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

>Osa06LNT0353100.2

TAAAACAGTTCATGCGATACGCGATCTGCTTCAGTCAGCAGATCGCTCCGATAATTACCATTATTTGTCAATGATTTCTTTCAGTAATCTGACAATTCTACAATGATACAGATCACATTGCCAACGCTCTTAACTTACACATCTAAACTAATGCCCTGGTGTGCCTTGTGTGATCTAGGCTCTTACATGTTACATCTACTGCTACAAAACTGGAAGGTTAATGGTACATGGTCGCGCCCCAAAGAGAGTTAGTCCACAGGAGAAGCAGATTACGAACAGCACACGGTGCGCATTCTTCCTTGAATCTCCAGGTTCCCTCGGGAAGCAGTGAAGCACACGCAGCCACGCTGGCTACAAACTCGGGAAGCACAGGCATGCCAATCAATGTTGGTTCCTCCCCTCTGTTCTTCGGAGTGAGCTTAAATCTCATCATCATCATCATCATCATCCATAAGTTCATCTGGAAGGTGTACTTTCTCCATTGCAGACTTGATTATAGCAACGTCAGCAGCAGGAGGTTTCAAATCCAGGGCAATGCCAAAGCAAAATACAGCCTTGTCAAGAATGTTAAGTTGCTTGTAAATCTTTCCCATCAGTGCATACATACTACTTTCATGAGGTGCAATTTCCTTTAGCCGTTCCAACTCATCCAGAGCATCAGGGTATTTTTGTAGGCCTAGAAGGATTAAAGCCTTTTGATACTTGGGGAGTGGATTCTTCTTATCAGCAAATATAGCGTTCTCCATCATTTCCAAGGCTTCCTCATTCCTCTTTAAAGCATGCAAGGCCATCCCAAGATAGCACATAAGAACAGAAGAGCAAGGATTTATCTGGAATGCCCTTCTGAAATGATGCTCAGCAAACTCAAACTTTTCCTGGCGAAGGTACACCACTCCAAGGCCATACCAGGCATTGTAGTGTCTTTCATCTACCTGAAGTGCAGAGCGGTATAGTTTTATACTGTTCTCATAATCCTCCAATGCAGAATACTCGTGACCGCATAGCGTGTGAGCGTATGCAACTCTTGAGTCAAGCTGTACAGCACGTTGAAAATTCTTCAAGGCAGTCTCATGATCTTTCCTCAAGGCAAAGCAATTTCCCACAGCACACCATGCTTGGGGAGATAGTCGATCAATAGAAACAAGATCTTGAGCAAGGTAACTTAGCCGCATTTCCTCATTCAAATGATAAAGAACAGTGGAGTAAATGTCCATTCCCTCCAACGTGCATGGTGATAGTCGATGCGCTAACTCAAAAAAATGATCGGCTTCTAAATAATTGACGAGTTCAAAATATGTCTTCCCAACCTGGCAAAGAACCCATCCAGTATTAAATTGTGCCTCTGGGAGCTTTCTATATACTTCCAATGCTTCCTGACACTTAAACAAGCAAGAAAGCCTATACCCTTCCCCTAGTGTCCGCAAGAGTGCCATTAGCTCCCTGATACCAATAGCTAATTTGGAGTCCTGTGACAGAACTCGTTCAGATTTCTCTTGCTCGGGATATCTTCCATCAACTATACTTGTAGAAGACGAAGTTGAAGTTACATTATCTGTCCACATTTCATCAACAACGTGGTACCTGTTTCCTTCATCAAAATTTTCTGTTGCCTGTGGTTTCCCTTTCCTAACTTGCACGGAACGTAGAGCTGTTGAACACAATTTTGATGGTGTGGACGAGTTTACTCGCAATTTACCTGACGAGTGATCTGTTCCATTCCCTCCAAATTGAGAGATATTTGAGTTTGAGTTTATTGTTGTATCTCTAGAAAGTCTTGCACTTCTTCGAGGAACTGAATCACTACTCTGATTAAACAGCCTTCCAGAAACCTTCTTTAGGCCTGCTTCATCGATGTATTTTCTTCGGAGTGTCAGGTTCGGAGCATTAACCTTTGGTTTGGAAGGAGCATTGCCACCTGCTGTATTCTGATAAGCATGCATATTCCGAAAGAGTGGTGGTGGAGCAATGCCAGAAGCCTGCGTTGAAGTTGGCGATGGAGTGTCAAACTGTGATAAATTAGATGGTGCACCGTTCTGCATATGCAATGCAGTTGACTTTACATGAGGATAACCAGATACTTCTGCAGTGGTGTTAGCATGCAGCTGTTTAATTTGCTTAGGACTATCACCAAAACTTGCTGACACATTGGAAGATAGAAACCGATTTTCATTAACAAAGTTTGACTTTTCCACATTTGATGTGGATGTGAGTTCCTGCTGAAGACGTAGAGCTGTTGCTTCACTGAAACATTCATTTGCATCTTCAGCAACACCTAGTATGCACAATTCCTCGTATGCTGCCCATAGAAGAGGATCAAGAGTCAGAGCTTGTACAAATTGCTCAGCTGCAGCTTCCACTCTGCCAGTGTACCTGTAAATTACTCCAAGAAGGTAGTGCCCTGTTGCACCACTTGGAACCTCAATATTTGGTTCATTGACAGGACACAAGGCTTCTTCAGCTTCCCGTAAGAGGTTCATTCGGAAGCATGACATAGCAAACAAGTACCGGGACTCTGGCAGCTTCTTTCCTTTCAAGATGTGGTATGCAGCATATGGCTGGTTGTTGTGAAGGTAGCAAGTCGCTAGCAACTGGACATTTGTCTCGGCGGGGAACTGGGCGCAGAGGCGCTCGCAGAGGAAGACGGCGTTGCGGTGCATGAAGAGGCGGAGGCTGCCGTGGACGCGGTCCACCATTAGGGTTTCCATCGCCGCCAACGCTCCAGCGGCGGCGGCGGCGGCGATGCGTGTCGGGCTACTGCGGCGGCGCGCGGCGGCCGGCGGCGAGGGTGGGCACCGTTTGAATCGAGGAGGAGGAGAGGGGAGGGGTTGGGTTAGATTCGAGGGGGATTTTTTTTTTTTTGGTGTTGTGTTGGGATTTTTGATTTTTTTGGATTGGGGATTCGGACGAACGGATCGGAGTTTGGGCTTGCGCCTGTGCGCGTTGGTGTGAGTGAGTGTGGCGTTTGAAATGGTGGGCTGACTGGC

