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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Sequence

>Osa03LNT0227300.1

GGAAGCAGATGAGCAAATTTTCCATATATGCTTTTGTAGCAACAGATGAGCAAATTTTCCAAGATCCAGCTTCACAAATAATAAAATAGCTAATTCGTCGAAATGGACCTACATAAATATCTATTCTTGAATGGTTACATAAAATTGTGGCGGTGGTATGCCAGTATAATACTAATCTAACTCATCCCAAGCTCGCCTCACGATCACTTGCTCCAATGCTTTCACCGTCTTCTTGATTTGTTGAAGGACTTCGATTTTCTGGAAACAGGAGCATTGCGCTCCTCCTCTTCCTCATCATCTTCGTTCTTCCTCCGCTTTTTCTTGTGGCCACCGCCCTCCTTCATCGTCGTCAGCGCAATCCTCTTCGAGTCAGAGATACGTTCACGAAGTATCATGATTTCTGCGTTATCCACCTTACGATCAGGAATCTCGTATCCAAGGAGCTTCTCTATCATCTTAAACCACATGGCCTCGTATTGATTCACCAAAGATACAGCATATCCTGTATTCCCTGCACGTGCTGTTCTACCCACCCGATGAACATAATCCTTGGAATTCATTGGAATATCATAATTGATAACCACATCAACTCCTTGAATATCAAGACCACGACTTGCCACATCGGTGCAAATAAGGATATTGCAGTCTTTCGTTTTGAACCTGTTTAAGGCGCCTAGTCTCTTATCCTGACTCATTTGGCCACTAATAGAGATAGCTTTAAAACGAAGATTCCTTAGGGTGAGAGCAAGGAGCCTTGTTGATTCACAGGTCCGGACAAAGATCATGATCATGCTCCCTGGCAACTCATTCAGAACATGAACGAGAAAACAATCCTTGTAATCTGCAGGAACAAAATAAAACTCCTGTCTAAGTGTGTCCACTGTAGAATATTTGGACGCTACCTCGACCTTAACAGGATTTCTTAGACAAGCACGCTGCAGTTTAGAAACCTGGAGAAAATAGACGTTATTGCAAAGAAAACCAAATTCAGTCTAAATGTAAACAAATAGATAGCATAATAGCCATCAGGTGCCATAAAAATAGGCCATGATTTAGAAAATACAAAATATCAGTAAATGGTAGCACAGTAGCAATACAGCATACGTCAGAATAAATAGAATGTCTACCATTTCATTACCTCAAGAATTTATAAACCAGTGTCATAATTATAATATTAACCTAAGCTGCTAGCATGGCCACATCAATCTGATAAAGTAAACAATCTATTGATGGGATACCAGCAATGTTTAATTCCGTTCTTTCTTGAATCCAGAGGAATAATAATTCTTCTCTGAAAACTACCAATTCACCAACCTTATTGGTCATTGTGGCTGAAAAAAGGAAAGTCCTCCGTTCTTTAGGGATAACATTCAGAATATCATCAAGGGCTTTCTGGAACTCCACATTAAGTAACTTATCAGCTTCATCCAAAACCAAGTACTTCAATTTATTAAGGCTAAAACCTTTCGTATCTGTCAAATGATCCAAAAGACGTCCAGGAGTTCCAACCACAATATGTGGGCGTTTTGCAAGGGATACTGCTTGTTGCACCCGATCAACTCCTCCAACAAGCACCGTGCAACTCAGACCGATCGCGGACCCGAGTGCCTCAAACTGCTGTCCAATCTGAAAAGCCAGCTCCCTTGTAGGCGACAGCACGCAGGCGAACAACGCCTGGGGCTTGTCCTGCTTGAGCAGCGCCTGGATGATCGGCAGCGCGAAGGCGCCCGTCTTGCCGGAGCCCGTCTGCCCCAGCCCAATCAGGTCCCTCCCTTCGAGGGCGTGGGGGATGGCCTCGGCCTGGATCCTGGTGGGCTCCTTCCACCCCATGGCGTCGCACGCCGCCACCAGCTCCGGGACGACGCCCAGCTCCGCGAACGTCGACGGCCGACGCGCCGGTGGCTCGGCCTCCTGCTCCTCGCCACCGTCCGCGGCGGGGGCGGCGGCAGCGGCAACCACCTCCTCATCCAACTCCTCCACCTCCACGTCCTTCTTCTTCGCCATGGCTACGGAGAGACGGGGGAGCTCGCCCGAGTGGGAGGGAAGCGGTGGTGGCTTCGGCGGCGGAGGTGGCTTGGCGATGAAGCTGCGGCGGCGGCGGTTAAAGAAGGAAGGAGGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.854641
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0227300.1 3 26381331 T 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
Osa03LNT0227300.1 osa-miR166l-5p Translation 3.0 16.25 1 21
Osa03LNT0227300.1 osa-miR396e-3p Cleavage 5.0 13.639 1 24
Osa03LNT0227300.1 osa-miR1428b Translation 4.5 14.394 1 21
Osa03LNT0227300.1 osa-miR1428c Translation 4.5 14.394 1 21
Osa03LNT0227300.1 osa-miR1428d Translation 4.5 14.394 1 21
Osa03LNT0227300.1 osa-miR396f-3p Cleavage 4.0 13.639 1 24
Osa03LNT0227300.1 osa-miR5524 Translation 4.5 12.784 1 21
Osa03LNT0227300.1 osa-miR5524 Translation 4.5 11.86 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0227300.1 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0227300.1 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0227300.1 3 QFlw3 Morphological trait Culm/leaf RZ474 C746
Osa03LNT0227300.1 3 Yd3-13 Morphological trait Seed RZ403 CDO337
Osa03LNT0227300.1 3 nan Morphological trait Panicle/flower RZ448 RZ403
Osa03LNT0227300.1 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
Osa03LNT0227300.1 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0227300.1 3 nan Resistance or Tolerance Blast resistance RM16 RM168
Osa03LNT0227300.1 3 qSB-3 Resistance or Tolerance Bacterial blight resistance R250 C746
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