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

>Osa05LNT0317600.2

AGTAATCTTGATCGGTTTTATTTTTGTCATAAACAAGCAGACATGCATGTCACAACTCATAAGTCGTAGCACGTCTATATACGGGTTTTCACCGTAGTGGCATACTAGAACAACGGCAGGCTGCTCTTGTGTACCAGCCTAGTCGCATCCACGGCAGCAGCAGCCCGAGACCAATTCAATAGCCGGCTGCTTATAGCTTACTTGCCCGCAGGCCTAGTCGCGGTCCCAGCAGGACCAGCTTGTCGCAACAGCTGGAAGTAGGACTCCCACTTCTGCCTGAGGACGGCATGCTCCCTCTTCACTTTCTGGAAGGATCTCGTGCAACCTTCGGCGTTTTCTTCTCCACAGAAATTCCTGAATGAAGTGCATTCATTCTTCACCCTGGAGGCACCAATGCTAGAACAGCTGCCTTTCAATTGCTGCATGTGTGTGTCCCATCTGGCGAAGTCTTTCGGATGCTTCTCAATAGCTTGCTCAAAATTCAACATTACCCTGGTTGAATCCTTAAAAAACAAGGAAACAACCTCCTCTGCAAAATTTGGATTTGCTTCATCCTGCAAATCCTCAACCTGACAAAATTGCTCATCCAAGTAACCCTGTCAATACAAAACGATTTGTTAAACCAGCACACTTAACACATGTTAAACTAAGATAAAGACCAGAAAAGAGAGTTCCGAAATGGTGAAAGGCGTTGATTTTAAAGCATTTCTTTGCTAACTGGGGTGGGGATAAGTACGAAATGGAATGAACTCTACAGAAATATCGATAACCCACTTATATTAATATAATGTGCTTCAATCTGATTCTCCTTAGCTTTGTTTTCATTATCTGTGTGCAATAGTGTCAATCCATGGTATGGCAATTAAAATGGCATGACTGTAAGGTGATGTCCATCAAAACACTGTATTCTATGTCTTGCTGAATGATAAATAGCAGAAGAAGATATAGCAAAAGGACTGATGGATATATTTGCAGAGTCTCAGATATGCCTCAACTATAATGCTTGAAATTTGAGATGAACAGAGCACAAGCCTGATCGAAGAGGCTCTTTTTCAAGGAAGCTGCTTGACGTCGCAAATTACCGTACTCCATTCACAAGTATTGAACAGTCAGGAAAAAAATGAGGCGAAGTGAAGCCTTTAAAGTAGGAGTCAATCCCAAAAATGAATACACAGGTTGCCGATCACCTAAGTTACAGAAAGTAGAACATGAGGTTCATTTATATAGCCCAGGAGCCTGTTACTATTCCTTCACCAACATAAGTGAAGATATTTTAAAGTTCGTATACAAGTGAGTTATCCCAGGGTGTGCAATATCTATCCACATTTTAGACAGTGACTTGAATAGCTGCAGATTCTGGAGATACTTTATAGGATACTATTTTGTATATTTGGTGTTCAGAAATCAAAATTGCTCATCTATAACTAAGTGATCATTTATAGAGGCTACAGTACAAAAATATTGTCAGTATTTCAGTTGACATAGGACCCAGTATTATAAAATCCGCCCATTAAATTTTATAGCTAAATTCTACTAAAAATTATAAAACTAACAAAAGGATTTGTGATGAAAAATACATTCACACCATTTTCTAATGGTCAACTAGATTTTTAACAAATTATATTGCAAATTACTAAAGTATCTTTCCCACATCAACCCCAACCTTAATAATCTCGGTTATTTAATAAAGATCCAAGATGAAAGTATCTAACCTTTGTAGTTGCTTTTAGTTCACTCAGTTTCTCATTCAATGAAAAGACAAAATTAGTGCCTCTCGGTATCACATAATTATGTAGAAGCATGCAAGCGACAACTTCTGATATGTCGTAAGAACTCTTTCAAGACTTGATGCATCAAACTTAATATCTCACAGGCACAAACAAATAACCGTCCAGTTGACAATTTATTTTCAAGGCCATAAGAATTCACACATGCAGGGCTTAGAACAAGAATAATCATTTTTGGGAAAATAAAAAAAATGAAAACTATGAATTACTTCATCTGATATAATGTTTTAGTTAGTAAGTACCTCTTATATTCAAATAACATATGTTGAGTCCAAATATATGAATCATAATAACTCCTAAAATAAGAAATTTTCTAGGGTGACACATTGCAGGAACAATCAAATAGGGAAATGATACTATCATTTTTTTCACCTCAAAGTTCAAGCATAATGCGGTGATAAAATCATTGACACCGATGGGAGGATTATAATAGGCCGAAAAGATTCTTACTTTGTACACATCAAAAAAAAAGTTGGAGAAAGAAAGCGATTTCAATAGCTCCTTTGAAGTTACAAACAAAATTCTCTCAAATCAGTGGGCCACGTGGCAAACTAGTAGCCTTTGCCCTTGCAGAAAAAACAAAGAGTATCATTTACCAAAAGGTGTAAAATAAGTTCATTCAATGATTGGTCGAAAGAGTACATTCAATCACATCTTGATAAGAGAATCTGACGTGGGTTCAAACACAAGGAAAGTTTCAAACATATCACAAAAGCAAATTCTAATCTATGCAGATCAAACTGCCATGGCAGCGAATGATAAATGAATGGGGAACAGAAATAGAGTACATGAAAGCTAGCAGTTGCTACCTCCCCTGGATAACGGGTAATGTGTTTAAATAAAGGGACAATGGCATGGCTCACTATTCATCCTTACAGTGGCATCGCTCTCCCTTTAGCTACGGGACATTCTCATGACGACATCTTTCTACAGAACATTTCAACCTCCCACCAGTGACCTTTCCCCCCCACCCCCCAAACGAAAACATTTCAACCTCGATATGCAGCAAGCAGTAAAACATCTCCCAGGACCAGCCACACAAGCAGAGAGCAATAATTGTATTTCCTGTAAAGATGTTGAAGATAGTACAAAAACTACAAATACATTATTCACGTATTGCAATTCTAAACAAAAAGCAACAGTGGAGTATTGAGTCAGGAATTCTGCTATGAATAGTTTACATATAATGTCACGACAGCACCTTAGCACACAGAATTATCAATTTACTTACTGTTCATTGAAACAATAATCACTGCCCAGGTTTTGGTTGGAATTTTAATGAATGCTTATCTCTGAAGCTATTATCCTGAACACAATTCCTCTCAGACGTTGATTTACACCTCCTTTTCGATGTTTTGATTCCTTGTCTGATGTGGTGGCAGCCAATCCATTCTTTCCTAGTGGCATCCAAATTGGGGACAAAGGTGCAATGATGCCTTCCGGGTTCCGGCGCATCTCGACGGCGGCGGCGGAAGACTGCATCACCCGCGGTGAGCACTCATCGCCGACGGATCTCACTGCTTTCGCGCTCCCCAACTCTACACTCTGGTGGAATGGTAGAGCCAATAGGCCATGGAAAAATACGATTAGGGAGCTTGCGCTTCCAGCGGAAGAGAGAGCAGCGAGGAGATGCGGCGACTCCGGTGGGGAAGAGGCTCATGGCGAGGCCGCGACGGCGAGGCGGCTGTCGGCTTCGCCGGACGAGCGGCGGGACCCCGGGAGAGGGAGATCAGAGAGCCAAAATACAAAAAAAAAAAAAAAGAACGGAAACGAACACAACGTGGCCCTCTTTGCACGGTCCGATGCGGATCGGAGCAAGGGCCCAAGAAGAGATTAGTCGAGGACGAATAAAAAAAAGAGAGAGAGAGAGAGAGATAAGTCGAGGACGGAGAAATTCCCCAAGCCGCCGCCACTAACCCTAGCTTCCGCCAGCACGGTATTAAAACCCTTCCGCTCTAATTTCCTCGCACCATTGATTTTTGTTCTGTGCGTTCGTTTCGATCCAAGTAGTTCCCCAACAATCCTGCTACTGCGGAACTGCCGATTTTGCTGTCAGTTTATTTTGATCGCAAACAGTAAATATTAGCCGAGCGTCGTTTGGCATTATCTTTCAATTCCATGCTTCTTTCAAATTTGACCCATCATGCATGTTATCAAAATTTACTAGAGACCCAGAAATATGCCGATGTTCTGTGGTGACATACCTATGTCCTGTTTTTTCTAGTTAGTTTGCATGTCTTGAAATAGGCTTGTGGAAAGAACTTGTGTTTCGAGCTTCATGTTAGAGAGTGGTGGGATGGCACCCTCTAATAGGCCACTTGAGGTCTCTAATTCTTTTGTTTTCCCAGTCTGAGTCAGATCTGTGTAAGAATCTTACATTTCTAGTAATAGAAATTGGGGGTTACTCCCTTGTTTTAAAAAAAAAAGGAAAGACCCAAAAAAAATTCACTAGACTAAGGGCATGTTGGGATGGTAGCCATTGCCAAAATTTTGGCGAAGTGGGTTTGTTTGATTTGATGTGAATATATTTGGAGCTTTTTTTAAACCTTGCCAAAATATTGGCATTGCAATTTTCCTTGTATCAAAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.88973
