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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Sequence

>Osa05LNT0296400.1

GGCTCGGTAACAGGACTTTTCAGTTAACAATCATATTATGAAGCTCAACAACACATATGTACAGAGAGTAACATACTACTCCACTACATTCAGACTTGATCGGAACTCACAGAACTACACCAATGGTTTCTCTAGAGACAAGAGAACAACCGGAGAGGACGATATTCTAGGTTCAAAGTTTCAAATAATGTTTTTGTAAGGTGAATAACCAGAGGAACACAAGGACGATATTCTAGCTTGCGGTGTTCTTATAATGCTCATGTAGCCCGTTTAGTTTTTCTTCTCCTATAAATCCTTGTAGGAGAACGAGTGTCTCCAGCACCGGTATTGTTGCTACTCTGATCAGGGTCATTCACATCTTGCTCAGGTTGAGAGGTATTTGATGTCACACTTGTTTCCGCAAGTTCTGTTCTCAGATATCCACTTGCGCTGATCTGCCGCCTCAGTCTCAATATCTCACCTTTTGCTGTGGCCAATTCCTCTTCAAGTTTCTTAGACATCGTTTCAAAATTCTCCCTCTCCGTTCCAATCATTCTCATAAGATTCTGAGCATCCTCCATATCTTTCTGAGCTTCCATTGTACTTCTCTTTTGTTGCTCAAGAGCCTCTGAAAGCATCTCTTTCTCTTGTTCAATAGAAGAAATCCTAGAATTTGCGCTATCCAGCCTCTCAGACAGGAACTGTGTACTCTCATCCACCTCTTTTTGTGAATTGGTCACCTCATCAAGGTCTGCTTGAAGAGCTTGTCGTGCTTCAGATTCTACAATCGATTGTTCCACCAATGCCTCAAGCTCCCTGTTTAGAGTAGCATTAATTTTACGTTCTCTAACAAGCTCATCTGTTGCAGACTCTAACTTCTTGTATGCATCCAGCAGTTCTTTATTAAGGTCCTCACGTGCTTCCATAGTTGACACTAATTGATTAGAAGTGACATCAAGCTTTTCTTGTGTCTTTTGAAGTACATCCCTTACTGATGCTAATTCATCTGAAAGAACTTTAGAAACTGCTTCTGCCTCTGCAATTTTGTTAGTCAGAACCTGTTTCGCTATATTGGACTCGTCTGTCAACTTCGTAATCTGGGTTATCAATTGCTGATTTGATATCTTCACTCTATTAAGCTCTTCAGAGAGGTTGAACACCTTGTCTCTGTAATCTGTTAGTGCCCCTTCAGTGGACTGAAGAATCTCTGATAATTTCTTATGAGCTTCAGCCTCATTATCTAGCATAGTTCTGTTGGTGTCCAATTCATTGTTCAGCTCAGCAATTATAATTTTGTTCTTACTAGTGTCACTTAATGCAGCAGATAGTTTTTCTTCAAGCTGGTTGAGCAGGTTATCTTTCTCGATCAGTAGTTCAGAATCACAAGATGCCCTCAACTCAGAAGCAGCTGCAAGGTCTGCATACTGTTTCTTTAGTTCACTTATCTTTTCTTCTGCTCCAGTTTGTGCAGTGTATAGTGTTTGGACTTCCTTATTCAATGAATCAATTGAACACATCTTTGAGTTCAGATCATCTTTAGTTGCAGAATAACCCTCCTCCAGTTGCTCTATTTTAGAATCTGCATATTCTAGGCTTGCTTCGGTTTCATTGTAGATCAACTGCAGCTTCTGATAGTCTTCTTCCTTGGAAGAGAGTGATGAGCTTAGTTCCCTGATGGCTTCCTCCTTGGCATTCACCTCTTGGCTGAGCAGATTTACTTTGTCCTGTAAACTATCAAGTGCTTCCAACTTCTCTCTCAGTTTGCCTTCAAACACATGTTTGTCGTCTTCTGCTTGTGCAATGCTACTCTTAAGTCGATGTATCTCTTGTTTAAGCTGCTCAACTAGTTCTTTCTCCCTTCTCACTTCCTCGTTTAAAGATGTTACTGTTCTCTTAGTCAAAGTCAATTGATCCAGAAGGGAAGCTTCCTTCTCCTGGAACATCCTAGCCTGTTTCTTTTGTTCTGCATGTTCATTCCATATCTGTTTCTCATAGTTTTCCCTAAGCATGGACATTGCTGCCTCATTTTCAGCCAACTTGATCTCCATAGTTGAGACGGTAGATTGCAACGCCTCTTTTTCCCTTTGAGAAGCACCAAAAAGTCCAGCAAAAACACCAGAAGCAATAACTGCGATTGCATTCAGAAGACCTGCAAGTGGATTCACTGCAGGTGGTACTTTCACCTCAGCCAGAGATTCCTCAGCCGAAGGTTCTTCAGGTTGAGTCTCCTCAGTCTTCACAGTGTCCATTCTATCAGTGACGAGATCCACCGTCGTCGTCGACGGCGGCCGCGCCGCGGCCGCCGCGAAGGCGGCGTCGCGCAGGCGGAGGAGCGGGAGCACCGAGACGCCGACCAGGAGCACGGCCCTCCTCCCCGCCGCCAGCGCCGACGGCGACGGGGAGCAGGCGGCGGCGACACGGCCCGCGCGCGGGCGGCGGCGGGAGGTGACGAGCGAGAGGCGCGCCGGGTGCGGGTGCGGCGGCGAGAGGAGGAGGTGGTGGTAGGCCATGGCCGCCGAGAGCTAAAACCCTAGCCCCCTCAGCGCCCTCGCTGTCGCTGCTCGGCGGCGGCGGCGGCGGCGCGGAAGCGGAGCAGCAGGAGCAGGAGTAGGCGGGCTCGCC

Coding Potentia
Explanation CPC Score
noncoding -1.06061
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0296400.1 5 4833312 T C
