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

>Osa02LNT0166400.1

CCCACAATCCTTATAGGATTGTTCATCCCATAAAAATGTTATGAAGGATTTATAGAATTCAATTTTAATACTTAGTTTCGAAGGTTTTTATAGGATTTTTTCTATAGAACTGAAATCATCAAAATTTACTATGCTTCTTACAAATCAAAGAGAAGCACAAATTGGTGACAGGTGTAAACTAATCTTCAGTTGACCAATTGATCTGAACTCTTCAAGCTTCAGGTAGCCTGCAAGTTTCTCCAGCTAAGGTTGCGCCTTCGTTTGGTGCGAAATTAAGATGCCGTGTCACAACACGCACGGCGCACGGCGTTGCAATCCTGCATCTCTCCTTTTCGACCGTGGCTGCTCGTGAATTCGCGACACGAGATCCCGCGGACTGGACGAGTACCATGGATGGCGCTGCTTCTTTTCACTAAACCAACTTGCCTGGCAAATATAGCACGTAGCAGCTGACTAGTGGGGCCACTAGGCTAGCCACTATCCATGCTCCATGACAGTCAGCATCAGCACCATGACCACTGGCGACAAAATATGATTTTTTATTAGCGCCACCATCACCAGATCCAACACCGTTGAGCCCGCACATAACCCCTTGCAAAATCAACCACGGCTTCCAAAATTTCGGTGCCATGTTTGACAGCTCAGTTCTTTGGCAATGCTCAGTGAAAATGCACGATTGGATGCAATTACATCAGATGGTGTGCATTCCTGTAATATCTATTGATGTACCTTGCCTTTACGTTGCTTACATCAGGAGTATCTAGAGTTTTTACAGGATAAAATTTGTAAAATTGGATATTTTCAAATGCCTCTTTGATCTTAGGATCCATATCATCAATAGCTTTCTTTCTAGCTTCCTTAGCCTGTTTCAGCTCTCTTTTTCTCTCTCTAACCTTCTCCTTTAGGAATTCCTTCATTTTTTCTCTCTCATCCTCCGGTAGCCCCTCCTCTTTAACTTTCTCATCAGCAAAGTCCTCATAATCATCCATCTCCCAGTTAAACTCACAAAATATCTGCAACAAACAGTACAAAGTAAATACAAAATTATTCGACAACATACTGAAACGTGGAAGCAAATATAAAAAAGATCAAAAATAGAGGTATTTAACTAAGTTTTTTTTTAATAATTTCAGTGTTGACATTAACTAAGCATGGGCAGTGGTATAGTCATTTTACCTTATCGTTTCAGAGCAATCAAAAATTTGCATCAATAGCAGGAAAAACATCACAATTAAAATTTCCACCAATGGATAGAAGTGACCAGCCTGATAAGCATGAAAACAGAACCTGGACGCCTAGGCAATTACACAGACAACTAAACAACCCCATTAAGCTAACAAACAGCAGCAATTAGATTTTGCGTGAAATAACCAGTATGCAACAGCAATTAAGAGGAAATTAATAAGCATGCAGCAGAAGTTAGAAAATAATCAGCCCGCAGTAGCAATTATGGAAGAAAATAATTGATGCAGCAGCAATGAGAGGAAAAGGCAATCCCTCGCTCTCCAGGCTGCTGATGGAGCAGCTAAAAAGAAGTGATGGTAAGAAGGTACGAAAAATTCAGTGATGACAATTAGGTTGGCAGCAGCAGTTTCAACAGCAAACTCCACCCCATTTCGATCTGCCTCCCATGCCCCCCGTCCCACCCCACCCCCAAACCAATCTCTTTAGGCAAGGCAATGGCAGTAGCAACCTCTCTAGAGTCTAGACCACCTCGACAATTTGAGCAATGCATTGATAAGTGATAACCATGTTGATAAGCCTAAAAAAGGGCAGAGCTGATGTGTTTCAGGCTCAATACATGGACCAATTTAGGAGGGCAATCAGATTAATAGGAATAAAAATCTCTCCTGATCCAACTGATCATGATGAAGGTAACTACATTGTAGGAATGCTAGTATGAGGATAACAGCAGTAAAAGTCAAAAGATAGTGCTTCGTCAAAGTTGGCAGGGGGCACCAGCAGCATGCGGTTTGGTTTTGACCTCAAAAGCTAGTGCAAATGAAGCATCACCAACATAAGCCTAGAGGTGCGTAGAAATAAGACAGAAAAGGTCAACTCGAGCTGCATATACGATAAAATTTATCTTCTCACACAAGCTACAGCTTGAGTTGACATTTTCTGTCTTGTTTCACGGCAGCTTATATCAATGAAAATGAAGAGAAGCTACAGCTGCATTTTGGTCAGAGGTTCCTTAAATGTTGTCTTAATGAACAAACATCCCAATTATAGGCTATAGTAAAAAAATATATTACTTTGCAGATTACACATAATGTGATGATTACAGAAAATGTCATTTTGTTACAGTATGTGTTGATCACAGGACTCAATAACATTAACAAACAGCTGTGTTAAAAGATTGTTTAGGCAAAACTGGAAATGAAAAACATACTAAAAGAAGCTTACCGGTGGTTCAAAAGGATATAGGATATTGATAACTGTATCATCTTCATTTTCAGGAGGATTTAGTGGCATATAATATGGCATGCAGTAGTCAAACAGCTTGACTCGTTCGGTTTTGAGATGCCTCAGTGCAGACCTCCGCTGAGTGCAGCCAAGAGTAAATATTTTTGTTTTCAAACTGTCAATCCTACTGAGCCGGTCCTCTAGCGGAAAATAAGGCACCCAGGCCATCTTCATTGCTTTCATTGGCAATATCTCTTCATTTTCCCTTTGGACAGAATTTATACCAATTTTATCTGAAGGAGGAAAAGGACAGTCAACAGCAACTACAATAGGAATAAGTACTATCTTCGATTCGCCATTCACACCCAATAGTTGAGGTTCAGTGCTTCCAAACAAGTAAACTGTTTTCTCATAAAGCTCTCCCCCTTCTTCTAGGGCTTTCTCCAAATTTTCAAAGTTCCAGTTGAACTCCTTTATCTTATCAATATTTTCCCACTCAGTCCCAACAGGAAAGGCTGACAACCAAAGATCTTCCAGATTCCGCTTATCGGGGAAGTACTCCGCCTCCGTCTCCGGCTTGGGCGACGCCTTGACACGCTTCCCCCTCCCCCGCGTGGCCGCATCCTCCTCCTCCGCCGCCGCCGCCGCACGCTTCCTGCCTCTGGGACGCGGCATCGCTCTCGATTAGGGCTTCGACCCAGGCGGCGAGGCTGTGAGTGGAGTGACGCTGTGTGTCACACCGGCTGGTGTGCCATCGGCGGCTGACAAGGTGGATACCGGAGAAGTGCT

