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

>Osa09LNT0442300.1

ACAACCAAACTGAAATCGCATTCACATCGATTGTTTTTTTTGGACGTGAGTGAGTAAAAGTTAGAAAAGGAGAGAGAACGAACTACCTAAACAGCTGACGACCCCGCGTTGCATCTGCTGTGCTGCTGCTTGCCGCGCCGCACGCAGCCGTCCGTGACGCTGCCCCCCCCTTTGCTTGCCTACAGCTAAATAAAGCCGCAAGCCGGCACCGCGCGCAAACCGCCGCCCGCACGAAAAGGACGGGAGAAAAAACACAGCAAAAACACCGGGAAACCCACGCGCGCGTCGCGTCGCGTCCGCCTCCGCTCGCGTTGCGCCTCCGCCTCTGCCGTCTGCGGGCTGTCGCTGCCGCGAGGATCGGGCACCACCACCGGCACGTGCCGCGCGGGCCTCGCCTCGTCTCGACATCTCGCCATCGTGCGGCGCCCCCACCGACCGACCCGGTGCCCGTAATCTATCGCTGCCTTTCGCTGCTCCCCAGCTGGCTAGCTACAGGCCTTTTCACCTCACGGGATCGACGCAGCTGAGCGAAAATCCCACCGGAAATGCTGTGAAATACTGCGCCAGCGTACGTACCAATAATTCCTCTTATTTTTAGATGGGAGTATTAAAGGAGATCGACCAGATCTGGAGCACAGTGAGTGCATCATCAGCTCAGATCCATCGGTACAGCAACGGATCGATCGGCTGCAGTACGTGTACATAACCCAAACGAAAACGGGGGCTCAAAGATCTGATCTGCTGGTACGATGATGCTGGCTCAGGCTGCACTGTAGGCGCTTGATATTCAGGTGAGATTGGCAGGAGAGGCGAGTTAACCTTTCACATGCCTTGGTTAAGAGCAGCACCGGCTGGCCCAGCTCTGTCAAATGGCCATGTTATCTTGTCAAGTCGAAGCTGGCTCTTCTCTTGGCTGCATTGGAGAACAGGTTGGTGCCTGCCTGGGAACACTGTAGCTTGCCGCCGTTGCACATGTGGAAGCTTTCCCTCCGTACCAACCGGGGTCGCCGTCAGTCGGGAGCCTGCCGCCGCAGCCCGTACCGGGAGGTGCAGGCGCAGAATATCGCAGCCTCTGCATCATGCAAGAAATACACACTGACATATGTTCATACTTCATGGGACTAATAGCATTGTTCCTTTTTTTCATGAATTTCCAGCAAAATAGATGCTGGCATACATTCTCATGGGAGTTGAGTGTTTGATGACACATTATTACGAAACAGGACCTTGATAAATGATAGGGTGACCATAGCCAGGTCACGCTCACATGAAACCGAGACGACACCTCGAGCTTTGCTGCCCCCAGAGGGCCCTAAGCCCTAGCCCATTCATTCCTACAGTAATAACTGGAAGAAATTCCTGAATGCCAAAAGTGGCCTCATCTGCCAAAGCCAACTATGATTCGGCAGTTGTTATTAGACATTCTCTATACCTGTTGCCTTTTTGAAGTGCAGACTGCTAATGTGATCAACCTGTTATTAACCAACCAAGCCAGCATTGGTGGCATTATTTTTATGCTCTCAACTACTAACTTTTCTAAGGCTTTGCCTTGAGCAGAATGGAAGAGTATGGAGCAATTCTGTATTTTGGTCCTGTAAATGGCACCCCTTCTGGTACAATATCATTTGGTGATTCCAGGTTGGTATCCACCACACGGTTCCAACATTTATGGTGTGGTGGTGGGGGAATTACAGCGTCCACAAAATAGTCATGTGCATTGAATGCCAAATAGATATCTCCACCAGAGTTGTGATCATGTACTGTGAATGCCAAAAATTTGCTTTCCTGGTTCTCCCAACAATCCTCGTGCCAGGTGACATCGTTTTTATTAAGAAACCTGTCTCGTCTTAATATTGGGTTGCTGTGACGAAACTTTATCATCTCTGAGAAAAACCTGAAATGGCCATCTCTTCTTTGTTCCAACTGTTCCCATTGGAAATTATTAATGCAAGTATCATGTCCATAGCTATTGTTGTTCCCATAACGTGTATGACCATATTCATCGCCCATCAACATCATTGGGGTGCCCTGAGAAATCATTAAAGCTACATGGAAGTTTTTCATTTGTCTTGAACGCAGACTTAACACATTCAGATCATTTGTTTCTCCTTCAACACCACAGTTCCAGCTAAAGTTGTCATTGCATCCATCACAGCCACCTTCTCCATTAGCATCATTGTGCTTTAAGTTGTAAGAAACAAGGTCACATAAAGTAAATCCATCATGTGCAATCACAAAATTTACACCATGGTAAGGCTTCCGCTCGTTCACCTGATAGAGATCAGCAGATCCAGACACACGAGTCGCAAACACCCCCTTCATACCAGGGTCACCCTTAATAAATCTTCGAAGATCATCTCTGTATTTGCCGTTCCATTCAGCCCACCTGTCCCAGTTAGGGAAACGCCCTACGAGATAAAGGCCGCCGCAATCCCAAGGTTCAGCAATGATCTTACATCTAGATAATACAGCATCTTTGGCAATTTCCTTGATGAGTGGAGGTGCATCAAGAGGACAACCATCTGGTCCACGACAAAGAACACTTGCAAGGTCAAATCGAAATCCATCTATGTGATACTCCTCAACCCAGTGTCTCAAGCTGTCAAGAATGAGCTCCTTGACAACAGGATGGTTGCAGTTCAGTGTATTCCCGCAGCCTGAGAAGTTCAGTAGTTCAGCATTTTTGTTCAGGTCTAACATGTAATAGACCTTGTTATCAATGCCACGGAAAGAAGTCATATACGGGTGAGCATCATCCGCCTCATTTGTATGGTTGTAAACAACATCCAGAATAACCTCTATGCCAGCTTTATGCAATTCTTTGACCATCTGCTTGAGCTCTTTGGAAGCAGCCACTGGTCCACCACCGGCACTAGCATAACGGCTCATGGGTGCAAAAAAGTTTATCGTAGAATAGCCCCATGTATTGACCATGTGGTCCCTTGGGTTGGGGTACCTCTTGAATTCCAGCTCATCATACTCAAAAACAGGAAGTAGTTCCACTGCATTAACGCCAAGTTCCAGCAAATGAGGGATTTTATCAATGAGACCAAGATAGCTTCCACGAGAAGTCGAATCAAGGCCACTTGACTCATCCGCGGTGAAAGCACGGACGTTCATTTCATATATGACTAGATCTGCCTCAGGCAAATTCGGAAGCCTGTAGTCATCACCCCAATCAAAAGGAGAGCTATCAAAATCATATGTTCCAAAATGCTGGCTTGACTTCTCTTCAGCAACCCCAAAGTACTTTCGACCAGAAACTAATTTTGCATAAGGGTCCAGAAGAACAGTGCTGCTATCAAATCTATGGCCTTGGTCCCATCCTTGAGGGCCACCAACACGATACCCATAAAGAACACCAGAAGCAGGCAAGCCCTCCACTATCACATGCCATATATCCCCAGTTTTGTTCTTCTGCTGGTCTAAAACAAACTCGACAACATCTGCACCTTTCTCATCTTCAGTTCCCCTCCCAGGAAGCTTTAAGCAGAGAATGACAGAAGAAGCATGCTGAGAGAAAAGTGCGAAGTTCAGCCCGCCTTCAACTTGAGACACTCCTAATGGGAAGGCTTTACCAGAGGAATATTTAAATGGCATTTCAGTATCAGACATTGTACATCCTCTTTCCTCGGTCATGCTTCTCCCAGCGTTCCCGTTCTGAGCTCTCGCCGTGGTGCTTCGTACAGAATCAAATCGCCTAACCTTCTCAGAACACGCTCTGAGCCCAGACGCGTCCCCGAAGCCGATCGTCGCCACACCCACACGGTTCGTACTCGCGACGGAGCGGCGAGCCGGGCGGAGCGCGATGCCTCGACGAGCTGTCACGGCGGCGGCGGAGGAGGAGGAACCCAGCGGGGCGCGATTTATACCAATGGAATCCATCCAAAATGGGGACGGGGCGGAGCGACGGGTGGGGGGGAGATCCGGGACGGGGACACGGGTGCCTAGTTATAGGGCGCGCGCTCCAAGAGGCTCGCGTCGCGAGCGGCTCTCGAAGAGAGGAGAGTGGAGGAGACTGGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGGCGGATGGGGGAAGAGGACGAGCCAACGAGGAGGAGGCGGAGGAGACGGTGATCTCGCATGGGGGGAAGCGCGCGGACGGACGGGAGAGCGGGGGTGGTGGGAGTGGGACACGCGGTGGAGCGGAGCGGCCACGGTGGACAGTGGTGGATAGAGAAGTGGACGGACGAGACGGTTTCTCTCTCGGTCGCGGCCATCCCCATGGACGAGATGACCGCGAGACGGTTTCAATGTGTCATCTCGTCATGCGCTTCTCGAC

Coding Potentia
Explanation CPC Score
noncoding -1.04381
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0442300.1 9 17853464 T C
Osa09LNT0442300.1 9 17853542 C T
Osa09LNT0442300.1 9 17851604 T G
Osa09LNT0442300.1 9 17852046 T G
Osa09LNT0442300.1 9 17853022 A G
Osa09LNT0442300.1 9 17853635 A G
Osa09LNT0442300.1 9 17853650 A G
Osa09LNT0442300.1 9 17854044 C G
Osa09LNT0442300.1 9 17854969 A T
Osa09LNT0442300.1 9 17856297 A T
Osa09LNT0442300.1 9 17858255 C T
Osa09LNT0442300.1 9 17861773 G T
Osa09LNT0442300.1 9 17862352 C T
Osa09LNT0442300.1 9 17864230 T G
Osa09LNT0442300.1 9 17864754 T C
Osa09LNT0442300.1 9 17866392 G T
Osa09LNT0442300.1 9 17866762 C T
Osa09LNT0442300.1 9 17860502 A G
Osa09LNT0442300.1 9 17859429 A G
Osa09LNT0442300.1 9 17859561 C G
Osa09LNT0442300.1 9 17860583 G A
