCTGGGAGCTCGTAGGCAGTAGCAGGGTAACTGCAGTGGCGAAATGGAATCCGTAGGCTGCGATTAAGTTAACGCAGAATTGCGGACTCGTTGACATCTCTAGACTTCCCACACGGTTTCCACACTATTTTCACATCACCTGCAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAAGTACCCAAGAAACCAAAGAAAACGACGGTCGTCTCGTCTCGTCTCGAGTCTCGACGCGCCTGAGAAATGGTCAGGGCTTCCGCGGAGCACTTGCTTCGCTCCTACTACTCTACTAGTCGTTACTGCCACGACCGCAAACAAACGCGCCGAGCTCCCGGAGCCGGAGCAAACCGGCGCCCGGAACGGCTCCTCCCGCTAAGGCATTTGTTCGAACACCTTGCGGGCGTGGACTGCGGGGGCGACCCCCTCGTCCCCGCCTTTGGCGTTCCGTCGAACAGGCGGGCGGGGGTGGGCGGCGTGAGTTGGGGCAGTCTCGTGCCCGGTCGGCATCGATCTGTGGACCCATCCTCGCCGGCCGCCGGGGTCGTCGTCGACTGGTCCGCCGCCTTGATGAGCAATCGCTGCAGTAAACAAAAGACCCAATTCGCGTCGTCGTCGTTGTCTCGTCTCGTCACAGGGCTGAGTGGTGGGT

Coding Potentia
Explanation CPC Score
noncoding -1.08742
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0339200.2 6 10739272 T C
Osa06LNT0339200.2 6 10739559 A G
Osa06LNT0339200.2 6 10740662 T C
Osa06LNT0339200.2 6 10740749 T C
Osa06LNT0339200.2 6 10740899 T C
Osa06LNT0339200.2 6 10740957 A G
Osa06LNT0339200.2 6 10740975 T C
Osa06LNT0339200.2 6 10741778 C T
Osa06LNT0339200.2 6 10742022 T C
Osa06LNT0339200.2 6 10742085 G T
Osa06LNT0339200.2 6 10742709 A G
Osa06LNT0339200.2 6 10742748 C A
Osa06LNT0339200.2 6 10743006 G A
Osa06LNT0339200.2 6 10743176 G A
Osa06LNT0339200.2 6 10743204 G A
Osa06LNT0339200.2 6 10743980 A G
Osa06LNT0339200.2 6 10743991 A G
Osa06LNT0339200.2 6 10739682 C T
Osa06LNT0339200.2 6 10738720 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
Osa06LNT0339200.2 osa-miR5796 Translation 5.0 17.977 1 21
Osa06LNT0339200.2 osa-miR5804 Translation 4.0 14.694 1 21
Osa06LNT0339200.2 osa-miR156k Translation 3.5 19.127 1 21
Osa06LNT0339200.2 osa-miR159a.1 Cleavage 3.5 23.275 1 21
Osa06LNT0339200.2 osa-miR159a.1 Translation 5.0 16.501 1 21
Osa06LNT0339200.2 osa-miR159b Cleavage 3.5 23.275 1 21
Osa06LNT0339200.2 osa-miR159b Translation 5.0 16.501 1 21
Osa06LNT0339200.2 osa-miR159c Cleavage 4.5 23.275 1 21
Osa06LNT0339200.2 osa-miR159d Cleavage 4.5 23.275 1 21
Osa06LNT0339200.2 osa-miR159e Cleavage 4.5 23.275 1 21
Osa06LNT0339200.2 osa-miR159f Cleavage 4.5 23.275 1 21
Osa06LNT0339200.2 osa-miR319a-5p Translation 5.0 19.194 1 21
Osa06LNT0339200.2 osa-miR319a-3p.2-3p Cleavage 5.0 22.354 1 20
Osa06LNT0339200.2 osa-miR319b Cleavage 5.0 22.354 1 20
Osa06LNT0339200.2 osa-miR166g-5p Translation 4.0 20.314 1 21
Osa06LNT0339200.2 osa-miR408-5p Translation 5.0 15.226 1 21
Osa06LNT0339200.2 osa-miR408-5p Cleavage 5.0 22.879 1 21
Osa06LNT0339200.2 osa-miR417 Cleavage 4.5 9.001 1 21
Osa06LNT0339200.2 osa-miR435 Cleavage 5.0 24.517 1 20
Osa06LNT0339200.2 osa-miR444a-5p Cleavage 5.0 18.217 1 21
Osa06LNT0339200.2 osa-miR1847.1 Translation 4.0 15.297 1 21
Osa06LNT0339200.2 osa-miR1849 Translation 4.0 24.154 1 21
Osa06LNT0339200.2 osa-miR1865-5p Cleavage 4.0 22.447 1 24
Osa06LNT0339200.2 osa-miR1870-5p Cleavage 5.0 13.801 1 24
Osa06LNT0339200.2 osa-miR1883a Cleavage 3.5 18.627 1 24
Osa06LNT0339200.2 osa-miR1883b Cleavage 3.5 18.627 1 24
Osa06LNT0339200.2 osa-miR2095-3p Cleavage 5.0 14.881 1 20
Osa06LNT0339200.2 osa-miR2864.2 Translation 5.0 11.965 1 21
Osa06LNT0339200.2 osa-miR2929 Cleavage 4.5 11.719 1 21
Osa06LNT0339200.2 osa-miR5080 Translation 5.0 17.7 1 21
Osa06LNT0339200.2 osa-miR5083 Translation 5.0 14.755 1 20
Osa06LNT0339200.2 osa-miR5515 Translation 5.0 19.147 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0339200.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0339200.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0339200.2 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0339200.2 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0339200.2 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0339200.2 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0339200.2 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0339200.2 6 Pi-2(t) Resistance or Tolerance Blast resistance nan nan
Osa06LNT0339200.2 6 gw-6 Morphological trait Seed C235 G294
Osa06LNT0339200.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0339200.2 6 qSF-6 Physiological trait Source activity RM136 RG456
Osa06LNT0339200.2 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0339200.2 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0339200.2 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0339200.2 6 qNFGP-6 Physiological trait Source activity RM136 RG456
Osa06LNT0339200.2 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0339200.2 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0339200.2 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0339200.2 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0339200.2 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0339200.2 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0339200.2 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0339200.2 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0339200.2 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
Osa06LNT0339200.2 6 nan Physiological trait Flowering R2171 R2123
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