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0317600.2 5 25928622 T C
Osa05LNT0317600.2 5 25928744 A G
Osa05LNT0317600.2 5 25928785 T C
Osa05LNT0317600.2 5 25932100 G A
Osa05LNT0317600.2 5 25933219 A T
Osa05LNT0317600.2 5 25933238 A T
Osa05LNT0317600.2 5 25934239 A G
Osa05LNT0317600.2 5 25934823 A G
Osa05LNT0317600.2 5 25935492 T C
Osa05LNT0317600.2 5 25930086 G C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa05LNT0317600.2 osa-miR5817 Cleavage 4.5 13.57 1 24
Osa05LNT0317600.2 osa-miR5818 Cleavage 5.0 22.016 1 21
Osa05LNT0317600.2 osa-miR5828 Translation 4.0 12.221 1 21
Osa05LNT0317600.2 osa-miR396c-3p Cleavage 5.0 19.801 1 21
Osa05LNT0317600.2 osa-miR159c Cleavage 4.5 12.414 1 21
Osa05LNT0317600.2 osa-miR159d Cleavage 4.5 12.414 1 21
Osa05LNT0317600.2 osa-miR159f Cleavage 3.5 12.414 1 21
Osa05LNT0317600.2 osa-miR444b.2 Cleavage 4.5 23.493 1 21
Osa05LNT0317600.2 osa-miR444c.2 Cleavage 4.5 23.493 1 21
Osa05LNT0317600.2 osa-miR444f Cleavage 4.0 23.493 1 21
Osa05LNT0317600.2 osa-miR1850.2 Cleavage 4.0 13.26 1 21
Osa05LNT0317600.2 osa-miR1850.2 Cleavage 5.0 11.206 1 21
Osa05LNT0317600.2 osa-miR827 Cleavage 4.0 10.586 1 21
Osa05LNT0317600.2 osa-miR2870 Cleavage 5.0 15.438 1 21
Osa05LNT0317600.2 osa-miR2863b Cleavage 3.5 10.88 1 21
Osa05LNT0317600.2 osa-miR2873b Translation 4.0 12.412 1 21
Osa05LNT0317600.2 osa-miR5072 Translation 5.0 24.392 1 22
Osa05LNT0317600.2 osa-miR5147 Cleavage 4.5 9.745 1 21
Osa05LNT0317600.2 osa-miR5490 Cleavage 4.0 10.399 1 21
Osa05LNT0317600.2 osa-miR5501 Cleavage 4.5 17.84 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0317600.2 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0317600.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0317600.2 5 QFla5 Morphological trait Culm/leaf RG470 RG346
Osa05LNT0317600.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0317600.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0317600.2 5 nan Physiological trait Eating quality RM163 RM31
Osa05LNT0317600.2 5 qRFC-5 Physiological trait Eating quality RG470 RG474
Osa05LNT0317600.2 5 qRGR-5 Physiological trait Germination/dormancy RM421 RM480
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