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

>Osa10LNT0078000.2

ACGCTTTCTTTTCCTTTTTATTGAGCTACCTTCTAGTCTTTTACATATTGCTTCCCAGGTTGGTTCCTAGGTTCTCCCTACTGTCGAGGAGCCAAAAAGATTTACACACCACGTGCTTGCTTATACACATTTTGGGGATATAAACCAAAAGGGGGAACACTATCCTATACAGAGCAAAAAAAAAAAGGACTGGAAATCTATATGTCTGTATCTGATCTCAAAAGTCTAGCTATCTGCCTCTGCACTTTCAGCTTTATTTTCTGCATTGCCCTGGCCAGGTTCTGCTGCTTCACCCAAGTCCCCTTCCGTCCATCGCTGTTCAGGAACAGGCGCTTCATTTGAAGCAACTCCCGAACCGTCAGGCTGCGCCTGGCAATGAGGTTGTTCTGCACCTTCGAGTGTTACTTCAGTACTGCCCCTGTTTGGTGAACCTGACGTGTTGCTCTGGTGGCATACTGCTTCGCACAAGTCACCTGACATCCCTCTCTGCTCAGGGATAACCGGTTCCTGGGAAGCAGCTCCAGAACTGTCACCCTGTGCCTGACAATAAGGTTGCTCTACACTTTCAGGCCTTACTCTTGTGCTGTCATTTGGTGATTCTGATGCTTCTGCCTTATAGCTGTCTGTTTTCATCTCACACTGCTGCTCGGAAACATCTTCGGGCTTAATTGCAGGCAGTTGGTGAGATGCAGTTCCATAACCTCCATGTTCGTCATGCAAATGAGGTCGATCTGCACTTTCGGATCTTATTTTTGCATTGACCTGCTGGGGTGAATCTGATGCTTCTGCTTCGCACCAGTTTCTTTTCATCCCTTGCTGCATAGTAACTGGCATGTTACAGGTGGCATTCTGCACCTGATGAGGTTCTTCCATCCAATGGTTATTGGTCCGTTCATACCATCCTCCCCTACCTCTACCATGATATGTAGGTCTCCCTCTACCCCGACCACCAAAAGTCCTATATGGTGCTTGTTGTGGATAACTACTGAACTCCCTGTGCTTATTCATACTTTGAAGTTCAGGAGCACCGGCTTCATATGTATTTGGCCTAATTTGAGAAGAATTGCGCCGGCATGGATAACCAGAAGTCCCATCCTGAAATCCTTTATTGCCGTCACCTCCTAAAGGTTGCCGTTCACCAAGGATACTAGTTTGCCTCTGTGATTTCTCCCTCTGAATTGATCCAGAATAAGGAAACCTCCCATTGCCTGTTTGAGGAGTACTGCACATGGTTTCATGATAACTTCTAGTACGTGAGTCCTGACCAGAATGATGATTTGGATGTTCTCTAAACACTTCCAGATAACCATAACTGCCACGGGATGGTCTGTTGCCATTGTGCCAATATTGATTAGGAGGAGCAACTTGTGAATAGTCACCACTATAGGACTTGCGTTGCTGAAAGTGTGTTCTATGCATGTCCTCTTTTGTGTGACACACATTTAGTCGTGAATCGTGGCCATTGCTTCTCCTTGTGTTTCCAGAACCTGGAAAGTGACTCCATCTCATTGGTCGACTGTTGCCAGCAGCAATTATGTCATGCCTCGATGACCCTGATGACCATCGATTTGCATTGTGGGCACTCCTCTGTTCTCTTTGGTTCCTCTGCTCTCCCTCCTTGGTTGCATGCATAATTATTTCTGCTAAATTCTTGTCGTCAAGGGCATTAAAGAAACATCCACGTCGTTTTGAGTCATGGACTAATTCTGCCCATATTGAATTGCTTGCCAGCAAAGTGGCTCCATTTCCAAGGATCCAAAGGCAATACTTTGCTCTTGTCAGAGCCACATTAATTCTCCCAGCATCCGAGAGGAATCCTACTTTGCCATTTTTGTTGGACCTAACGGTTGAAATCAATATTATGTCCTCCTCTCCACCTTGAAATCCATCAATGGATTTTACTGTAACAGACAGAAACTCATGATTCTTGAACTGTTTTCCAAGTCTTTCTTGCAATGCAATTACTTGGGCAGTATATGGAGATATCACACCAAGGCTGGTTCGCTGCCTCTTCTCAGAGCACTCTTTTGCAAGTCTTTCAACAATATTGGTCGCTACAGCAACCTCAACCATATTTTTGGAACTCTGGCCAAGTTCATCAAGCATTTCCATATCGTTTTCAATATGAATGAATGAATAAGCACCATAAATAGGGCCAGGGAGATAACTCTTCATATAGTCTTCCTGTTGGACACTGGGACCATCAGAAATTCGGTTATCATAAAAGTTGGCATTTGGAAATTTGTTGATGCCAGGGTGCATCCTATATTGTACTTCCAGCAAATGCTTTCTATAACCCATTGTACACAATCTCTCATAGAGACTTCGGCCAAAGTCAGCATCTTTAGCAATCTAGAGTAGCAGTAAGGAGACAGTATGAGCAAAGCTATAGAAGTCAGAATAATTATTGGCAACAATATACTCATAATAAAAGAGAACATGTCCATGTATATTATCCCATACCAATGGCATACCTTACTCTTTACCAATGATGATAATTGGTTTTCATCTCCAATCAGCAGAATGTGCTCTATCCCTGGGAGCAAGAGAGGAACCAGTGCTTCGCATTCTTTTAGTTGTGCTGCCTCATCAATAACCAAGATGCTTATAGGCATCACGTTTTGCAACCTGAACAACTCAAATGAACTAGAAGCAGTGCAGAATACCAGTTTCGCTCGTTTCAAGCATAAGTCCCGAATCGAACTCTCATTGTCTTCACAAGGAAGCCGCATTTTTGAAAGATCCATCAGGGTTTTGATACAAAGAGACTTTATCTCCAAAGGGTCATCTAGGGAGATATCATGGTCATGAAGATCAACAGTTGCATCATCTGTCTGGTCATGGCTATCAAAAGAGTCAATAGGTTCATCGGAAGGCTTGAAAATTGTGAAAAGAAGCTCATCAGAGACATCATCTGCACACAGCAGTTGTTGCAATTTATCTAACAAACTTTTGGCAAACATCATCCTGTCCAAATTCCTGCCCAGGGAATCAGTTGGAAGATGATCAAAGAATGTATCAATACACCTTGCTAATTCTTTTACTAATGTGCTGAATTTACTTGTGAAATACTTCTTAAAGGTAAGATTGCATCCATCACTGCTTGCCTGCTGTATATCTAGGGACATTTGGTAACGAGAAATGCAATTCATAAGGAATTTCATGACAGAATCCACACGTGCCTTCCAACCATCTTCTCGTTTGAAATACCTCAGCAGCTTATGGACACGATCATCCAAATATACTTTTGACAACTCCTTTCCGATGTGCAGACGGTCCTTGTTACCAAATAAGACAATGTCACCAAATGAATAACAATGACTTGAAGAGAAGTCCTGAATCAGCTCAATAAGACGAGATGCCACTTGCAAGACAGCCATGTTGGTTGGAGCACATGCAAGAATTCTCTGCTCCTTCATCAAAAGCATGTGTAGCATCACCGAAACTGTTGTAGTTTTACCTGTCCCAGGAGGGCCCCATATTAGCCCCACCGAAGAGTTATGACAGCATTCACTTGCCGAAATACAACTTGCTACTGCATCAAGCTGCGAGTCATTCAGCTTAAAATTGCAGAGATAATCCTTGATTTTGTCGTGTGTTTCACTTCCGCAGTACTTACAATGCCCTGTAGCTTTTTTTTTTTTGCCAAACATACTGAGAACAATTTTTGAATCCATTGTCAAACCCCTTCGGAGCACAACCCAAACACGATCATATGTTATCATATTAGTCAGGTAGGTAGCACAGAAGGACCATCGCTTCGATGAATTTCCACATGTCCCCATCTCATTCTGTTCTTGCAGATCACTACACTTCTCAAAGCACTTTCGAACTTTTGAATGTTCTTTACGCCCATTTTCATGCATAAATGAGTTGCTAGATTCTGGAGCAACTGCTTCTTGGTCCAGCATTTCCCAAGACTTGTCAAAACCTTCCGCATACAACTTGTCATACCTGTTCATGCCCATTTGTTGTCGTTCATCTCCATGAACCCCTGTCTCCATCCTCCGTGATGCCTTGACTGTCATCTTATTACCCTGGACCTTACCAACCCATACAATGACACAGGATTTAGACTGTTTGAGAATATCAGATTGATTTGCCGGTCTCGTTTCTGAAATCAGTAGCAAATCTGCCGCTTTAGGCTTATAACCTTCTATCGCACAACCATGAGACACCCCCCTCCATTTGTCAAGCTTGATCTCATATGATCCTTTCCCCTTCCTCATTGCATTGACAGACAGAACACTTGCATATGGAGCTTTGGAAATGTCCTCCATGCTTGAACACATGTCACCCCTGACTTCCTCCAAAAGTGGACCGAAAAATGATGTCATGTACTGCTCCATGCTGCTGAATGTTTCTGGGATCTTAGCCACCTTGTCGCGGAGCAGGTCCTTGTTGAGGATTTGGTCCACCGACCACGAGAGCACCACCTCGGACAGCCCCTGGCTCCGCCACTGCCACAGCGAGTCCCCCGACGACGACGACGACGACGACCCCTTCCCCGCCCCCGCCTTCATCGCCGCCTGGTGCCACCCGCCGCCGCCGTCATCGTCGTCGCCGTCCCTGCCGCCGTCGAACGCGTGGGAGGAGGAGGGCTCCGCGGGATCCGCCTCGCGCCCCCAGTCTCCGCCGCCGCGGCGCCGCATTTCGCCGGCGACCGGGAGAGGAAGGAATCGCCGCCTCGCGATTGGTGGGTCAGATTTGGGGGCTAAATTGGAGTAGGTTTTAGTGGATTTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.918323
