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

>Osa10LNT0059900.1

AAAATATCCAGCGTGCCACGCGCCATTTTCTAATCATAATGTTAGAACAAGCTCGAAATTGTTACAACTCACATGCAAATTAAATGCCATCGACTAGTGAACTTTGGTTTAGTGATCGTGCTAGTCTGCAAATTAAGCTGCATTTTTGTTAATATCTCGATGGAAGGATGGCAGCCACGACGACAGCAACGCCGAACATGAGGATGGCGAGACCGGTGAAGTTGACGACGAACGCTTCGCTCGGATAGCCGTGGAAGGGGAAGATGAAGCGTGCTAGGCCGGTCTCGGCGGTGCAGATGGCCATGAGGAAGATGACGATGCCCAACAAAATGTGCCATGGCGCGTAGTCAGCCCTCATCGTCATCACCGCCCCCGGGAATACAAAGTAGACAAAACCCACCAGCCACTGAAAGGCATAGAGTGCTGCAGTGGTTATCCCAAGCCAAGCATGGAGGGAGCGGATGTCAGGGGCGCGGAGATCATGGTGGAACTTGAAGGCGGCGTACAGGCCGACGGCGGCGAAGGCGAGGGCGACCAGATGCAGCAGCAGGTGCACCGCCTTCTTCACCTCCCTTGACCCCAGCATGATCCTGTACGCCATTATCGCTTCTCCCGTGCAGATGACAAGGCCAATCACCATGAAGAGAGGATGTGCCGTGTAAACGAGCTGAGGGGTAGAGCTCCTATGCCAGGACCAGGAGACGCCACCCCGGAAGTGCAGCACCCAGACGAGCGTGAGCGTCAGCACGGCGGCGGCCAGCAGCTGCGCGACCACCACCACCGGCAGCGCGGTGAGCCGGAAGCTGGCGCTGCTCTTCACCGGCATGACTATGCCTCTCTACTCTTCTTCCCCGACCCGCCGCCCGCCGGCTGACACCCACGTCGAGCTCGCCGCCGGCACCACCACCAATCACCACCAGCAACCACGGAGAGATGGCAATGGCATACAAATGATACAATGCTGCAGTACACGGGTTATAAGGGCTTTGTTCTGGTGATGCAACCAAGGAGTGCTCAAGTAAATAAGAACCGGGTCAATGCAATCGTAAATTTATTTGATAGTTTTCAATCCTGCTAAGCTAGCTATTGGAGGAGATGAATTAGGGTGCGACAAAGCCAAGGAAAGGATGATAAAACCGGAGGAAAGGTCTAAGTTTTGGACTGTTTCGGATTTGTCCGGACGGCAGAGGAAACAGCTTAGATTGAAATCATCCCAGCTGGGACAGATTTAGCTGGAGTTACTACAAATTGCCCATTCATCAGGGATGCTGGAGTAAAAAACAAGGGACGTTATTATGATTTTATATTCGTATCAACCTGCGCGTCGCCGGCTTGCTTCAAGCACATACTAATAGCTTGTCCGTTCCTGCTGGTCCATATGTTGTGTTGTTGTGTTGTCGGTCCCCCTCGCAAGCTTGAAAAGTACACCACACCGGGAAGGCAAATCAATCCATCAGCTCAAATGCGGCCGTCCGTCTGGACTACTTTGCTTGTCATTGCAAGAATTTCTGCTTGTTTGCGCCGAGCAGGTTCTTCTCATCTCCAGCCAAACTGAAACTGAAATTGGTCCACAACCACCTCAAGCCCCACTTCTCTTCTTGTAGTATGTACGTCCAAGACCAACATAGCCGTCCTATCTTGTCCTATGTCCTGGCATCGACCTTGGTAACCACTGGGATCTCAGATGACAACCATAGAAACCAGCATCCAGGCTGCTTGCAAAATGGAAGAGAGAACCAGCATCCTCCCAAACAGCAGGAATTCAGATATAGACCAAGCCTGCTCTAGAGCCAGTGAGAGTTGTTTTTCTCCCGGCATGTTTTCAAAATGAAAATGCCCATGCATGTATATCTATGAGATGATAGGTTCTGTTAAAGCATGCTAAAAAGCAAGCATTGCAATGTCAGGCATAATCTGTCCAGCTGACACCTTGCTCAATTCTGGTCACTAGATATGGAAATCCTGTGATGTTTCGAAACACTGACGACATGAAGCAACTTTGTTCCATGAGGCACCCATCCAACAAAATGCCATCTCTAGGTACAGGCACCTGAGGCTTACAACCCATTGTCACTAGAGGCTTGGTTTCATAATCAATCGTCTGGTGTTGTGAATACCAACACCTTCCCATCACCATCCCATCCACCGGTAGAGCCAAGTGCACATCTTCTGAATAGACGCCACCTTGTCCATCCAAGACTGTCCAGGGCTGCACAGACCAAGCAAATGTACAGTTACAGCAGTGCATTCTTTACACTTCTCTTCTTGAACCATTCGACGAATTCGGCCTCCTAGGCATTCCAAAAGGCAAATTATCTCTAGACCTATCACCAGGACGTCCCAGATCATCCAAATTTCTGTAACTGCCATTTCTCGGAACAGAGTTAGAACGTTCATCCTCATCAGGCCTCATGCTAACCCTGGAATCTGGAAGCATTTCCAAATGCCTCGGTCTTGGTCCACCAGTCCTCATGTTCCTTATGTTATTTGAAGTGTTCCTTCCTGGAGTGTTAGAGATCTTCATGGCAAGGAAGTCCTTGGGAATGGTATCAAGATCCATAAAACATTTCCTGGCCTTTGCATCTGCTATCAGTAAAGCCCAGTCCTCAGACTGCATAAGAGCACCGGCATTACCAACAACCCATAGAGCTCTCCTAGCTCTAGTAAGAGCAACATTCATACGGCGTATATCTGCCACGAAACCCACACCATGATTTGAGGCACGGACACATGACATAATAATCACATCACGCTCCTGTCCTTGAAAAGCATCAACTGTGTTTATGTAAATGTCCTTCCCATCCTCAGTACTCATAACCTCCTCGAATTCCCGCTGAAGACATTTCAACTGCAACTTATATGGTGTGATTATACCAACAGAAGCTTTCTTGCCACCATTAGCTCTCAAGAACTTCTGAAGATTCTCATACAAACGCAAAACAAACTGTGCTTCATGAACATTCTGGTACGAAGATGACCCACCTCTATGAGATTCACGACCATGTGAGATGTCATAGAATATGTAAGGTGCCATTAATGCATCTCTATAATATGCCTCGTCAGGCAATTTGACAACACTTTCACTATCTGTAAGGCGCCCTTGATAGAAGTGTCTTGATGGAAATTCACGGATCTGGGGATGCATCCGATACTGCACCGATAACAAAATGGTAGGGCAACCAGACAACTGGAACCTCTCAAAGAGACTCCTGCTGTACATTAAAGTCCCAGCTGCTTTGCTGATAACAGTTGCAGGGAGCTGTTGTGGATCACCAACCAAGACACACCTAGCTGCACCGAGCGAAAGTGGAGGGAGGACTGCTACTTCACTAGCCTGAGCAGCTTCATCAATTACCACCATATCAAAGCCATGACTAAGGCGGGAAAATAACTTGCGACCACTGCTTGAAACTGTTGTAAAAACAATTTCTGCTTCATTGGCGAAACTTGCTTCTAGACTAGCCCTAGCATCTTCCATATTGAAGTTGCTGCCAACACGGAACCTGCTTTCTAATATCAGCAGGCGTGACATCTCCACCAATACTTTATCCCTGCTTTCTACTGAAGCAGCAAGTTTCTGAAGTAGAAAATCACGACTACGATCTCTTTGAGCGAGCACATCAGGGTCTACTCCAACTGAACCCTGCGATCTGCCAGCCGCTGCAACCATAGTAAGTTCCCTTTGTAGAAGGGCTATCTCCTGTGATAATTGCTGCTCACGGCATTTTAGCTGTTGCAGCCACCCAATCACTTCATCACGGCCCTTCATTAAAAGCTGGTCAGTCCTTCGCTCAACTGAAACAGCTTGAGCAGCACGAGATTGTGAATCAACTCCAACACGGGCAACATCAGGACGATAGACCTTCATTTCACCATCTATAAAACCACGATCAAGAACGCGAGCAAGCAGCTCATCTGTGGCGGCGTTTGATGGAGCACATACAAGCATCCGTGGTTTGGGGCAAAGCTTGGGAAGAGTGCGGAAAAGGTTCTGATCCATACTCTGTAAAACTTCATCAATGGACCCTGCAGCAACAGTCTCCGAGCTGTTGCTTGTGTTACCGCTAACTTGCTTGTAACTTTCAGGAGCAAGCTTCTTGAGCAGAGCAGCATAGTAATGTTGATACTGAACAAGATGGATAACATTTAGCATCCCCCATACCGTATGGGTTTTTCCTGTCCCAGGCGGCCCTTGCACTAATGTGAAAGGCCAGGGTTCTTGTTTCTTCACAGCTCCGTTGCTTGTGCCAGCAGCTGTATGCATTGCAGCCCAATGAATCGCTGATAGCTGAGGCCCGTTGAAAGTACGATGCAGATGATCAGCAAAATTTGGAGTGAAACAATCAGGCATAGCAGGTGGCTGCTCTTCATACTTGGGGAAGTGCTCTGGACTTGGCTGAAGAATAGCATTTTGCATCTGAACATTGAGTCTGCGGAATGCATGCAAGGCAACATATTCCCTTTGTGTTGTTGCTAGGGAACCAAGACTAGTCAGATACCAGGTGCTCCGAGGTTGGAGTTTCCTCAAAACATTGGTCTCACTGCTAGAATCAAATGAATCCCCAAGATAGAAGTGAATGATTGCCCCAATGGGATCGCGTGTATCAATAGGCGTATGGCGTCTGACTGTACCAACAAGCCGTCCACACTCTGACTCAGTGTCTTCATTTGAACCAACATTCCGCCTATTAGATCTACTTGATTGGGAAGCTGAACCAGGCCTAGGAAAGGACAAAACTGCAACTTCACCTTCTTTGAAAGTCCATTTATACTCGTGCATTGGTAGAACAACAACATCATACCATCCTCTTTCACGCCTCTCCACTGTTTTCACCCGCACCATAACATGTGCATCCCTTGATACAGACTCAAGACTCTCCTCATAGGAACTATATAACTGAGCTCGACATTCCTCAAAGAGCAAAGGCTCGAAAACTCTAATGTACTCCTCAGCGGATTCAAAACTTTTAGGAACACATTGAAGTTCTGCCTCCTCTGGATTGTGCCAGAACTTGTCACTTGTCACCTCCCGTATAAGTCGTTCAACAGAAGTGTCTTGGTATTGCATGTTATTTGCTGGAGTTTGTTTTTTGGAAACAAGAGACCTCTTGTTGACTGGTTTCTGATCTACAGTATTCTGTCCTGTTACAACCGATCTCTGAGAAGAAATTTGTCTGCCCTTTAACTGTCTTGGCATTGGTTGTTGATAACCATCTGCAGGGGCTTCTTCAGCATTCATTTTCTTTGGCCGGCCTTGAGATCCCGTCTCAGCATCACCATTGGATTCAGAAATTTGATCGATTGGATCTGCAGAATTACTTCGTTCCGAACCAAGCATTTCAGATTGCCTCTGATCCCTGATGGTTGGCTGACTTTGTCTTTCTGCAGCTCTTTCAGCAATACCACCACCACTGCGAAAAGCTTCCTTCACAGTACGTGTGACAATTGGTGCTGGAAAGGATGACTGTCTTCTGGGTGTTGATGTCTTCATTGTGCCAGCTTGCTTTGCATCCTCAACATTAATGAACACAGTTTGCCTGGCTCTCTTTTTACCTAGCATTGCCTCTTTGTGTTCATCCAACTTAGGTCTCTTTGAAGGGTTACTTGCAAACTTCAACGCATAATTGGCTTCTACACCTCTAACATCCTTTGACTTGTTGGACAGATCTGAATCATCCCCAAGCTGATTTCCTTTGTTTTCTAAATTTTTCGTGCTCTCAAGTCCTGTGGGACCACGTACCACTGGATCCTTAGGCACATCCATCATTTCGGTGTCACTGGGCTCAGCGGCGGCCTCATCTTTAATCATGTTACCAGATTTGACAGCAGTAGGTTCACTTTCTTGGGAATCCCTTTTCACTTGTGTAGTTGCAGTACCAGCCAACTCTTCTTTGTTGCTAACACTACTCCCTGCAGTGTCAGAAGCAACATCTGCATCAGACCACTCTCCTTCCTCTCTTTCCACTGCCTGAGAAACCTGATTGGAGGACCCAATCATTTTAGCAACACCATCAGAGCTATGGTTGATTAACATAGATGTAGAGGCTATGCTAGCATTCAAATTATCTTCTGCCTTGATTGGCTCCTTTGTAATTTGTGAATCTTTGCTCCTCACAAAAGGCTGAAAACCTGAACCGGACGGTGCGTGCTTAAAGGCATTATTGTTTAATATCCCCTGCGACTGTGTTACTTCCTGTTGCGGAAATAAAGAGGGCCCTGCTGTGGGAACAGGAAGGGTCTTCTGAGGTTGTGACACAACAACTGCGGCTTCTTCTTCTTCAGCTTCTGTTGGGAGCTCATTAAGGTCAAATAACATCCTTCCACGAGACCCCATGTCATGGGTAAATGCATATAGTTTGAACCTTTGGAAACTATTGGACTCGATAACAATCTTCTGGGGTAACAGAACCTACTTTTTGAAAGCTATAATTGACCTTTTGTAGAAAATATCTGAAAATCATTCTTCGCTGGATTCCTTTTGTGCTGTGACCCTGCCCACTCCGTCCTCTTGTTGTCCACTTCCTACCCATCTCAAGAATTTGGGTTCTAGCAATACAGGATCTCAGCATCCAGGCAGACCCAGGCGATCGGCGGCGGCGCGGCCAGATCCGGCCCTGTGCCTCGTCTCCTCCTCCTCCTCCTCCCGCGGCGGCGTCGGCGGCTTTGACTAGGGTTTCCCACCGCGCGCTCCTCCTCCTCCTCGTGTGATGCGGTGCGGTGCGATGCGATGCGTTTGATTTTTTTTTTCTCAAGTTTTTTTTCTTGCCCCCCTTTTTTGGTCTGGGTGGTGGTGTGTGTCTCCTCCTCGCCTCCTCCCACGAGCGAGCGAGCGGTCGGTGAGCGTGACGACTGCTTCCTTCTTCGAGAAATCGAGAGAGGAGGAGAGGGGGGGTGG

Coding Potentia
Explanation CPC Score
noncoding -1.03816
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa10LNT0059900.1 10 1193113 A G
Osa10LNT0059900.1 10 1198445 T C
Osa10LNT0059900.1 10 1196878 T C
Osa10LNT0059900.1 10 1190416 G A
Osa10LNT0059900.1 10 1190441 A C
Osa10LNT0059900.1 10 1190841 C G
Osa10LNT0059900.1 10 1190876 G A
Osa10LNT0059900.1 10 1190896 A G
Osa10LNT0059900.1 10 1190944 A G
Osa10LNT0059900.1 10 1190953 T C
Osa10LNT0059900.1 10 1190987 A G
Osa10LNT0059900.1 10 1191030 A T
Osa10LNT0059900.1 10 1191032 A G
Osa10LNT0059900.1 10 1191230 T C
Osa10LNT0059900.1 10 1191344 G T
Osa10LNT0059900.1 10 1192067 A G
Osa10LNT0059900.1 10 1192203 G A
Osa10LNT0059900.1 10 1192295 C T
Osa10LNT0059900.1 10 1192764 A C
Osa10LNT0059900.1 10 1197134 T C
Osa10LNT0059900.1 10 1197168 G C
Osa10LNT0059900.1 10 1197211 G A
Osa10LNT0059900.1 10 1197237 A G
Osa10LNT0059900.1 10 1197395 T G
Osa10LNT0059900.1 10 1197776 T C
Osa10LNT0059900.1 10 1198232 T C
Osa10LNT0059900.1 10 1198815 T C
Osa10LNT0059900.1 10 1198854 T A
Osa10LNT0059900.1 10 1200034 A C
Osa10LNT0059900.1 10 1190851 T C
Osa10LNT0059900.1 10 1192765 A G
