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

>Osa08LNT0404300.1

GCTAGTACTAAACATTACCACCTCGGATGCACAAAAGATAACAAACGAGAAGCAGTGGCGACACATTGGGTAATGCACAAAAGCAACTTCGCTATATTTTCGCCCTCGGAAACATGGGAAATGCTTCGCAGTAAGCATTTCTGCGGTCACTACTTGACTAGAAAAAGAGGACGCGATCCACACATCTGATTCACGAGATGTGTCTCAACATAAGGGCAGAGTTCATGTTGCCTTGGTGCCTTTAGATGATATCTTCAGAGATTCCATAGCTTCCCGTAATGCACGCTCAATCTCTGCATTGTCCGGGTCCAACTTGAATCCATCAAAAAGTGCATCGCACGCGCTCTCGAAGTCCTTCAGGGTCATCAGAGCAGCACCAAGCCGGTAGCAGGCCTTTGGCCAATCGGGCCGCATTTCTCTGCATTCAAGAGCATCCAGAAAAGCCTTCTTTCCATCACCCATGCAGAGCCAGCAAAGGCTCCTGTTTGAGAACAAGGTTGCATCATTAGGGTCAAGATCCATTGCCTTAGTGTAGAACGCTGAAGCAGAAATGTAATCTTCTCTATCGACTGCTTTATTCCCAGATGTCTTCAACTCTTCTATTTTCTTTTTATTCACATGTTGATCATCATTAGGGCCACCATAGTTGGCACCAGCCTCCATTAAGAAATTTAAGCACTCAGTTGAACCATCATTGCCCATTGCAGAATCAAGTGCAGCAGTTGAGATACAATCTGAGTTGACATCAGCACCAGCCTCAACCAGGAGCTTCACACATTCCACTGATGAAACATTTACAGCCTGAAAGAGGGGTTGTCATAGGATACAATCCAAACATCATGTACGTCTTGTTGCAATCTGCATTATGATCCAATAAAACCTTCATAGCACCGACTTGTCATTCCTTAGTAGCAAGATGTAGTGGCGTCCCACATTCATCAGCTACCGGATCAATATCAGCCCCCTTTGCCAGCAACGTTTCTATCATTTCACAATCTCCTATTCCAGCAGCGGAATGTAGAGGGGTTAGCCCGTCATCATCAGCTTTGTCTGGATCAGCACCATGATCAAGAAGGTACTTGACAATAGCAGCATTTTCACCGATCACCGCAAAAACTAGAGGTGTTCTACCCTCATCATCGGCGGCGTTCACATCCACGCGCAGCCCTTCGACGAGGTAGCGGCACACCTCCAGCTGCTCGTTGCCCGCGGCGAGCTGCAGCGCCCAGATGCCGCCGTCCGTCCTCGCCGCCTCCACCACCTCCTGGAGGCGGCCCCTGACCTTATCCAGCGCCCGCACCAGCCTCTTGAGGTGGCGGAGGTCGCCGCTGGCCGCCGCCTCGAGGAGCTCGTGCTGCATCGAAGCGGCCGCGGCGGAGGAGGACGTCGGAGCGGCGAGGCGAGATCGCCGCGCCGCCATGGCGGATGGGTCGGGGAAGCGCGAGGGAGTAGGGTTTTGCGAATGGGGGTGAGACTGAGAAGAGGAGGGTGAGAGAGAGAGAGAAAGGAGGCGAGGTGGGGAAGAGAGAGGCGAAAAATGGTTGGGCATTTGATTTTTGAAAACTGAGGCGAGAGAAGACGAGAGAGAGGGCGTGGAGGAGGCGTACGCGGCAAGCCAGCGCGTGGGACCCGCCCAACCCCTGTAACTGCGGACACCTGGAGGCGGTAGGCCAAAATGCCCAACCGATTCCATCGTTTCGTCTACCAGTAACCTGTGCACGTTACTGTGCACGTGTAGTACACGTCGTAACCTGTATTAAAATTATATTATTTTTAAAATCAAATTTATAGTAGTATATAATTAAAAGCTACGACATACATTTAAAAAATCAATATACTTTCACTTATAAGTTTGAATAACATAACATAACTATTTTTTTTTGCTATTTAGTACCAAGGAAATCCTCCCAATCTTGCATCATAATACTTTTATATGAATTGAGAAAATATGAATTGCGCTTGAGGTATCTTTAATGATAATGAAACAAGTCACATATATACATAACTTTTTAACAAAATTATCAGTCAAGCGTCATGTCCTACAAGTCAATAATATTATATATTTTAAAATGGAGGAAGTAATATTCATGCATCAAAGTGTGACTGCAATCTTGGATTTTTCATCAGCCTCCTTGAATGAGCAATATAGCTGTTAGAAAAACTTAAGAGAAATAAAATTTGCTCATGTTCAGTATAAAATTTCTTAGAATTTTAACTGTTCCCTATCACCCTATGTGCCAAGGGGGCAAGAAGACTAAAGGGAATGCCTTGGTTAGGTATAAAACTGCTCGGATTTTTGTTTAACACTAATTTATTTGAAAATTGTAAACATAATCCCTTTCTCACTCCATGCCAAATTTTGCAAAGAACAAAATATAAAGTCCTGCTAGGTTGCTATAGAGTACAACCAATTCAACATTGGTAACACTTGATGAATTACAACAGCTAGACAGCTAGACGATTGTAAGGGTACAAAACACCAGATGAGAAAAAAAATAGTTTAACCTAAGATAATATATTGTTCAAAACATCTTCCTCATGTATTGCCTTTCTCCAACTGAATCATGTATTCTGCACTTTATGAATTACAGTATTGATATCCAAGATCCTAGCATGGTCAATTGGATCACCATGGAAAAGTTGTTTCCATTTCAGTTTCTTAACAATGAGTTTCCCTTTCATTTATGCCTATGAAGACATGGTCACAGACTAACTGTGCCCAAAAATAGTTTTATCACTGCCCTATGTTTTTGCCTTTTGCTCTTGAGCAGCAACCTGATTTTTTTTTCAATCTCAAACAATAAAAGCCACAAATGGATAAATTTTGATTTAACAAAGTTCATATAAGTAATGAAAGCTCCTTATGACAGACCATCCTAGATTCAAACTGTAGCTATTAGAGCGGCAATCTTGTGAGTTGTGATAAGAAAGTGATCTAGCTAGCTGCATACAACTTCCAACCTGCAGATAGGACTGAATAAATATGTAACCCTCTTTTCAATTTGGCAATTTAGAAAAGTATGAACTGGCATATGATGAACATCAAGAGTTTCTCCACAATTCCAGATTTGCAACAAAGTGGACATGCAGGAACGGAGGAATGGCAACGTAGGTGAAAAAAAAACAGTAGTTTTTTTTTAAATAAATTCAGCTGCAACCAATCAATAGAATATCAGTAGCATAGTGCCTCGTAAAAATAAAGAATTGTAAATATGTACCAATATGTTCATGTGCATAGCAGAAAAATGTTGGGCTACTTCTTTATGCGCAATCAACACAATCTGTTAAATATATCATATATGTCAACTCTCAGGTGTTCTGGAGTAAAGAAAAACTCTCAGATTGTTCAAGTATTACATAGCATGGAGTTGAGCTGATCAGTTTCATGCTGCTAATTCTAACAGCCATTATTGTAAGAGGAAATACCTAGCTAGTACGTATGCAGCAGGAATTCTAGTGACAAGAAGTATATAGTAAAATATGAATGTCAGATCATCAAATAGCAGAGCTGAGATTTAGAAATTACCTCCCAACCCAGATGACAAGTACTTTGAAGAGGTGAGTCCAAAATAACTACTATGAAACTTGATAATGTTGTATCATACAATTTAAGAGTAAATTGGAGAGATAGTAGAAGTGGGAAGCTACCAAGGTATTTTGGACATGTAGCTCTTGTACTAATTTTGCCCAAATCTTAATATCACCATTAAAGGACCAGAAGAAACCATGATAATTACGTTTAGAATCAAACAATCAACTTTGGTATTGAATCTGCCTCAGCTAATGGCATTCCTCCTTTTGTTGGTTCTAATGGCAAAGCAGCGGGATAAAGCAATATCAAACAGTGGGCTTTAGCTCGTAATGGAATAAATCAATTAACTTGTAATACTGTAGACAAGTGGTGTTATTAACTTCCTTGGATTTGCAACTCATGGGAATGCCTGAACCGGCTCCATCACCGAAGAGGAGAAAACTCAGGTAATAAGCTCGATCCACAAAAATCTGACTGATTAGTGATTAGCCCCCACGCCTCCAGTACATCCTCTGTACCTGGTTCACCTGGTGGGCGCTGGAGATGGGTGCTGGCCTGCTCGATCGGGCGGCGAGCCAGCGAGCGGCGGTGGCAGTTGATGACGCCCGACGATGGGCGACAGCCTTGATCCAATAGCGAGGGCAGTCAACGCCGGACAACGACCTGCATCCAACAGCGACGGCGATAGACGCCGGGTGGCAGCCGATGATGGGAGGGGATCCGGCGACGGGAGGGTGAGCAGCGACCGACGGATCGGCGACGCTCCCTGAGGAAGAGAGAGGAGCTTAGGGATTCCGTGGGGAGGGATTCTCGGAGGAGAGACTTTTGTGGGGCCGGCGCGGGCTTCGCATGAAGCTCAGGAGCTATTTGCGGAGGAGCAATGGGGGCGTGCGTCCATAGTCGTCGGGGGCAGTCCCAGGCGTGGCACCGGCGGAAGGGGATGCGATTGTGCGGTGGTGGCTCAGCGCTGGTCGAGTGAGGAGCAAGCGAGAGAGGATGCGCACGGCGGAGTCATCGCGGCTGGGTTTTGTGTGGCGGAGTCACCGCTTTGGGGCGAAATTGGTGGAATCGATGGAATTAGTGGAGATCCAACAGCGGCGGAATCGGTGGAATCGCCGTCGCTATTGGAATCAGCGAGGAGGAGCAGCGTGAGAGGAGCGAGGCGTGGTCAACGCGCGGTCATCA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.925663
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa08LNT0404300.1 8 8114592 T A
Osa08LNT0404300.1 8 8109648 A G
Osa08LNT0404300.1 8 8119623 T C
Osa08LNT0404300.1 8 8110804 T C
Osa08LNT0404300.1 8 8109504 A C
Osa08LNT0404300.1 8 8117122 C T
Osa08LNT0404300.1 8 8117812 T C
Osa08LNT0404300.1 8 8107799 T C
Osa08LNT0404300.1 8 8108497 A G
Osa08LNT0404300.1 8 8108529 G C
Osa08LNT0404300.1 8 8109045 A T
Osa08LNT0404300.1 8 8108415 A G
Osa08LNT0404300.1 8 8109778 T C
Osa08LNT0404300.1 8 8109892 G C
Osa08LNT0404300.1 8 8110168 G A
Osa08LNT0404300.1 8 8110512 A G
Osa08LNT0404300.1 8 8110842 A C
Osa08LNT0404300.1 8 8111176 C A
Osa08LNT0404300.1 8 8111575 C G
Osa08LNT0404300.1 8 8111783 A G
Osa08LNT0404300.1 8 8111812 A T
Osa08LNT0404300.1 8 8112770 A C
Osa08LNT0404300.1 8 8114295 A G
Osa08LNT0404300.1 8 8114332 A G
Osa08LNT0404300.1 8 8114375 A G
Osa08LNT0404300.1 8 8115017 T G
Osa08LNT0404300.1 8 8115065 G A
Osa08LNT0404300.1 8 8115076 G C
Osa08LNT0404300.1 8 8116149 T G
Osa08LNT0404300.1 8 8116349 C G
Osa08LNT0404300.1 8 8116756 A G
Osa08LNT0404300.1 8 8116987 G A
Osa08LNT0404300.1 8 8117439 C T
Osa08LNT0404300.1 8 8117608 T C
Osa08LNT0404300.1 8 8118825 C T
Osa08LNT0404300.1 8 8119479 A G
Osa08LNT0404300.1 8 8119684 A T
Osa08LNT0404300.1 8 8119817 A G
Osa08LNT0404300.1 8 8119970 G A
Osa08LNT0404300.1 8 8120021 T C
Osa08LNT0404300.1 8 8120095 A G
Osa08LNT0404300.1 8 8120208 C T
Osa08LNT0404300.1 8 8120232 C G
Osa08LNT0404300.1 8 8118803 T A