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa10LNT0078000.2 10 20941737 C T
Osa10LNT0078000.2 10 20942141 A C
Osa10LNT0078000.2 10 20944033 A G
Osa10LNT0078000.2 10 20945895 T G
Osa10LNT0078000.2 10 20946135 C T
Osa10LNT0078000.2 10 20946956 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
Osa10LNT0078000.2 osa-miR5525 Cleavage 4.5 20.029 1 22
Osa10LNT0078000.2 osa-miR5532 Cleavage 4.5 16.815 1 22
Osa10LNT0078000.2 osa-miR5542 Translation 5.0 12.59 1 21
Osa10LNT0078000.2 osa-miR156k Cleavage 5.0 12.333 1 21
Osa10LNT0078000.2 osa-miR172d-5p Cleavage 5.0 22.164 1 20
Osa10LNT0078000.2 osa-miR530-3p Cleavage 3.0 12.431 1 21
Osa10LNT0078000.2 osa-miR812a Translation 4.5 14.758 1 22
Osa10LNT0078000.2 osa-miR812b Translation 4.5 14.758 1 22
Osa10LNT0078000.2 osa-miR812c Translation 4.5 14.758 1 22
Osa10LNT0078000.2 osa-miR812d Translation 4.5 14.758 1 22
Osa10LNT0078000.2 osa-miR812e Translation 4.5 14.758 1 22
Osa10LNT0078000.2 osa-miR444d.3 Translation 3.0 18.889 1 21
Osa10LNT0078000.2 osa-miR1865-3p Translation 5.0 15.474 1 24
Osa10LNT0078000.2 osa-miR1874-3p Translation 4.5 12.676 1 24
Osa10LNT0078000.2 osa-miR2093-3p Cleavage 4.5 22.016 1 20
Osa10LNT0078000.2 osa-miR2864.2 Translation 3.0 16.915 1 21
Osa10LNT0078000.2 osa-miR2871a-3p Cleavage 5.0 15.807 1 21
Osa10LNT0078000.2 osa-miR2871b Cleavage 5.0 15.807 1 21
Osa10LNT0078000.2 osa-miR3982-3p Translation 5.0 23.58 1 21
Osa10LNT0078000.2 osa-miR5077 Cleavage 5.0 20.22 1 19
Osa10LNT0078000.2 osa-miR5498 Translation 5.0 18.19 1 21
Osa10LNT0078000.2 osa-miR5519 Cleavage 5.0 16.353 1 21
Osa10LNT0078000.2 osa-miR5522 Cleavage 5.0 19.467 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa10LNT0078000.2 10 nan Morphological trait Seed RZ811 RG561
Osa10LNT0078000.2 10 qRf-10 Physiological trait Sterility RZ811 RG561
Osa10LNT0078000.2 10 Rf1 Physiological trait Sterility nan nan
Osa10LNT0078000.2 10 nan Morphological trait Panicle/flower RM171 RM333
Osa10LNT0078000.2 10 nan Physiological trait Sterility C701 C16
Osa10LNT0078000.2 10 nan Physiological trait Sterility RZ811 RG561
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