Osa10LNT0059900.1 10 1192979 A C
Osa10LNT0059900.1 10 1192980 T A
Osa10LNT0059900.1 10 1193051 A C
Osa10LNT0059900.1 10 1193327 T C
Osa10LNT0059900.1 10 1193813 G T
Osa10LNT0059900.1 10 1194318 T C
Osa10LNT0059900.1 10 1196514 G A
Osa10LNT0059900.1 10 1196650 C T
Osa10LNT0059900.1 10 1196705 G C
Osa10LNT0059900.1 10 1197087 C A
Osa10LNT0059900.1 10 1197116 G T
Osa10LNT0059900.1 10 1200101 A G
Osa10LNT0059900.1 10 1200638 T C
Osa10LNT0059900.1 10 1200794 G A
Osa10LNT0059900.1 10 1200904 G C
Osa10LNT0059900.1 10 1200905 T C
Osa10LNT0059900.1 10 1201104 T C
Osa10LNT0059900.1 10 1201163 C G
Osa10LNT0059900.1 10 1201171 A G
Osa10LNT0059900.1 10 1201740 C A
Osa10LNT0059900.1 10 1202044 A T
Osa10LNT0059900.1 10 1202155 A G
Osa10LNT0059900.1 10 1194526 A G
Osa10LNT0059900.1 10 1194784 G A
Osa10LNT0059900.1 10 1195696 C T
Osa10LNT0059900.1 10 1195960 T A
Osa10LNT0059900.1 10 1193572 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
Osa10LNT0059900.1 osa-miR5530 Translation 4.0 19.672 1 21
Osa10LNT0059900.1 osa-miR5534a Cleavage 5.0 21.048 1 21
Osa10LNT0059900.1 osa-miR5805 Cleavage 5.0 15.818 1 24
Osa10LNT0059900.1 osa-miR166c-5p Cleavage 4.5 16.051 1 20
Osa10LNT0059900.1 osa-miR169a Cleavage 5.0 10.596 1 21
Osa10LNT0059900.1 osa-miR166l-5p Cleavage 3.0 16.051 1 21
Osa10LNT0059900.1 osa-miR169b Cleavage 5.0 10.596 1 21
Osa10LNT0059900.1 osa-miR169c Cleavage 5.0 10.596 1 21
Osa10LNT0059900.1 osa-miR169n Cleavage 5.0 10.596 1 21
Osa10LNT0059900.1 osa-miR169o Cleavage 5.0 10.596 1 21
Osa10LNT0059900.1 osa-miR419 Cleavage 4.0 17.721 1 21
Osa10LNT0059900.1 osa-miR444a-3p.2 Cleavage 3.0 19.741 1 21
Osa10LNT0059900.1 osa-miR169r-5p Cleavage 4.5 10.596 1 21
Osa10LNT0059900.1 osa-miR444b.2 Cleavage 3.5 19.741 1 21
Osa10LNT0059900.1 osa-miR444c.2 Cleavage 3.5 19.741 1 21
Osa10LNT0059900.1 osa-miR444d.2 Cleavage 3.0 19.741 1 21
Osa10LNT0059900.1 osa-miR444e Cleavage 3.0 19.741 1 21
Osa10LNT0059900.1 osa-miR444f Cleavage 3.5 19.741 1 21
Osa10LNT0059900.1 osa-miR1442 Cleavage 4.5 20.035 1 20