Osa08LNT0404300.1 8 8108084 G A
Osa08LNT0404300.1 8 8111658 T A
Osa08LNT0404300.1 8 8112005 A G
Osa08LNT0404300.1 8 8112174 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa08LNT0404300.1 DTM_#DNAt_MULE_japo_Os1127 Chr8 - 8111859 8112238 379
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa08LNT0404300.1 osa-miR5543 Cleavage 4.0 8.266 1 21
Osa08LNT0404300.1 osa-miR5543 Translation 5.0 15.903 1 21
Osa08LNT0404300.1 osa-miR156j-3p Cleavage 5.0 24.209 1 22
Osa08LNT0404300.1 osa-miR398a Translation 5.0 15.198 1 21
Osa08LNT0404300.1 osa-miR168b Cleavage 3.5 19.812 1 21
Osa08LNT0404300.1 osa-miR166g-5p Cleavage 5.0 18.868 1 21
Osa08LNT0404300.1 osa-miR166g-5p Cleavage 5.0 15.677 1 21
Osa08LNT0404300.1 osa-miR393b-3p Translation 5.0 21.096 1 21
Osa08LNT0404300.1 osa-miR172d-5p Cleavage 4.5 22.034 1 20
Osa08LNT0404300.1 osa-miR417 Cleavage 4.0 17.942 1 21
Osa08LNT0404300.1 osa-miR1426 Cleavage 4.5 12.721 1 21
Osa08LNT0404300.1 osa-miR1435 Cleavage 4.0 8.786 1 20
Osa08LNT0404300.1 osa-miR1435 Translation 4.5 9.322 1 20
Osa08LNT0404300.1 osa-miR1857-5p Cleavage 3.5 13.884 1 21
Osa08LNT0404300.1 osa-miR2093-3p Translation 4.5 19.958 1 20
Osa08LNT0404300.1 osa-miR2096-5p Translation 5.0 20.006 1 21
Osa08LNT0404300.1 osa-miR2099-5p Translation 4.5 13.461 1 22
Osa08LNT0404300.1 osa-miR2868 Translation 5.0 7.703 1 20
Osa08LNT0404300.1 osa-miR5491 Cleavage 3.0 12.062 1 21
Osa08LNT0404300.1 osa-miR5509 Cleavage 4.5 13.121 1 21
Osa08LNT0404300.1 osa-miR5518 Translation 4.5 24.505 1 21
Osa08LNT0404300.1 osa-miR5828 Cleavage 4.5 13.536 1 21
Osa08LNT0404300.1 osa-miR5499 Cleavage 4.5 9.678 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa08LNT0404300.1 8 nan Resistance or Tolerance Drought tolerance RM72 RM331
Osa08LNT0404300.1 8 qDSR 8 Resistance or Tolerance Other soil stress tolerance RM3572 RM404
Osa08LNT0404300.1 8 qALRR-8 Resistance or Tolerance Other soil stress tolerance RG978 C1121
Osa08LNT0404300.1 8 hd8 Physiological trait Flowering RZ562 RG978
Osa08LNT0404300.1 8 dth8 Physiological trait Flowering RG333 RZ66
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