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

>Osa06LNT0332400.2

GCTAAAAAGTCAACGGTGTCAAACATTTCGAAACGGAGGGGGTATTTTGTAATAATTTAAGGGTTCTATTTTCTTAAGGTATCTTAAAAATCCATTCATAAACTTTTGAGTAAGAGATGGATTAAGTACTTACTACTTTTGAATCATGTTCTTTTTCTCGAGTAAATAATAAACTATTGCTTGTAGTATGGCTATAAATGAAAAGGTGAGAGCAAGATACTTAAAATTCTTGTGATTAAATCGTCTCATGAAGGTGCATGATACAATAAGAAAGGGAGGGAAGCGTATACATGGAGAAAAAGAAGAAAGGGGAAAATGGATAAAAGGGAGGGGAAGCGTAGGTACCCACGTACGTAGGTGCATACCGAAGGTGGAGAGGTGGAACCTCGTAGTATTTAGTTTGTTCTAAGATCAATTTAATCTAATGGTTTATAATATTGGACCCATCGATTAAGTGAAAATCAAGTAATAGATACTTTGCTTTTTTTCTTAGAATTTCTAATATTTTTTCTAATTTATTAGAGCACCACGTGGCAGCTTGAGGGCATTTTAAGAAATTTTAATGTACTTACCACATGTAATTATAATATTAACCATGTAATATATATGCATGGGATATATGTTAATATTCATTATAGCTTCGTCCGTGTTTATATACAGACCTATTTACAATTGTTTATAGTAGCTCTTACAGATTCATCTTACGACTTTGATTATGCGTTGATCACTAATTTACTGATCACCATGACTCGCATGAAAAAATTATAATTATGTACTACTTAGGGTTTAGGGTTTAGGACAATTGAAATTGATGAATTATTTAATTTATGTGATAGCTATTTGAGATTATAAACGAATGAATTAACTTCTAAAAAGTTATAAAGATGTTTAAGAAAAGCACCATTTAGAAACTTGGAAAGCGTGGAGCGTGCAAACGAAAATCCAAAAGATGGAATCAGGGAAAAAATAGGGCCTTAAACTCCCTTATAACACTCTTATCCTAGTAAGAGTTCTATTGATATTCGTTAATATTGTGCTCACATTTGTAACATAATGATTTACGAACAAATAATACAAAATCTGAATGCAACATAACACAATACATTATAATTATTATGTAATCAACTATCGATTTCGGCTTAAACAGAGCTAAGTGTTCCCACGGTGCTTAATTCTTCTCTCACTGCATCACATTTAATTTTCTTTTCATGTTATTAACAAAATCGGTACCTGCAGCGGTCATGATCACCTGAGATGCCTCAGACATGACGCTTTGTCACACATGCGAAAGGAAAAGGTATAGACGTGCATTATGCAGCGGGCCAAAAAGAGAACTTTAGACACTTTAGTTATTAATAATAAATCCGATGATTTAAATAATGGGTCGTACTTGTTCTAGTGTAAATATAAATTAGTTAATATATATTTTAAATTGTTAATTTAATGGGTACACAATATAATGGTGTAGACTTTATTTTAAAACAATGTATTATTTGAGAATAATAGTCCAAAGTAATTATAAAAATAGATCTAATGATTTAAATAATGGGTCTATCTGTTTAAGTGCACGTATATATTAGTTAATATAGATCTTAAATTGTTTATTTGATAGGTACACAATATAATTGTGTAAATTTTATTTTAAAATAGTGCATTATTTAAAAATAATAGTACAAAGTAATGAGTACACCGGTTTAAGTGGAAACTATCTTACATTATTGATTTAATGGGTAAACATATAATATGGTGTAAATTTTATTTTCAAAGATTATAGAGCTAATTTAGTTACATGTGTTTATAAAGAATTATATGATGGTATATTCTTTGTTTGTAAAATTATCAATTGTATAAATGGAAAAAAGAAGTAAAAAAAGAAACAAAAGGGAGGGAGGCGTACGTACTACATACCCGTACGTGACCTACCTATGCACGTATAAAGAGGAGAGGTGGGACCCATAGTATTTGGTTTGTTTTACGATCAATTTCATCTAACGGTGTATAATATTGGACCCACCAATTTAAGTGAAAATGAAGGGGTAGTGTTTTGCTTTTTTCTTAGAATTTCTAGGATTTTCTCTAATTTATCAGAGTGCCACGTGGCAGCTTGAGAGCGTTTGTAGAAAGTTTAATGGACTTTTAGTATATAATAGAAGATAGATAATAGATAGATAGATAGATATGAATGTGGGAAATGATAGAATGTCTTACATTGTGAAACGGAGGGAGTAACACATACGGCTTGTACAGTGTTGAATTGTTCATGCAAGGTGATCAAGATTCAAGAAAGCCAAAATAATCAAGCCATCCCCTCCCGCATATCTTCATAAAGCATTTAGAGCATCGACATACCTGATAGTCGTGTGATGTGATGTGAAGTCATGTAACAATGTATCTCATGTTCCTGACAAGATTAGTGCATGAGTGCAACAGATAAGCAAGAATAATTGAATTGCAGGGGTTTATACTAAGCTGGTTTCATTCACCCCCATCAGGCAGCAACATGCTCACACAATCTGGAGGAATAATATATCAGATCTTCTGCGTTATCAAATCACCAATAAAATTTAAAATATCACGTGAGGTTTTGTTGTTTTGCATCCCAGTGTCACAGAGTGAAATATGCTATCTTCACCATTTGTTCATCTCTGCAAAGAAACTCGGATGAAACAATCAAATACTATGTTCTCTAAAGAACAAACTTCGATCGCACTACCTAATGTGAGCAATGAACACCACGGTAATATCACCATTGCTTCTCACTGATGTAGGCAAATCTGACACTAAGTAAAGCAAATACTACTTCAGAACCTCCTGTGTGCTTTGTTGTTTAACAAATTTCCCTCTCCGAGGCCCTCTTTTAGATCTCTTTGCTATGGCAAGACCCTGTTTTTTCATTTTCTCCAATTTTTCTTTCCTTCCTTTTATATCAGCTTTAATAACTTCATCCCTGCTTTCTTCTGACAATAGAGCTAGTCTGGAAAACTTCTTTGGCCATACTTCTCCAAGTCGCTCATGTATATCTTTAAATACAGGTACAAGACCGGCTCTCATGAAATATCCTTCAGTAAGCTTCATTGAGTTCGTTTTAGGAAGAGCGGGAGCATCTTTCAACTCAAGGTCCAGGCAAAAAGGAGAGTCTTTCAGCCACATCTTAAGAGAGTAAGCCTTCACCACAAAGCGACCTGACCGACTTCTGCATGGTAGGAAAGGGGAGCCCATTTCCAAAAGGTAAGCCCTGATAGTTTTACGCAAGGATACCATGTTATATTCCCCCTCTCCTGTGACCAATACAATAGATTTGGGGGATTCTGGTGCACCCTGCAGTGAAGCATCTTGCATCTGATCAAGCCACAATGTTAGAGCAACAAGAGCAGCCCCAGCAGACAACTTGCGTAAGTCAGCTCCCCAATCTTTTTCTTCCACTCGAAAGATATTATGATGGTATATGCTTCTTTTTACAGCCAATTGGAAAATCCATGAAGCGGTTGCTCGACGTTCAAATGCCCATAACAGGTCTTCCAGTGCATTTACAAAGTTCAATGAAGCAGAATCTTCTAGTGTCCCAAGTTTTTCTAGAAAGCTGTCAACCTCAGTAAACAGAGACGAAGTCCTCTCAGTAAGGAGCCTAATGGGAAGGTCAAATCCACAATCCTGCAAAGACTTTAGAAGAAGAATGGCATCATCAGTCTGCTCGCACAAACTAGCAGCCCTGATGAAACTTGTCCAGACTTGATGATCTGGTTCTACACCATCTCTTTTCATTTCTAAAAGCTTTGTGATTCCAAGACTGTAGTCACGATTTCTCAAGTAAGCATCGAGAACAGTACTGTATGGTAAAGTGCTAATTTCCAAATTAGAAGATTTCAAGCTGTTCAGGACTTTCTCAGCTTCGTCTGGGTGCCCAGAAGTCCCATAAGAAGTCATGAGGATATGCATAGTAGCGATGGTTGGTTCAATCCCATCCTCTTTCATTGCTGATAGTAAGTGCTCGGCTTTGGAATGGTTGCGGGCATTCCTATATATTTTCATCATCATGTGGTAGATAGATCTATTTAACCGATATCCCTTTGTTCTCATTTCTTCAAAAAGCAGGTCAGCTTGCTCCCAGAGTTTAGCTTTTCCAGATGCAGCAAGCAAGATTTTGTAGGATTCTAACTTGGGTGTCAAACCCCGTTTACCCATTTCATACAAGAGAGTAAAACCTTCTTCAGGCCTAAAGTTTCTACTGTACATGACTATAAGAGTATTATATGTATCCTCATCAGGCTCTAATCCAGCTTCCAGAATACTATGATATACTTCTATTGTCCTGTCAAAGTTTCCTGTCCCAGTATACATTAAAAGAAGGGTATTAAGTACCACGAGATCTGGTTTGAATCCTGCTCCCTCCATCTCTGCAACCATCAATTCGACATCTCTGAATCGTTTATTATGGCAGAGCAAGGAGATCATAATTCTGTAGAGGTGCATATTTGGCAAGTATCCTGCTGCCTTCATCCCATTATATATTTTCATTACCTCGAATACATCCCCAGCTTTTGCAAAAGCTTCAAGCATAAGGAGTACTGTGCTTTTGCTGATCTTGATGTCTAAATCTTGAAGCTCCTGAACAACCACATACAACTCATCCAGCCTGCCATCAACAATCAATGCTCTCATCATTCCATTAACTGATTCAACAGTTGGTAGAGGACCCTTTTTAATCATAATGTCAAAGATTGCCCTTGCATGCTCATAAAGGCCACTCTCAGCATATGCATGTATTAAAGCATTCCAAATCCTTCTATCAACACCAGACTCCTGCTTCAATCCTTTCACAAAATTTTCTGCCTGCTGCCAGAGTTTTAACTTACCATACGCTTCAATCATTGCTACTCTGCATGAAAGAATGTTCAAGGAAATATCAGATCGCGCAGCATCATCCATCAATTGATAAGCCGTTTCTGGGAAACCCAATCTGCAGCATGTGTAAATTATACTCTGGTATATCTTTTGGGAAGGAACTATGCCAAGAAACTGCATATCGCAGAACACTTGACAAGCTTCGGGAAATAACTCAGCCTCCTCAAGGTAAGTAATCAAGTACTCATACAAGTCGCAGTCTTGACCAAAGGATCCACGTTTTAACATTTGTTTTCTACTGTACTCCTGAATGGCATCAACAATCTTCCCATTTTTGCACAAAAGCATGATCGAGCATTCAGATATTAAGTTGTGGGAGTTGGGAACATGCTGCCGGATCCATTCAAGCAAAGAGAGACCTTTTTCATGCTTACCCATTTTTTCATATGCGTCTAAAATGGACAGTAGGCTCTTACCGTCAGGCTCATATCCTTGGAGGCATGCCCTCTTTAACAGACTAGCACCCTGAGAAATGCATTCAGCCTTGATGAGTATACTGGATATTACTAGTGGATTCATTTCAAAAACGGCCTCCATGTCTTGGATAACTCCTTCAATCTCATCGTGTTCATTTCCCTTTGCGAGTGCAGCAAGCAAGACCTGATATAAACCATCATCTGGCTTATATCCATCCTTGATCATAGCCCGGTACAGAACCATCAGCTTTCTAGTCTCATCAGACCTTGCAAAAACATCTAACATAACCAAATAGGCTAAACGATCAGGTTTGACACCTGACTCAACCATACGATCAAATGTACGCTCCGCATCATCCTGCCTCCCACTTTTGGCGTATGCACATATCAAAGCACTGAAAGTTACCAAAGTTGGCTTTAATCCTGCATCAGCCATCTCCTCCAGCACCTTCCCTGCCTCAGAAATCCTATCCATCTTCCCTAAAGAATCAACCAAAACAGTATAGGTCACAGCATCTGGAGTGCAGCCTATAGCCCTCATCTCATCATACAACCCAAGCGCCAAGTCAAGCCTGCCCATCTTTCCATACATATGAATCATGGTATTATAAGTAATCCCATCCTTCCTGAAACCAGCCTTAACCAATTCCTCACACACACGCTCCACCCTCTCCACATCGCCTTCCTTCGCGAAAGCATAAAGGAGCGAGTTGTATGTGACTGCATCCGGCTGAAAACCCTTCTCAACCAGCTCCTTAAACATCAGCTCAGCCTCCTGTGCCTTCCCGCACCGGCCATGCACGGAGACCATGGCATTGTACGTCCACAAATCTGGCCGACACTCTGAAGCTATCATCTCCTCAAACACCGCCACTGCATCATCCAAATTAGAACCTTGTGAGCAAGCACTGATGAGGGTGTTGTAAGTGATAGCATCCGGTCTCAGCCCAGCTTGCCGGACTTCATGTAGGAGCTCAAGAGCGACACCAGCGGCCAAACACCCAGACTTGGCCCTGGCATTGATAAGGGTATTGAAGCTAACGAGGTCAGGCTCGATGTCCTGGTCACGCATTGCGTCAAGCAGCTGGCGCGCGTCGTCGAAGCGGCCAGAACGAGCGTAGACGCCCATCATGGCATTGAACACCTGCACGGTGGCACCCTCGCGGGCGAACCGGAGGAAGACATCCTCCGCGAGCGCGTCCTGGCGGGCGCGCCCGAGGACGCCGAGGACGACGGCGACGACGCGGGGGCCCGGGGCACGCCCGCCGCCGCTCGCGAC

Coding Potentia
Explanation CPC Score
noncoding -1.02273
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0332400.2 6 5025577 A G
Osa06LNT0332400.2 6 5026815 T C
Osa06LNT0332400.2 6 5025633 G T
Osa06LNT0332400.2 6 5025792 A G
Osa06LNT0332400.2 6 5026145 T C