Osa10LNT0059900.1 osa-miR1439 Cleavage 4.5 15.561 1 21
Osa10LNT0059900.1 osa-miR1858a Cleavage 2.5 14.557 1 21
Osa10LNT0059900.1 osa-miR1858b Cleavage 2.5 14.557 1 21
Osa10LNT0059900.1 osa-miR1871 Cleavage 4.5 17.733 1 24
Osa10LNT0059900.1 osa-miR1879 Cleavage 4.5 18.209 1 24
Osa10LNT0059900.1 osa-miR1879 Cleavage 4.5 14.319 1 24
Osa10LNT0059900.1 osa-miR1320-5p Translation 4.0 15.353 1 21
Osa10LNT0059900.1 osa-miR1846c-3p Translation 4.0 16.048 1 21
Osa10LNT0059900.1 osa-miR2091-3p Cleavage 4.0 20.402 1 22
Osa10LNT0059900.1 osa-miR2099-3p Cleavage 4.5 17.7 1 20
Osa10LNT0059900.1 osa-miR2122 Translation 4.5 12.189 1 22
Osa10LNT0059900.1 osa-miR2275a Cleavage 4.5 16.3 1 22
Osa10LNT0059900.1 osa-miR2275b Cleavage 4.5 16.3 1 22
Osa10LNT0059900.1 osa-miR2863a Cleavage 4.5 14.287 1 21
Osa10LNT0059900.1 osa-miR2920 Cleavage 3.5 16.748 1 23
Osa10LNT0059900.1 osa-miR2926 Cleavage 4.0 19.412 1 20
Osa10LNT0059900.1 osa-miR3979-3p Cleavage 4.5 18.363 1 20
Osa10LNT0059900.1 osa-miR3980a-3p Cleavage 5.0 24.413 1 21
Osa10LNT0059900.1 osa-miR3980b-3p Cleavage 5.0 24.413 1 21
Osa10LNT0059900.1 osa-miR5144-5p Cleavage 4.5 20.033 1 21
Osa10LNT0059900.1 osa-miR5487 Cleavage 4.0 12.064 1 21
Osa10LNT0059900.1 osa-miR5491 Cleavage 4.0 12.768 1 21
Osa10LNT0059900.1 osa-miR5509 Translation 4.5 13.774 1 21
Osa10LNT0059900.1 osa-miR2275c Cleavage 4.0 10.245 1 23
Osa10LNT0059900.1 osa-miR2275c Cleavage 4.5 18.963 1 23
Osa10LNT0059900.1 osa-miR2275c Translation 5.0 14.282 1 23
Osa10LNT0059900.1 osa-miR2275d Translation 4.5 14.911 1 22
Osa10LNT0059900.1 osa-miR168a-5p Cleavage 3.5 18.925 1 21
Osa10LNT0059900.1 osa-miR168b Cleavage 5.0 18.925 1 21
Osa10LNT0059900.1 osa-miR444b.2 Cleavage 4.0 23.095 1 21
Osa10LNT0059900.1 osa-miR444c.2 Cleavage 4.0 23.095 1 21
Osa10LNT0059900.1 osa-miR444f Cleavage 5.0 23.095 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa10LNT0059900.1 10 hwd1 Physiological trait Lethality nan nan
Osa10LNT0059900.1 10 nan Physiological trait Sterility C701 C16
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