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

>Osa04LNT0289500.2

ACAAATACGAATCAACGTTTTGATTTCCAATGTGCAAGAAACGCATGAACAGCTGCATGTTAAATTGGCAAAAAAATACTTGCCTTGTAACAATCTAAATAGTAGTATTCTTTGGTTCGGAAAAACTTCTCTAGTGTAGTACTACTACTGTAAGTAACTTGCAAGATTTGATGGCCCGGGATGTATCAGGTGTGAGAAAACTAATCTCTGGCTGCAGACCAGCAAAGGAAAATCTCCACTGCAATGCGACGCGCCAGCCCCAGCAGCTGATCAAAATTACCAGGCAGGCAGGAACTGCACCCAGGAAGAGGAAGACTCAAATGAAACATCTGACAAATGATCTGTTGATCACCAGCATTGTGATACTTGTCTCGATAGCTTGGTATCTGTGCTTGTTTCGAGGACGAAATTGCATTAGTTTCTCCGCTCAGTTTCATTAAACTTTGCAACGCGATCCCCATTAAATAGTCACTCATACAATATCCACTATGGTCCACCATGGTCACTCAAAACAGCTTCAATGGCTGCTAGGTGCAACCATTCATATCTTCCGCAGGGTTAAATGTTAACCATGTTTCTGCAAGTAACCCTTCTGGCCACCATGCAGCTTATACGACCCATCAACAGTGACTGCATACAGCTTAGGTAAATCCCTATCAACATCACTCAGAAAAGGGTCAGTCATGTTCTGCTTTTGTCCAAGTGATCGCGACTCAGGTGCTTCACTCAGTAAAGCAAAAAAATACAGTTTCGCATTGCATCTCAAACATTCATTTTTCATATTGCAGGGATAGATGAGACCATCTATCCATCCCTTGTTATTTCTTGCATGACTATCTGCTCCATTAACCAGCTGCTCAGAGGTAATTGAATCATGAACTGCAGTTGGAAGATACCCTCATTTTTCATATTTCAGTGATAGGCGGGAACATTTGAGTATCTGATGATGCCATCTTGTGTCCCTCAGATTTCTTAGCTTCACTGTATTCAATATAAAATCTAGCTCGACCAGCTCAATTTGATCCATTAACCTGCACCTCTGAGGGAATTGAATCATGAACTGCAGTTGGAAGATGTCTTTCTGTTTTGCAATAAAAGAGCTGTGGTCCGGTAAATTGCATCCGGGAGAATTCATTGCATAGTACTGGACTGGAACTGGAAGGATGAGTAGCCTGAACAGTTGCCCAACACAGAGTAACAGCCAGAGACAGCCCAGAAATTCGATTTAAAATAAAATCACACTTCCCCAACAGCTAGCTTGGCATGATTAAACCATGTTGCAGGACCACATTCATGTTTCAGTGCTCTGAAAGAAGCATTGGTTGCATCCTCAGTATTCAACTCGGCCTCTAACAAGTCAAGATCATGGAGTTCAAGATGCCCGTTTCCTTTCCTGCTAGGCAAACACTTACCATTAGGTAATCCAGAAACATTGTATGCATCCTTGTCCTCTTCTGATTTGGCAGCTGTAATTCCATCCAATCTTTTAGTTAGCAAGGATGTTCCAGGAAATAACATCAAGTTCACATTACGAAGTTGTTTCTTCTCATTATCTTCAATGGGTTTGAAACCAAATCCTGACACCCATGTATTAACCAACTCTGGGATGGCAGAAAGGACCAATGTCTCAACATGGAATGATCTAAGCATCATTTCAATGGTGTCCATAAGTCTTCGGCACATTCCTTGGCGGCGATAATCCACAGAAGTAGCAATAAATGGAAGCTCAGCTGCTTTGGTCCCATGTACTCTGATAGATGCTACACATAAAATCTCATCACCTTTCTCCAGGATTACTGTATAGAACCCCTGGTAATCTAAGCGAGCGAAGTTTGATCCCTTATTGTACAAGACATGCGGTATCATGTCTACACCAGTTCTAGGATCCACCATGCGAACAAAACATTCCTCCAATATAGTAAGAGCCACAGCTAATTTTGTATTGCATTCTGTCATATGCGCAATCTTCTTGGAAGAATGTAGCTTCTGCCCATCAGTGTTGCACTTCAATATGCTCCATGAAAGCTCGTTGTCAAGAAAATTCTCTATTCCAACGTGATTGTGTAATCCAATAAATATCTCTTTACAGTATCTCCCACAAAACCATATGTTGGATTGTTTATCCCCACAGGGGAGCATCTCCTGGTCAATGCAAGTATCATGGTATGAATCTCCACACTGCAAACATTTCAAGATAGCCGAGAATGTTGAAACCTCCTTTTCACTAAGTGGATTCCCACAACTCCGGCATGTGCAGTTATGGCAGTACCAACTGCCTTCTGGAAGTTCCTGGTCAGACAAACAAGTTTGATGATATGTTGATGGGCAATTGTCGCAGCAAAGTAATTCACCACCATCTCCACAGAAACCACACGTATCATCATTTTCATCCATCGCCTCAACTTTTCTACCAGATGCATCACATTTCCTACTTAGAAATTCAGCAGACCAAGCTTCTACCTGGCATAGAGTGTACGATTTGCCAGACTGTAGAAAGAGGCCCAATGAGGACTTTGGTAAACTGCAACCGCCATGAACCTTGAAGTCTGATATAGAAAAGGTCTTGGTGCAACAATTGCACAGAATGCCTTCCCAGGTAACCTGCCCATCCTTAACAACTTCGTTGCTCTTCAGATTCTGGTACTGTATAACATCTTTTACGGTCAGAAAGCCAGTGGCAATCAACCAGCAGAGAACTGTTTTCCGTGCCAAACTTACTCTCTTCCCACCCAACAGATTTGATCCTCCTTTTCCGGACATTCGAGCAAGTAGCCTGCCACATTTCTTTGAGCTCTTAAACTTTGTAAACTTCTTTGCATCCAAAAAAATGGAGTCTGCAGCAAATTTGTGGCAGGAGCCAAGATCCCTATTTTTCACCATAGCTGTGATCAAAAGATCATCGTCATTGATACGTAACACACGGGGCCTTTTCTTGGCATACTTCTCCCAAGCTTGAGGTTTTCTTTTAGCAGCAACTGCCTTGCACGTCGGTGACTCCTGAGATAAATCAGTTTTCAGGACAGCAGCATTAGATTCGTAGGATAGGTTAACAGGAACAGAGTTGACCGTTGGAAGATTATGTACATCCTTGGGGAAAATTCCAATGGATGATTCCTTCAGCGACAGCAACTTCTTCTCTTCATTTCCTATGGGGATGAACTTGCTGGAACCTGATTCCGTTGGAGTAGAACCATTTTCTGGGAGTATGTTGAATCCTGCAGGTTGCTCAACAGTCTCCTCGCCCTGTAATATGCTGGTTTGCATGACTTCTGAAGGCAAGAGCACGTCGAGCTTGTTGCTTTGGTTGTTTGCATTTAGCTTTGCTAATTTGGATTCAGCTTTCAAGTGCCTTTTCGATGTGCCAACAGATGAACAGATACCATGTTCCTCAGAGCGCATATTGTTTTCTGCAAAAGACAATTCCACACTTGCTAGTTCGGTTTCTTGGTTTAACACAATTTCCACAGCAGGCTGCATAAAACTTTCAGAATGCAGTCCATCTAGTCCAGTTGAATCAATATCTGATATCCTTTTGGATTTCTTCTTAGTCTTTTTCACTGCGCTATTAATAAGTGTTGCTCCAGACCAAAGTTCCCTTTGTCCATTACTTTCAGAAATGGGATTTTCTGTTCTTTGACTTGTGTCACCTGCCGCGCAATACAGCTGGCTCTGTGTGCAGAGAGTACTCAGGTTAGTATCCCCGTTGTGGCCATCCTCCAAGTCATGGCAGCTCTGTAAAGCATGATTCCCGTTGCCACTCTCAGTTGCTAGTGTGCTACAATCAGAGTCCGTGATCACTGGAGTAGGTTGAATCATGCGAGTGGGCAACAAATCACTGGATTTCAGCATGCTCTTACTTTCTGAGGGGACATTCCTGCTGTCATTGAGAACATAGGTCGAACTATCAACAGCTCTAAGAGTTTTATGTTGTTGCAGAGCAGTAATTTTCCTACCAATGAACACAACAGCTATGAAAGGATCCAAAAGCTCCCACCGATGAAGAAGAGTGGGTGCATCTTGGCGGTTCACGAGCATCTTATCGACATAAGCCATTGTATCTGTGAGGTCCTTCCAAAATGTATCGACATCTGACCACTCCTTAGGACACTTTCCGCGTTGTGAACACGGGGTAGCTTCATACAATTTCTTGCCACAGAACTTCCAAGCCTGAGTTAGAGAGGTATGAACAACCTCCCTGTGTGGTGCAGTGAAATAGGATGCCATCTTAGCCCTGTCATTCCTTTTCCGTGGCTTGATGGTCCAGCCGGCATCCATGAAAAGGTGCTGAGCATGTACCTCCAGCTGATCAGGGAGTTCCCTGCTTAAATTCCTCTTGGAAGCAACAGCAGTAGTGCCGTAGTGTTGAGTGTTGTCAGCAGCGACATCAGCAGCATCATCAAGCGAACCAATACTTGCGCCTGGCGTACCAAAATTCTGACAGAGGTTGTCAAGTTGGACAAAGTGAGCAGAAGCAGTAGAGTCGCGGGACAGGTGAGGCAGAAGCGTAGTATCATAGACTGTGTTGCTGTAGAGTGAGAAGTGGTCTGGTCCTGTGACAGACAGATCTGGTGTAGTAGCTGAATATAGAGTATGGCTAGTGGTGTCAAGCATTTGGGGTTGATCATAGGTGAAGGACATATCAGTGGGGAAGTGGTTGTTATCTTGGAGCCACTGATTCAAGAAGGGATCGGAAAGAAGAGCGTCATTGTGGAAATCAGAGAAGTCTGCTAGTGCCTCCATATAGGAAGGCAAAGGATCTTCGACTCCACTGTTGCTGCTGCTGGCAGCCAAGGCGGTGCACATTCCAGCAGCAGCAGGAGGGGGAGGAGGAGGAGGTCCAGCGGAGTGTTGCGGCGGCGTTGGTTGCATCATGTCATGGAAGAGGTCAGCGTCGGTTACACTTAGAGAGCTGCCTCCGCCTTGCCAGTAAGCAACGAAGCCCTGCAATGCGGCGTCCAACTCGAGGCCTCCATTCCCATTCCCATTCCCATTCCCATGTAGCACGGGGCCGTGAGAATGTTTGGGATCGATGGCGGCGGCGTCGACCTCCACGGGCGCGGGTTGAGGCTGCAGCGCGTGCAGGTGGTGGTGGAGTGAAGGCGCAGGCGCAGGCGGAGGCGGAGGCGCAGGCGCAGCAGCAGCAGCAGTGGGGAGCAGGGATGAAGTCTCGGCCACATGAAGAAGAGGTGGAGACGGAGAGAAGACGTCCCTGAAGACCTGGACCTCGGGTTGCGACCTGTCGAAGGAGGAGGCTGCGGCGGAGTGGTGCATGGCGAGGAGATCCTCGCCGAAGAGGAACCTGAGGGCGTCCTCCTCCCTGAACCCTAGCTTGTGGGCGGCGGCCATCTGGATGAAATCGGGATTCCAGTTCCCCAATTGGCCGGGAGGGGATGGGATGGATGCAGCCGGCCGGCGGAACCCTTCCCTTGCAGCAAGCTTAGAGTGGAGGAGGGAGCCCCAGCCCCGGCGGTTGCGGCTGACGGCGAGCTCGGGGGGGTGGGGTGGCGGCGCCCGGCGCCCCGTCGGCGAGTAGAGAAACACTAGTAGTGAGCAGAGCAGAGCTCCCCCGCGCCGCTTCTCTTCTCTTCTCTCACACCTCTTCTCTTCACTTGGACTTGGGGACAATTCCTCCCTG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.571231
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0289500.2 4 35383618 T C
Osa04LNT0289500.2 4 35383680 A T
Osa04LNT0289500.2 4 35383693 T A
Osa04LNT0289500.2 4 35384756 G A