Osa06LNT0332400.2 6 5026379 A T
Osa06LNT0332400.2 6 5026585 A T
Osa06LNT0332400.2 6 5026729 G C
Osa06LNT0332400.2 6 5027414 A G
Osa06LNT0332400.2 6 5028975 C T
Osa06LNT0332400.2 6 5029517 T C
Osa06LNT0332400.2 6 5030171 T C
Osa06LNT0332400.2 6 5030553 T A
Osa06LNT0332400.2 6 5030723 A C
Osa06LNT0332400.2 6 5032149 A G
Osa06LNT0332400.2 6 5034084 A C
Osa06LNT0332400.2 6 5034114 T C
Osa06LNT0332400.2 6 5034234 T G
Osa06LNT0332400.2 6 5034326 T C
Osa06LNT0332400.2 6 5034362 A G
Osa06LNT0332400.2 6 5034506 T C
Osa06LNT0332400.2 6 5027996 T C
Osa06LNT0332400.2 6 5026686 G C
Osa06LNT0332400.2 6 5032130 G 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
Osa06LNT0332400.2 osa-miR5796 Cleavage 4.0 10.968 1 21
Osa06LNT0332400.2 osa-miR5799 Translation 4.0 12.749 1 24
Osa06LNT0332400.2 osa-miR5815 Translation 4.5 19.449 1 24
Osa06LNT0332400.2 osa-miR5821 Translation 4.0 16.902 1 21
Osa06LNT0332400.2 osa-miR5179 Cleavage 5.0 10.314 1 21
Osa06LNT0332400.2 osa-miR5837.2 Cleavage 3.5 9.654 1 21
Osa06LNT0332400.2 osa-miR6251 Translation 4.5 12.02 1 21
Osa06LNT0332400.2 osa-miR6252 Translation 5.0 9.489 1 23
Osa06LNT0332400.2 osa-miR159a.1 Cleavage 4.5 19.382 1 21
Osa06LNT0332400.2 osa-miR159b Cleavage 4.5 19.382 1 21
Osa06LNT0332400.2 osa-miR159c Cleavage 5.0 19.382 1 21
Osa06LNT0332400.2 osa-miR159d Cleavage 5.0 19.382 1 21
Osa06LNT0332400.2 osa-miR159e Cleavage 5.0 19.382 1 21
Osa06LNT0332400.2 osa-miR159f Cleavage 4.0 19.382 1 21
Osa06LNT0332400.2 osa-miR319a-3p.2-3p Cleavage 4.5 19.867 1 20
Osa06LNT0332400.2 osa-miR319b Cleavage 4.5 19.867 1 20
Osa06LNT0332400.2 osa-miR160f-3p Cleavage 5.0 12.997 1 21
Osa06LNT0332400.2 osa-miR167d-3p Cleavage 5.0 8.549 1 22
Osa06LNT0332400.2 osa-miR169f.2 Cleavage 5.0 10.499 1 21
Osa06LNT0332400.2 osa-miR172a Cleavage 4.5 10.202 1 21
Osa06LNT0332400.2 osa-miR172b Cleavage 4.5 10.202 1 21
Osa06LNT0332400.2 osa-miR172c Cleavage 3.5 10.202 1 21
Osa06LNT0332400.2 osa-miR172d-3p Cleavage 4.5 10.202 1 21
Osa06LNT0332400.2 osa-miR413 Translation 5.0 10.431 1 21
Osa06LNT0332400.2 osa-miR444d.3 Cleavage 4.5 16.411 1 21
Osa06LNT0332400.2 osa-miR444d.3 Translation 5.0 9.428 1 21
Osa06LNT0332400.2 osa-miR1436 Cleavage 5.0 10.731 1 21
Osa06LNT0332400.2 osa-miR1439 Cleavage 4.0 14.139 1 21
Osa06LNT0332400.2 osa-miR812f Cleavage 4.0 12.606 1 24