Coding Potentia
Explanation CPC Score
noncoding -1.05851
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0353100.2 6 25031735 A T
Osa06LNT0353100.2 6 25026863 C T
Osa06LNT0353100.2 6 25026948 C T
Osa06LNT0353100.2 6 25027540 A G
Osa06LNT0353100.2 6 25027580 A G
Osa06LNT0353100.2 6 25027674 T C
Osa06LNT0353100.2 6 25027676 T C
Osa06LNT0353100.2 6 25027903 T C
Osa06LNT0353100.2 6 25028733 G A
Osa06LNT0353100.2 6 25031007 A G
Osa06LNT0353100.2 6 25031375 C T
Osa06LNT0353100.2 6 25031865 T C
Osa06LNT0353100.2 6 25032929 T C
Osa06LNT0353100.2 6 25033542 A T
Osa06LNT0353100.2 6 25033904 T C
Osa06LNT0353100.2 6 25027116 C T
Osa06LNT0353100.2 6 25034440 C T
Osa06LNT0353100.2 6 25025742 A G
Osa06LNT0353100.2 6 25027014 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0353100.2 osa-miR5542 Translation 4.0 18.767 1 21
Osa06LNT0353100.2 osa-miR5828 Cleavage 5.0 19.311 1 21
Osa06LNT0353100.2 osa-miR6250 Cleavage 5.0 21.592 1 22
Osa06LNT0353100.2 osa-miR166c-5p Translation 5.0 16.286 1 20
Osa06LNT0353100.2 osa-miR166i-5p Cleavage 5.0 20.693 1 21
Osa06LNT0353100.2 osa-miR1440a Cleavage 5.0 22.285 1 20
Osa06LNT0353100.2 osa-miR2122 Cleavage 5.0 18.529 1 22
Osa06LNT0353100.2 osa-miR2866 Cleavage 5.0 21.216 1 20
Osa06LNT0353100.2 osa-miR2874 Cleavage 4.0 20.657 1 24
Osa06LNT0353100.2 osa-miR5505 Cleavage 4.5 16.637 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0353100.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0353100.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0353100.2 6 qDLR6-2 Resistance or Tolerance Other soil stress tolerance RM1340 RM5957
Osa06LNT0353100.2 6 ostd(t) Physiological trait Sterility nan nan
Osa06LNT0353100.2 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0353100.2 6 nan Morphological trait Root RM4447 RM5509
Osa06LNT0353100.2 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0353100.2 6 RPLD4 Physiological trait Eating quality RG424 RG172
Osa06LNT0353100.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0353100.2 6 prt6.1 Resistance or Tolerance Drought tolerance R2549 RG716
Osa06LNT0353100.2 6 gw6 Morphological trait Panicle/flower RG424 R2549
Osa06LNT0353100.2 6 qGL-6 Morphological trait Seed R674 R2549
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