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

>Osa03LNT0206800.4

GGGCAAGTTACACTGGATTTTTCGCTACTTCTCCCTAATCGGAGCACGTTCTCAGACATGACATATCTTACACGCCCTCGTTTGGGCCAACGAATATATGTACAGGATGAAAGAATATTGTACAGGTGAGCGGTCAGTGCCGCTGGTATTGCAACGGGACGAGCCTAGCGTTAACGGCTTCAATGTATGTGCGCAGGCGGCGTCGATCATCTCTTGTTAGGGACAGAGCGGGGTTCAGGGCGAGTGACGGTGCCTCAGTCAGGAGAAAGCGCAGCATGGATACTGCCTTCGAGTACAGCACCATGGCAGATGCTGATTTCCCCATCATCTCATCAACACCACCATGTCTTCCCAGGTTAAGCGCGGTCTGAAATATGATTTCTATCGCATCTGGCATTTCTGTAGCATCAACTGTCTGTCCTATAGTGTTGGCAAGTTCTTCAGCATATTCCATTTGAACCAAAAACTGACTCTCTATCTCCATGCATGTATCATATAACAGTTGAGAGTTTGCAAGCAAATGGGGAGCATTTGAGCCAAAACCCTTCGCGGTGACATCATGGGAAGGATTCTCTCTTGTGGCAGAAGATGCATAAGAAGTGCAGATGTAAATTGCTTGCTTCCAGGTTGCAAGAACAACTAGCTGAATCGAGAATCCCTCTAAGTGCTTGGCATCTTTAATCTTTTCTTTCACCAATTCTGCTATGGTAGACGCATACTGCTCCAATAATCTAACCCTGGTCAGACAATCAGATGGTGGTTGATCCATAGCATCGTTGAGATCTGCAGATCCTTGTGAAGTACCAGATACTGGAGAGCAGTGACTGTCCAAGCTACCAGTTCCACCAGATTGCTGTCTGTTAATTGCCATGCCATGTATTGGCCTTGGTGCACTCACAGCAGTTAATAACTTCGGTGGTGAAAGAGAAGAACTGTCAAGTTTTGATGGCATGGTGCGCTGTCGGGAGTCATTCATCGAAGAGGAGGATCCCTCTGGGTGCACAAAGACATATTCCTGATCTACAAACTCTAATGAATCAATGATAGGGGAATCTACATTTACAAGTAAGGAAATAACAAATTTAGTAAGAACTTTTTCACAATTATAATGAAACATGTGATAGTCACAACAGACTGCAATACCTTCTGGATAACCACCTTTAGGGTTGTGCCCTTCATCACCCTTGTTTTCCTTGATTCTCCTAGGATGGTCCAGGCGTTGACTACTAGATGCGTAATTATTTCCCCTAATATATTTAGAGACCAGACTTGAATGTTTCGTTGGACTCTGACCTGAAGTTTTATCAAGCCTTTTACTCGTGGCAAACCCATAGGATTTTATTGCACTCTTACTATCAGAAACAGGACCTTCATCCTGTCCAGTTGACTCATCATCCAAAGGAAAAGGCATACAATCTTCCTGAGAACTTTGGCTTGAAGGTCTCGTAGGACTGCTATTAATGAATGGAAAGCCATCTCTTATGTCCGATGGTGTCCGGCTCAAGGTTCTCTCCAAAGCATGTTCAGCGAGAAATGGATGGTTCACAAACTCTTCAACGGTAAGGCGTTCCACTGAATTGATTCGCAGTAACTTTCTGCATAAGTCAATGCAGCCATGGCTCAAGTCGCAATCAGATGGAAATCGTATTTCTCGTGTATTGAGTATATTTCTCAGCAACTGGATTTGACTATCCCCGGTAAAAGGAGGAGATCCGGTAACAAGTTGATATAGAATTATACCAACACTCCACAAATCTGCCTTTGCATCATACTTCTGAGCTTGCATGACTTCTGGAGCCATGTAAAGCGGTGAACCGCAAAGTGTTTCAGCCAGAGAAGAAGGTTCTAAAAACCTGCTTGCAAGAATAGAAAAGGTAAGTACACATTTCTGATACTATCCGCGTCTAACCCTCCCACCAAGCCTCACTTGATCCAACCATCGATGAATGAGAAGCAGAGAGAAAGCTGAGGTGCCAATTTTGTCATGGCTGTAATTAAATATGCAAGGAAGCAGAGAAACACAGGATCAAGCACAAAGCAACATGATCTTATTCTCTTTCCCTGCACGATACTTATCTAGTTGTCCTCAAGAATGTTTCGTACTTAGCTTTTATGCACAGATTTTTGTGTAAAACTCTGTGTGAATTCAAAGGACATTACATTACGGAGTAGGACTGTTCAATAAAAAAAAGTAGAATTGAGTGTAGAGAATTAATTGGACTCAAGATAGCTTTTTTTTTTGTAACAATGATAGCTTAATTGGAGTAATACATATGCGACATAGGTGTATTGGTACATGAAATATTTTTTTGTAACAATGAAGGCATGCTGTAGTTGTGGAGCCAAATCCTGAAGGGGGCCTAAAAAGTGATGCACATAATATTTCATTCTTTAAATGGAATGTCTCTAACATCTTTCAAGACATGAAGATGAGACTTTCAAATGATGCACCTTTTCTTTTGAAATAGTGCAAATTGACTGTATTTTTTTCAGAACTTCTTGAGAAGTTATTCCATTTTAAAATGCACAACACCGTTTCTTTCACAATACTGCAATTTCATTTCAGGTAGGAGCGATTTCTACAGACCTATTAGGGGATTCTTAAACCAGGTATCAAACTCATTGCTGATAAACTCAATAAAAAAGGCCATGTGGAAAATAAGATAATATAACTCCAAAATAAAAGCAATCAAACATAAGTAACTTACTTTGCAAATCCAAAGTCCGCAATCTTCAAGAGGGAATTTTCATTATTTGCAACTAGAAGAATGTTCTATTTGAACAGCCACAAATTCAGGATAGAAAACAAAACAAAATGTCAGGAAATTCCGTTTCTTTCATCAATTCTTTGTCATTAAATATGAAGATATAATGGAAATATCCACTCAATAACAGTAAATTAAATAATTTAACCTGTGGTTTTAGATCTCGATGAACCACGTTGTTTTCACGCAGCATCTGCAGACCAGATGCTGCATAAAGAAGAGAATGTGATTTTGGCTCTGGGGAGAGATAAAGCAATAAATAGTGCAAGACACTGAGGGTCTGAGAAAGTGCTTGCCTAGCTGCTGGATGAAATGCTTAGCAACTGTTTCAGAAACCCTTTTATGCTGCTGAAGGTATGAGTGTAAGTCACCACCTCGACAGTACTCTAATACAAGATATATTTTCCCACCATCCCTGATGGACTCGTGGAGGGCGATGACGTTGGGATGACGGATGCGCCGGAGGATGTCGACCTCGGAGAGGAGGCTCTCGCGGAGCTTGCTGCTAAGCCGCTCCACGGCGATCTCCTTCAAGGCCACCTCCGTGCCCCGCGTGCGGTGCTTCCCGAGCCAGACCCGCGCGTACGCCCCCGACCCGATCTGCCGCACCAGCACGTAGTCCCCTACCCTCCGCACGCCGCTTCCTCCCCCTCCCCCGCCGCCGCTCCCCGCGGCGCGGTCCCCCATCCCCTCTGGTCCCGCTGCCTGGAGCGCAGTTCGCCGCGAAGGACGTGAGCTCCGCCGCCGCCGGGAGAGATGCCGCCGCGGCCGCGGGGAGAAGCAACCGAATTATCTCGCCGCGCGGAACA