Osa09LNT0442300.1 9 17866901 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa09LNT0442300.1 DTM_#DNAt_MULE_japo_Os0284 Chr9 - 17859356 17860688 1332
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0442300.1 osa-miR5827 Cleavage 5.0 13.315 1 21
Osa09LNT0442300.1 osa-miR1440b Translation 5.0 17.027 1 21
Osa09LNT0442300.1 osa-miR7692-3p Translation 4.5 19.273 1 24
Osa09LNT0442300.1 osa-miR156c-3p Cleavage 4.5 16.214 1 22
Osa09LNT0442300.1 osa-miR156f-3p Cleavage 4.5 16.214 1 22
Osa09LNT0442300.1 osa-miR156g-3p Cleavage 4.5 16.214 1 22
Osa09LNT0442300.1 osa-miR156h-3p Cleavage 4.5 16.214 1 22
Osa09LNT0442300.1 osa-miR398a Cleavage 4.0 14.999 1 21
Osa09LNT0442300.1 osa-miR156l-3p Cleavage 4.5 16.214 1 22
Osa09LNT0442300.1 osa-miR817 Cleavage 5.0 15.011 1 21
Osa09LNT0442300.1 osa-miR818a Translation 4.0 13.805 1 22
Osa09LNT0442300.1 osa-miR818b Translation 4.0 13.805 1 22
Osa09LNT0442300.1 osa-miR818c Translation 4.0 13.805 1 22
Osa09LNT0442300.1 osa-miR818d Translation 4.0 13.805 1 22
Osa09LNT0442300.1 osa-miR818e Translation 4.0 13.805 1 22
Osa09LNT0442300.1 osa-miR1424 Cleavage 4.0 14.079 1 21
Osa09LNT0442300.1 osa-miR1427 Translation 5.0 14.713 1 21
Osa09LNT0442300.1 osa-miR1850.2 Cleavage 4.0 18.442 1 21
Osa09LNT0442300.1 osa-miR1857-3p Cleavage 5.0 14.111 1 21
Osa09LNT0442300.1 osa-miR1428b Cleavage 4.0 13.317 1 21
Osa09LNT0442300.1 osa-miR1428c Cleavage 4.0 13.317 1 21
Osa09LNT0442300.1 osa-miR1428d Cleavage 4.0 13.317 1 21
Osa09LNT0442300.1 osa-miR1428e-3p Cleavage 4.0 13.317 1 21
Osa09LNT0442300.1 osa-miR1320-5p Translation 4.5 13.657 1 21
Osa09LNT0442300.1 osa-miR2099-5p Translation 4.0 11.796 1 22
Osa09LNT0442300.1 osa-miR2275a Cleavage 4.0 16.619 1 22
Osa09LNT0442300.1 osa-miR2275b Cleavage 4.0 16.619 1 22
Osa09LNT0442300.1 osa-miR2876-5p Cleavage 3.5 22.048 1 21
Osa09LNT0442300.1 osa-miR3980a-3p Cleavage 5.0 20.512 1 21
Osa09LNT0442300.1 osa-miR3980b-3p Cleavage 5.0 20.512 1 21
Osa09LNT0442300.1 osa-miR3982-5p Translation 4.5 12.252 1 21
Osa09LNT0442300.1 osa-miR5158 Cleavage 2.5 13.661 1 24
Osa09LNT0442300.1 osa-miR5500 Cleavage 5.0 13.687 1 22
Osa09LNT0442300.1 osa-miR5519 Translation 5.0 11.97 1 21
Osa09LNT0442300.1 osa-miR398b Cleavage 4.5 14.999 1 21
Osa09LNT0442300.1 osa-miR1861d Cleavage 4.5 6.222 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0442300.1 9 qSB-9 Resistance or Tolerance Sheath blight resistance C472 R2638
Osa09LNT0442300.1 9 nan Morphological trait Panicle/flower RM257 RM566
Osa09LNT0442300.1 9 rdw9 Resistance or Tolerance Drought tolerance R79 R2638
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