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

>Osa05LNT0295000.1

CTGAAATTCCGTCCTATATAACATATTTAAGCTGAGCAGATAAATTATTTTTATGATACACAGGACCAGCAGCAGAACTGATTATTTCGATCAAGTCTACACCAGGGCTACATATTACATGACAATCAACCTTTTTGCCTCGAGTTCGTATAATTAAGCCCCTCGTATAATTAAACCAAACGAAAAACTACAAAAATCTGGAAATGTTCATACACAGATGGAAGCTACAGAAAGATCGGCGCTATGAACCTTTTTGCCTCGAGTTCGTCAGAGGCTCCTCACTTAACTATGGTTGCCGATTTCGTTTCTGGGAAGTGAGCAGGCGCGTGACGAAACTAAGGACCTTCAGGAGTGGTTGTGGTGGATGCTTTGGCTTGCGCTCCGGCCCTTCTCTAGGCTGCAACTGGTTCATTTACAGAATGAGAAACACCCGAATTAACCTTGGCTGCTTTAAAGAGTTCGTCCAGCACCTCGGACAATGTTGGGTGTGCATGAACAGCAAACTTGATGTCTTGCAACCGAGTTCCTAGGGCAATGGCATTTGATGCCTCGTGGATGAGGTCAGCAGCGTGCAAACCCAAAATGTGCACACCAAGAATTTCTCCAGTGTCAGGCCGGTAAATCAACTTAGCAAGTCCATCTCCTTCATTTTCTGCCAATGCTTTTGTATTAGCCTTAAAGCTGGTCTTAACAACACTTATCTCAAATCCTTCTTTATCAGCTTTTTCTCTGGCTTGTGGCTCTGTAAGCCCAACCATACTAATCTCTGGATGAGTGAAGCAAGCAGCGGGGATGCTTAAATGATTTAGGATGTGGTCCCTCCCAGAGATTTGTTCGACAACAGAGATTCCCTGTGCACTGGCAGCATGAGCAAGCATGAGTTTACCATTGGCATCTCCAATGCAATATAAGTTCGGAACCACATTGCCATCTGCATCCATGACTCGCATTCGCTCATCAACAGGAATAAAACCACGCTGTGTAACAACATTGATATTTTCCAAGCCAAGTCCTTTTGTGAATGGTGCCCGTCCTGTGGCTATAAGGGCTGCATCCACCTCGAGGGTTTCTTTGTGTTCCTTTGTTTTTGCATCAATGAGCTCAATCTGCACAGGTTTTCCATCCTTTGCTGGAGTAATCTTGCTTGCAAAAACACCAGTGTGATAGTCTATATTCCGAGGGTTGATAAGGACTCTCTGGGCTAATTTTGCAATTTCAGGATCAAAACCAGGCATTAGCTGGTCAAGAGCTTCAACAAAAGTAACCTCACTTCCAAGAGCTGTATATACATCACTGAATTCAAGCCCAATGTATCCACTTCCAACGATTGCTATCCAGTCCGGGACAGACTCAAGTTTTAGTGCATGATCACTGGTAAAAACAGTTTTCCCATCAACCTCTATGCCCTTGGGAACAAAAGGAACTGATCCAGTAGCAATGATGATATTCCTTGCAGTGATTTCTTTGTCTGGAAAACCAACTTTTCCATACCGTACCTTTTGTTTTCCAACAATTGCACCAAAACCACTCAATATATCCACTCCCAGAGCTTTCATTGAATTAGTCAAGTTGCTTCGGATTTTAGAGGCGAGATTGTTTGCATGATCAGCAACAGCTTGTCTGTCATATCCAGGGGATGAAACCTGTAGACCCAATGACTTCATGTGATGTTCATCATGAAGCTCCCTCATGCGACCGCTGACAGCAAGAAGTGCTTTTGATGGGACACAACCTCTGTTTACACAAGTCCCACCTACAACATCTCCCTCAATAATTGCAGTTTTCAAACCCTCCTCGACAGCGTGGAGCGCCGCGCCGTGCCCACCAACGCCGGCGCCGATGATGACGAGGTCGTAGTCGAACCCGCCGCTCCCCGCCACGCCGTTCTCCGCGGCCGCCCTCGCCGCCACCGCCGCCCGCCTCACCGCCGCCCCCTGCGAGATCCGCAGCGAGCGGAGCGCCACCGCCTCGCCCCCGAGCCCGCACACCCTGATCCCGCATGGCCCCCGCGCGGATCTGGCTCCCCCGCCGGCGCCGCCGCCGACCACCCACGCCGGGGCCGAGGCGCACGCCGCCGCCGCCGCCGCGGAGTTCATCGCCCTCACGACGAACGCAAGAGGAGGGGAGAAGAGAAGCCGGAGTCGCGAGGGGAATGGGAGGCGGCGGCGGAGGAGGCGAGGCGAGGTGGGGGGCAGAAGGAGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.987603
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0295000.1 5 3318888 G T
Osa05LNT0295000.1 5 3314331 G A
Osa05LNT0295000.1 5 3314639 C T
Osa05LNT0295000.1 5 3315162 A G
Osa05LNT0295000.1 5 3315279 A G
Osa05LNT0295000.1 5 3316477 G A
Osa05LNT0295000.1 5 3318161 C A
Osa05LNT0295000.1 5 3318346 T C
Osa05LNT0295000.1 5 3317458 A G
Osa05LNT0295000.1 5 3315004 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
Osa05LNT0295000.1 osa-miR1861o Cleavage 5.0 10.382 1 22
Osa05LNT0295000.1 osa-miR1861o Cleavage 5.0 21.0 1 22
Osa05LNT0295000.1 osa-miR396a-3p Translation 4.5 13.672 1 20
Osa05LNT0295000.1 osa-miR396b-3p Translation 4.5 13.672 1 20
Osa05LNT0295000.1 osa-miR169r-5p Translation 4.5 11.951 1 21
Osa05LNT0295000.1 osa-miR1861a Cleavage 5.0 10.382 1 22
Osa05LNT0295000.1 osa-miR1861a Cleavage 5.0 21.0 1 22
Osa05LNT0295000.1 osa-miR1861b Cleavage 5.0 10.382 1 22
Osa05LNT0295000.1 osa-miR1861b Cleavage 5.0 21.0 1 22
Osa05LNT0295000.1 osa-miR1861f Cleavage 5.0 10.382 1 22
Osa05LNT0295000.1 osa-miR1861f Cleavage 5.0 21.0 1 22
Osa05LNT0295000.1 osa-miR1861i Cleavage 5.0 10.382 1 22
Osa05LNT0295000.1 osa-miR1861i Cleavage 5.0 21.0 1 22
Osa05LNT0295000.1 osa-miR1861l Cleavage 5.0 10.382 1 22
Osa05LNT0295000.1 osa-miR1861l Cleavage 5.0 21.0 1 22
Osa05LNT0295000.1 osa-miR1870-3p Cleavage 4.0 14.778 1 24
Osa05LNT0295000.1 osa-miR2096-3p Cleavage 4.5 20.291 1 21
Osa05LNT0295000.1 osa-miR2868 Cleavage 4.0 14.833 1 20
Osa05LNT0295000.1 osa-miR1863c Cleavage 4.5 18.502 1 24
Osa05LNT0295000.1 osa-miR396a-3p Cleavage 4.5 11.687 1 20
Osa05LNT0295000.1 osa-miR396b-3p Cleavage 4.5 11.687 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
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
Osa05LNT0295000.1 5 3316477 Leaf-angle-cultivated 8.654643059 -