Osa04LNT0289500.2 4 35385396 C T
Osa04LNT0289500.2 4 35385685 C A
Osa04LNT0289500.2 4 35385732 G T
Osa04LNT0289500.2 4 35387834 G A
Osa04LNT0289500.2 4 35388900 G T
Osa04LNT0289500.2 4 35389259 C T
Osa04LNT0289500.2 4 35390627 T C
Osa04LNT0289500.2 4 35391250 C T
Osa04LNT0289500.2 4 35392039 G A
Osa04LNT0289500.2 4 35385145 C 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
Osa04LNT0289500.2 osa-miR5528 Translation 4.5 14.443 1 21
Osa04LNT0289500.2 osa-miR5815 Cleavage 5.0 19.19 1 24
Osa04LNT0289500.2 osa-miR5822 Translation 4.5 17.803 1 21
Osa04LNT0289500.2 osa-miR395u Cleavage 4.0 9.973 1 21
Osa04LNT0289500.2 osa-miR397b Translation 5.0 15.04 1 21
Osa04LNT0289500.2 osa-miR171f-5p Cleavage 5.0 21.061 1 21
Osa04LNT0289500.2 osa-miR172c Translation 4.5 19.891 1 21
Osa04LNT0289500.2 osa-miR528-3p Translation 4.0 22.733 1 21
Osa04LNT0289500.2 osa-miR444b.2 Cleavage 3.5 18.817 1 21
Osa04LNT0289500.2 osa-miR444c.2 Cleavage 3.5 18.817 1 21
Osa04LNT0289500.2 osa-miR444f Cleavage 3.0 18.817 1 21
Osa04LNT0289500.2 osa-miR810b.2 Cleavage 4.5 11.664 1 21
Osa04LNT0289500.2 osa-miR1851 Translation 3.5 16.838 1 21
Osa04LNT0289500.2 osa-miR1851 Cleavage 5.0 17.938 1 21
Osa04LNT0289500.2 osa-miR1861e Cleavage 4.5 17.037 1 22
Osa04LNT0289500.2 osa-miR1861g Cleavage 4.0 17.037 1 22
Osa04LNT0289500.2 osa-miR1861k Cleavage 4.5 17.037 1 22
Osa04LNT0289500.2 osa-miR1861m Cleavage 4.5 17.037 1 22
Osa04LNT0289500.2 osa-miR1862e Cleavage 5.0 24.085 1 24
Osa04LNT0289500.2 osa-miR2867-3p Translation 4.0 21.53 1 20
Osa04LNT0289500.2 osa-miR2863b Translation 4.0 19.135 1 21
Osa04LNT0289500.2 osa-miR2905 Cleavage 5.0 16.93 1 21
Osa04LNT0289500.2 osa-miR3980a-5p Cleavage 5.0 16.135 1 21
Osa04LNT0289500.2 osa-miR3980b-5p Cleavage 5.0 16.135 1 21
Osa04LNT0289500.2 osa-miR5073 Cleavage 3.5 20.6 1 23
Osa04LNT0289500.2 osa-miR5337a Cleavage 5.0 13.157 1 21
Osa04LNT0289500.2 osa-miR159a.2 Translation 4.5 15.997 1 21
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