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

>Osa10LNT0059900.2

AAAATATCCAGCGTGCCACGCGCCATTTTCTAATCATAATGTTAGAACAAGCTCGAAATTGTTACAACTCACATGCAAATTAAATGCCATCGACTAGTGAACTTTGGTTTAGTGATCGTGCTAGTCTGCAAATTAAGCTGCATTTTTGTTAATATCTCGATGGAAGGATGGCAGCCACGACGACAGCAACGCCGAACATGAGGATGGCGAGACCGGTGAAGTTGACGACGAACGCTTCGCTCGGATAGCCGTGGAAGGGGAAGATGAAGCGTGCTAGGCCGGTCTCGGCGGTGCAGATGGCCATGAGGAAGATGACGATGCCCAACAAAATGTGCCATGGCGCGTAGTCAGCCCTCATCGTCATCACCGCCCCCGGGAATACAAAGTAGACAAAACCCACCAGCCACTGAAAGGCATAGAGTGCTGCAGTGGTTATCCCAAGCCAAGCATGGAGGGAGCGGATGTCAGGGGCGCGGAGATCATGGTGGAACTTGAAGGCGGCGTACAGGCCGACGGCGGCGAAGGCGAGGGCGACCAGATGCAGCAGCAGGTGCACCGCCTTCTTCACCTCCCTTGACCCCAGCATGATCCTGTACGCCATTATCGCTTCTCCCGTGCAGATGACAAGGCCAATCACCATGAAGAGAGGATGTGCCGTGTAAACGAGCTGAGGGGTAGAGCTCCTATGCCAGGACCAGGAGACGCCACCCCGGAAGTGCAGCACCCAGACGAGCGTGAGCGTCAGCACGGCGGCGGCCAGCAGCTGCGCGACCACCACCACCGGCAGCGCGGTGAGCCGGAAGCTGGCGCTGCTCTTCACCGGCATGACTATGCCTCTCTACTCTTCTTCCCCGACCCGCCGCCCGCCGGCTGACACCCACGTCGAGCTCGCCGCCGGCACCACCACCAATCACCACCAGCAACCACGGAGAGATGGCAATGGCATACAAATGATACAATGCTGCGCGTCGCCGGCTTGCTTCAAGCACATACTAATAGCTTGTCCGTTCCTGCTGGTCCATATGTTGTGTTGTTGTGTTGTCGGTCCCCCTCGCAAGCTTGAAAAGTACACCACACCGGGAAGGCAAATCAATCCATCAGCTCAAATGCGGCCGTCCGTCTGGACTACTTTGCTTGTCATTGCAAGAATTTCTGCTTGTTTGCGCCGAGCAGGTTCTTCTCATCTCCAGCCAAACTGAAACTGAAATTGGTCCACAACCACCTCAAGCCCCACTTCTCTTCTTGTAGTATGTACGTCCAAGACCAACATAGCCGTCCTATCTTGTCCTATGTCCTGGCATCGACCTTGGTAACCACTGGGATCTCAGATGACAACCATAGAAACCAGCATCCAGGCTGCTTGCAAAATGGAAGAGAGAACCAGCATCCTCCCAAACAGCAGGAATTCAGATATAGACCAAGCCTGCTCTAGAGCCAGTGAGAGTTGTTTTTCTCCCGGCATGTTTTCAAAATGAAAATGCCCATGCATGTATATCTATGAGATGATAGGTTCTGTTAAAGCATGCTAAAAAGCAAGCATTGCAATGTCAGGCATAATCTGTCCAGCTGACACCTTGCTCAATTCTGGTCACTAGATATGGAAATCCTGTGATGTTTCGAAACACTGACGACATGAAGCAACTTTGTTCCATGAGGCACCCATCCAACAAAATGCCATCTCTAGGTACAGGCACCTGAGGCTTACAACCCATTGTCACTAGAGGCTTGGTTTCATAATCAATCGTCTGGTGTTGTGAATACCAACACCTTCCCATCACCATCCCATCCACCGGTAGAGCCAAGTGCACATCTTCTGAATAGACGCCACCTTGTCCATCCAAGACTGTCCAGGGCTGCACAGACCAAGCAAATGTACAGTTACAGCAGTGCATTCTTTACACTTCTCTTCTTGAACCATTCGACGAATTCGGCCTCCTAGGCATTCCAAAAGGCAAATTATCTCTAGACCTATCACCAGGACGTCCCAGATCATCCAAATTTCTGTAACTGCCATTTCTCGGAACAGAGTTAGAACGTTCATCCTCATCAGGCCTCATGCTAACCCTGGAATCTGGAAGCATTTCCAAATGCCTCGGTCTTGGTCCACCAGTCCTCATGTTCCTTATGTTATTTGAAGTGTTCCTTCCTGGAGTGTTAGAGATCTTCATGGCAAGGAAGTCCTTGGGAATGGTATCAAGATCCATAAAACATTTCCTGGCCTTTGCATCTGCTATCAGTAAAGCCCAGTCCTCAGACTGCATAAGAGCACCGGCATTACCAACAACCCATAGAGCTCTCCTAGCTCTAGTAAGAGCAACATTCATACGGCGTATATCTGCCACGAAACCCACACCATGATTTGAGGCACGGACACATGACATAATAATCACATCACGCTCCTGTCCTTGAAAAGCATCAACTGTGTTTATGTAAATGTCCTTCCCATCCTCAGTACTCATAACCTCCTCGAATTCCCGCTGAAGACATTTCAACTGCAACTTATATGGTGTGATTATACCAACAGAAGCTTTCTTGCCACCATTAGCTCTCAAGAACTTCTGAAGATTCTCATACAAACGCAAAACAAACTGTGCTTCATGAACATTCTGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.325616
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa10LNT0059900.2 10 1190851 T C
Osa10LNT0059900.2 10 1193113 A G
Osa10LNT0059900.2 10 1190416 G A
Osa10LNT0059900.2 10 1190441 A C
Osa10LNT0059900.2 10 1190841 C G
Osa10LNT0059900.2 10 1190876 G A
Osa10LNT0059900.2 10 1190896 A G
Osa10LNT0059900.2 10 1190987 A G
Osa10LNT0059900.2 10 1191030 A T
Osa10LNT0059900.2 10 1191032 A G
Osa10LNT0059900.2 10 1191230 T C
Osa10LNT0059900.2 10 1192203 G A
Osa10LNT0059900.2 10 1192295 C T
Osa10LNT0059900.2 10 1192764 A C
Osa10LNT0059900.2 10 1192765 A G
Osa10LNT0059900.2 10 1192979 A C
Osa10LNT0059900.2 10 1192980 T A
Osa10LNT0059900.2 10 1193051 A C
Osa10LNT0059900.2 10 1193327 T C
Osa10LNT0059900.2 10 1193572 C T
Osa10LNT0059900.2 10 1194318 T C
Osa10LNT0059900.2 10 1194526 A G
Osa10LNT0059900.2 10 1194784 G A
Osa10LNT0059900.2 10 1190953 T C
Osa10LNT0059900.2 10 1190944 A G
Osa10LNT0059900.2 10 1193813 G T
Osa10LNT0059900.2 10 1191344 G T
Osa10LNT0059900.2 10 1192067 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa10LNT0059900.2 osa-miR5805 Cleavage 5.0 15.818 1 24
Osa10LNT0059900.2 osa-miR166a-5p Translation 5.0 15.367 1 21
Osa10LNT0059900.2 osa-miR166e-5p Translation 5.0 15.367 1 21
Osa10LNT0059900.2 osa-miR1442 Cleavage 4.5 20.035 1 20
Osa10LNT0059900.2 osa-miR2099-3p Cleavage 4.5 17.7 1 20
Osa10LNT0059900.2 osa-miR2118e Translation 4.0 17.736 1 22
Osa10LNT0059900.2 osa-miR2118r Translation 4.0 17.736 1 22
Osa10LNT0059900.2 osa-miR3979-3p Cleavage 4.5 18.363 1 20
Osa10LNT0059900.2 osa-miR5338 Translation 5.0 9.612 1 21
Osa10LNT0059900.2 osa-miR5487 Cleavage 4.0 12.064 1 21
Osa10LNT0059900.2 osa-miR2920 Cleavage 3.5 18.474 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa10LNT0059900.2 10 hwd1 Physiological trait Lethality nan nan
Osa10LNT0059900.2 10 nan Physiological trait Sterility C701 C16
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