Osa05LNT0296400.1 5 4833479 C T
Osa05LNT0296400.1 5 4833695 T C
Osa05LNT0296400.1 5 4834323 G A
Osa05LNT0296400.1 5 4834534 C T
Osa05LNT0296400.1 5 4835105 G 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
Osa05LNT0296400.1 osa-miR5836 Translation 5.0 8.438 1 21
Osa05LNT0296400.1 osa-miR5512b Translation 4.5 15.314 1 21
Osa05LNT0296400.1 osa-miR528-5p Cleavage 4.0 7.87 1 21
Osa05LNT0296400.1 osa-miR530-3p Cleavage 3.0 16.665 1 21
Osa05LNT0296400.1 osa-miR1852 Translation 3.5 8.432 1 21
Osa05LNT0296400.1 osa-miR2090 Translation 4.0 14.456 1 22
Osa05LNT0296400.1 osa-miR2870 Cleavage 4.0 18.92 1 21
Osa05LNT0296400.1 osa-miR2919 Cleavage 3.5 8.654 1 19
Osa05LNT0296400.1 osa-miR5512a Translation 4.5 15.314 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
Osa05LNT0296400.1 5 4831608 Grain-Width(mm) 9.927902222 -
Osa05LNT0296400.1 5 4831923 Grain-Width(mm) 11.25414944 -
Osa05LNT0296400.1 5 4831926 Grain-Width(mm) 11.02141476 -
Osa05LNT0296400.1 5 4832023 Grain-Width(mm) 11.00997257 -
Osa05LNT0296400.1 5 4832093 Grain-Width(mm) 11.26141262 -
Osa05LNT0296400.1 5 4832103 Grain-Width(mm) 11.26329422 -
Osa05LNT0296400.1 5 4832118 Grain-Width(mm) 10.72083473 -
Osa05LNT0296400.1 5 4832156 Grain-Width(mm) 11.00032711 -
Osa05LNT0296400.1 5 4832176 Grain-Width(mm) 9.426827431 -
Osa05LNT0296400.1 5 4832280 Grain-Width(mm) 11.2722311 -
Osa05LNT0296400.1 5 4832282 Grain-Width(mm) 10.5844717 -
Osa05LNT0296400.1 5 4832283 Grain-Width(mm) 10.93262959 -
Osa05LNT0296400.1 5 4832297 Grain-Width(mm) 10.96896553 -
Osa05LNT0296400.1 5 4832311 Grain-Width(mm) 10.73194408 -
Osa05LNT0296400.1 5 4832316 Grain-Width(mm) 11.01663589 -
Osa05LNT0296400.1 5 4832318 Grain-Width(mm) 10.96003056 -
Osa05LNT0296400.1 5 4832407 Grain-Width(mm) 11.97633648 -
Osa05LNT0296400.1 5 4832410 Grain-Width(mm) 11.66359711 -
Osa05LNT0296400.1 5 4832437 Grain-Width(mm) 10.28683281 -
Osa05LNT0296400.1 5 4832439 Grain-Width(mm) 11.70210838 -
Osa05LNT0296400.1 5 4832759 Grain-Width(mm) 11.62013149 -
Osa05LNT0296400.1 5 4832812 Grain-Width(mm) 11.39164925 -
Osa05LNT0296400.1 5 4832827 Grain-Width(mm) 11.16862869 -
Osa05LNT0296400.1 5 4832852 Grain-Width(mm) 10.83542633 -
Osa05LNT0296400.1 5 4832941 Grain-Width(mm) 11.28365517 -
Osa05LNT0296400.1 5 4832991 Grain-Width(mm) 11.68667507 -
Osa05LNT0296400.1 5 4833038 Grain-Width(mm) 12.05186462 -
Osa05LNT0296400.1 5 4833125 Grain-Width(mm) 9.659952164 -
Osa05LNT0296400.1 5 4833157 Grain-Width(mm) 11.3402071 -
Osa05LNT0296400.1 5 4833166 Grain-Width(mm) 11.01862621 -
Osa05LNT0296400.1 5 4833226 Grain-Width(mm) 10.98868465 -
Osa05LNT0296400.1 5 4833273 Grain-Width(mm) 11.22282028 -
Osa05LNT0296400.1 5 4833312 Grain-Width(mm) 10.09671688 -
Osa05LNT0296400.1 5 4833340 Grain-Width(mm) 11.82862663 -
Osa05LNT0296400.1 5 4833347 Grain-Width(mm) 11.32097816 -
Osa05LNT0296400.1 5 4833451 Grain-Width(mm) 11.73173141 -
Osa05LNT0296400.1 5 4833479 Grain-Width(mm) 8.45727253 -
Osa05LNT0296400.1 5 4833520 Grain-Width(mm) 11.75686455 -
Osa05LNT0296400.1 5 4833607 Grain-Width(mm) 11.47158146 -
Osa05LNT0296400.1 5 4833812 Grain-Width(mm) 11.02047348 -
Osa05LNT0296400.1 5 4833824 Grain-Width(mm) 11.1821804 -
Osa05LNT0296400.1 5 4833827 Grain-Width(mm) 11.36481953 -
Osa05LNT0296400.1 5 4833828 Grain-Width(mm) 11.26670742 -
Osa05LNT0296400.1 5 4833864 Grain-Width(mm) 10.93930435 -
Osa05LNT0296400.1 5 4833898 Grain-Width(mm) 11.10296345 -
Osa05LNT0296400.1 5 4833905 Grain-Width(mm) 11.1592741 -
Osa05LNT0296400.1 5 4833937 Grain-Width(mm) 11.14613438 -
Osa05LNT0296400.1 5 4833955 Grain-Width(mm) 11.81662273 -
Osa05LNT0296400.1 5 4833963 Grain-Width(mm) 11.59244442 -
Osa05LNT0296400.1 5 4833969 Grain-Width(mm) 11.38297176 -
Osa05LNT0296400.1 5 4833982 Grain-Width(mm) 11.36449528 -
Osa05LNT0296400.1 5 4834012 Grain-Width(mm) 11.59415245 -
Osa05LNT0296400.1 5 4834050 Grain-Width(mm) 11.51992702 -
Osa05LNT0296400.1 5 4834057 Grain-Width(mm) 10.53516388 -
Osa05LNT0296400.1 5 4834082 Grain-Width(mm) 11.73387909 -
Osa05LNT0296400.1 5 4834100 Grain-Width(mm) 12.05152321 -
Osa05LNT0296400.1 5 4834106 Grain-Width(mm) 9.95685482 -
Osa05LNT0296400.1 5 4834196 Grain-Width(mm) 11.02306843 -
Osa05LNT0296400.1 5 4834285 Grain-Width(mm) 11.2540493 -
Osa05LNT0296400.1 5 4834333 Grain-Width(mm) 11.15883446 -
Osa05LNT0296400.1 5 4834369 Grain-Width(mm) 9.951205254 -
Osa05LNT0296400.1 5 4834382 Grain-Width(mm) 11.86915684 -
Osa05LNT0296400.1 5 4834430 Grain-Width(mm) 11.70187092 -
Osa05LNT0296400.1 5 4834457 Grain-Width(mm) 11.76915264 -
Osa05LNT0296400.1 5 4834732 Grain-Width(mm) 11.40069675 -
Osa05LNT0296400.1 5 4834740 Grain-Width(mm) 11.31697083 -
Osa05LNT0296400.1 5 4834751 Grain-Width(mm) 10.83985043 -
Osa05LNT0296400.1 5 4834806 Grain-Width(mm) 11.6709528 -
Osa05LNT0296400.1 5 4834850 Grain-Width(mm) 11.59004116 -
Osa05LNT0296400.1 5 4834899 Grain-Width(mm) 10.86448574 -
Osa05LNT0296400.1 5 4834918 Grain-Width(mm) 11.12714672 -
Osa05LNT0296400.1 5 4834929 Grain-Width(mm) 11.23466969 -
Osa05LNT0296400.1 5 4834935 Grain-Width(mm) 11.34677696 -
Osa05LNT0296400.1 5 4834950 Grain-Width(mm) 11.55866814 -
Osa05LNT0296400.1 5 4834952 Grain-Width(mm) 11.07449055 -
Osa05LNT0296400.1 5 4834993 Grain-Width(mm) 11.67420673 -
Osa05LNT0296400.1 5 4834996 Grain-Width(mm) 11.85295773 -
Osa05LNT0296400.1 5 4834998 Grain-Width(mm) 11.86860847 -
Osa05LNT0296400.1 5 4834999 Grain-Width(mm) 11.62360096 -
Osa05LNT0296400.1 5 4835007 Grain-Width(mm) 11.46465492 -
Osa05LNT0296400.1 5 4835114 Grain-Width(mm) 10.97094154 -
Osa05LNT0296400.1 5 4835174 Grain-Width(mm) 11.89224243 -
Osa05LNT0296400.1 5 4835346 Grain-Width(mm) 10.75537014 -
Osa05LNT0296400.1 5 4835566 Grain-Width(mm) 9.798872948 -
Osa05LNT0296400.1 5 4835571 Grain-Width(mm) 9.910128593 -
Osa05LNT0296400.1 5 4835577 Grain-Width(mm) 8.20405674 -