Coding Potentia
Explanation CPC Score
noncoding -1.03158
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0166400.1 2 18889981 G A
Osa02LNT0166400.1 2 18890219 G A
Osa02LNT0166400.1 2 18892362 C T
Osa02LNT0166400.1 2 18892832 T A
Osa02LNT0166400.1 2 18894705 T C
Osa02LNT0166400.1 2 18896043 A C
Osa02LNT0166400.1 2 18896754 C A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0166400.1 osa-miR5540 Translation 4.5 11.035 1 21
Osa02LNT0166400.1 osa-miR6252 Translation 4.5 15.643 1 23
Osa02LNT0166400.1 osa-miR437 Translation 5.0 5.421 1 21
Osa02LNT0166400.1 osa-miR1865-5p Translation 5.0 11.856 1 24
Osa02LNT0166400.1 osa-miR1865-5p Cleavage 5.0 11.017 1 24
Osa02LNT0166400.1 osa-miR1866-3p Cleavage 5.0 13.796 1 22
Osa02LNT0166400.1 osa-miR1866-3p Translation 5.0 19.893 1 22
Osa02LNT0166400.1 osa-miR2864.1 Translation 4.5 18.816 1 21
Osa02LNT0166400.1 osa-miR2864.1 Translation 5.0 12.017 1 21
Osa02LNT0166400.1 osa-miR5523 Translation 4.0 17.891 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0166400.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0166400.1 2 nan Morphological trait Root RG171 RG157
Osa02LNT0166400.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0166400.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0166400.1 2 2-3SY Physiological trait Source activity RG171 RG157
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