Coding Potentia
Explanation CPC Score
noncoding -1.16823
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0206800.4 3 8896685 C G
Osa03LNT0206800.4 3 8898210 C G
Osa03LNT0206800.4 3 8898317 C T
Osa03LNT0206800.4 3 8899028 A C
Osa03LNT0206800.4 3 8899272 C T
Osa03LNT0206800.4 3 8900561 A T
Osa03LNT0206800.4 3 8900887 G A
Osa03LNT0206800.4 3 8898674 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0206800.4 osa-miR5541 Translation 5.0 12.851 1 21
Osa03LNT0206800.4 osa-miR5820 Cleavage 5.0 11.904 1 21
Osa03LNT0206800.4 osa-miR5833 Cleavage 4.5 19.906 1 21
Osa03LNT0206800.4 osa-miR6252 Translation 4.5 18.194 1 23
Osa03LNT0206800.4 osa-miR395t Cleavage 5.0 12.971 1 21
Osa03LNT0206800.4 osa-miR395a Cleavage 5.0 12.971 1 21
Osa03LNT0206800.4 osa-miR416 Translation 4.5 21.416 1 21
Osa03LNT0206800.4 osa-miR530-3p Cleavage 5.0 10.885 1 21
Osa03LNT0206800.4 osa-miR1854-5p Translation 4.0 22.95 1 21
Osa03LNT0206800.4 osa-miR1868 Cleavage 4.0 16.849 1 24
Osa03LNT0206800.4 osa-miR1873 Translation 5.0 16.332 1 24
Osa03LNT0206800.4 osa-miR2093-5p Translation 5.0 16.802 1 20
Osa03LNT0206800.4 osa-miR2097-3p Translation 3.0 24.241 1 22
Osa03LNT0206800.4 osa-miR2879 Translation 4.5 14.854 1 24
Osa03LNT0206800.4 osa-miR5144-3p Cleavage 5.0 20.692 1 21
Osa03LNT0206800.4 osa-miR5517 Cleavage 4.5 24.001 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0206800.4 3 S34(t) Physiological trait Sterility nan nan
Osa03LNT0206800.4 3 qGW3 Morphological trait Seed C706 C12534S
Osa03LNT0206800.4 3 qOE3-1 Physiological trait Eating quality nan nan
Osa03LNT0206800.4 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0206800.4 3 gl3a Morphological trait Panicle/flower C63 RM232
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