Osa06LNT0332400.2 osa-miR2095-5p Cleavage 4.5 16.084 1 22
Osa06LNT0332400.2 osa-miR2101-5p Translation 5.0 14.893 1 22
Osa06LNT0332400.2 osa-miR2868 Cleavage 4.5 12.736 1 20
Osa06LNT0332400.2 osa-miR2875 Cleavage 4.0 13.656 1 24
Osa06LNT0332400.2 osa-miR2920 Translation 4.5 9.566 1 23
Osa06LNT0332400.2 osa-miR2920 Translation 5.0 15.522 1 23
Osa06LNT0332400.2 osa-miR2931 Cleavage 4.5 8.772 1 20
Osa06LNT0332400.2 osa-miR3981-3p Translation 4.0 16.526 1 21
Osa06LNT0332400.2 osa-miR5160 Cleavage 4.0 9.643 1 22
Osa06LNT0332400.2 osa-miR5511 Translation 4.5 11.03 1 21
Osa06LNT0332400.2 osa-miR2275c Cleavage 3.0 5.712 1 23
Osa06LNT0332400.2 osa-miR5518 Translation 4.5 10.714 1 21
Osa06LNT0332400.2 osa-miR5525 Cleavage 4.0 14.51 1 22
Osa06LNT0332400.2 osa-miR2931 Translation 5.0 7.205 1 20
Osa06LNT0332400.2 osa-miR5492 Translation 4.5 5.496 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0332400.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0332400.2 6 qRCRJ-6 Physiological trait Source activity RM217 RM402
Osa06LNT0332400.2 6 nan Morphological trait Seed RG138 RZ398
Osa06LNT0332400.2 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0332400.2 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0332400.2 6 qASV6-1 Physiological trait Eating quality RM111 RM314
Osa06LNT0332400.2 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0332400.2 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0332400.2 6 nan Morphological trait Seed RG138 RZ398
Osa06LNT0332400.2 6 qLW-6 Morphological trait Seed RM217 RM111
Osa06LNT0332400.2 6 qSPTF6 Physiological trait Sterility RM217 RM111
Osa06LNT0332400.2 6 alk6-1 Physiological trait Eating quality RM190 RM253
Osa06LNT0332400.2 6 hr6 Physiological trait Eating quality RM190 RM253
Osa06LNT0332400.2 6 qRCT6b Resistance or Tolerance Cold tolerance R1954 RM253
Osa06LNT0332400.2 6 rrsd6b Resistance or Tolerance Drought tolerance RM253 RM314
Osa06LNT0332400.2 6 QGt6b Physiological trait Eating quality RM253 RM314
Osa06LNT0332400.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0332400.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0332400.2 6 Xa7 Resistance or Tolerance Bacterial blight resistance nan nan
Osa06LNT0332400.2 6 AsTol Resistance or Tolerance Other soil stress tolerance RZ516 RG213
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