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

>Osa01LNT0058300.1

AACAGTAACGAGTATGGATCCCGATGGAAATTACTAACTCTAAAAGGTACTAACGGATTAGATTACACGAAGAACATACATAGAGTGAAAGAAACGAAATGGCATTGACAACAAACAGGAACCAATTAAAATTGACATGAAATACCCTGGGTAGCAAATAAAATCATGACTTTAGTGAAAATGTTATACAAACCTAATCCCTCATATCTCCCCAACAGTGATGGTACTGCAAGACAATATATCACCAGGAAAGGGTGCTTTCTCCGTATACGAAAATTTCGTTTTCCAGGTCCCTGATCCATTGGCATACTCTATTGCATACCTTGATTGCTTGACTCTTGTCAGCCAGTGGATTAAAAGCGGCGTACAACTCAAAATCCTGGGTTATCCAGCAGAACAGAACATAATCTTCATCTCTTCTGAATTGGGTTTTATGTGGACCAGTTGCTTTATCATGCATGGAAGCATACAATTTTTGATAAGCTTTGTACAATCTTTTCTGTTGCTTTGGATTGCTTATGATTAAGGGGAACTCAGATGATACATATTGATCAAGGTAAATGCTTTTATATATAAAATGCCAAAGTCCAGCTGGTCCACCAATTGCCATTTCAGAAGATAATAACTGAAAGTGCAGATCTTGAGAGAACTGTGGAGGTGGTGATACAGATTGAGAAGATGGATCAGCAGGGAGATCTTCAATGCGCAGTGCGCTCTCACGCAGAGACCTTTGGACTTCCACAAGGACATTTGCCTTCAAGAGAACATTCTGAATGCGGGACCTGGAATCTTTCAGATCATAAAAGGCGTCTGATCTTGCAGTAAGAAGTGTCAAGTATGTATTTTCATCAAAAAAATGAACATAAGCATATAAGAAAGCCATAGAATTGTATCTTGGAAGGCATATGGGTGAAAAAGACTCCGAAGTCCTAAAAGATTCAGAGGACAATATGAAATTTGAAAGTAGAAAAATATCATCAGGATGCAAAGTTGCCTTTTGTGCTCCCACTAGACTAATAACCTTGTGCTCACACATCAACAGTGCAAACAAAACTCCTGAATCAGCAATGTCTTGTAAAACTGCACTAGCCGCCTGCCTTGTGGATTGGGCGAGGGGAAGGCATGTGTACGCATGAAGAAATGTAGCAGGATTCCAGCTGAATGCATGTATAAGTGATAGGAAAACTGCATCTGTGCCACCTAGCAATGGTGCCATATCAAATTTAGGGTTCTTCTCAAAGCATCTGTTGACAGACTTGGTCAAAATCAGCAGCATCTGACCATACATGAGCTCTAGTTGTCCCCTCAATCCTTCATATGACTCTTCAGTGCAACTTATACAAACTAAGTATATTGGACCCTTGACAAGGAAAACTATCTGATGTTTGGCAGCCCTTACAAATTTGATATGGTCACCACTGTTCTCAACGAAAGAAATGATTGCTTGCAACGTGGCGGAAAACCCAGCAAGCTTATGCTCATCTCCATACCTAGAATAAATTGGCTTGCCAGAATTGCTCAAGATGAAGAAGTGCTTTTTCCGTTTGCGCCATGAAGCAGAAGTATCGTCCTCGTGGAGATGCTTCTTGTCGCGGGGCCAATCGTCGTCGTCGGGTTGGGGTTGGGGATCGTCGTTGGCGGCGGCGCTGGAGGCGAGGCTGGTGCCCCTCTCGGCGGCGTAGCCGCTGCTGCTGGGGCTGGGTGGAGCCACGTCGGCGTCTTCGAGGTCGTCCTTCCAGGCGGAGGCGGAGGTGCTGATGCTCCCTACCCTGGAGACGGCAGTGAGGTAGCCCTCGTCGTCGTCGTCGTCGTAGTCGTCGTGGATCTCGAAGTCGGGAGGGAGGTGAGAGGTGCGGAGGGAGAGGGAGGCGAGCCTCTTCTCCGGCGGCGGGGAGTCGGGGGGACCAGGGGGGCTAGGGTTATTGGTGGGAGGATCCATATCCATGGGGGGCCTTCCCGACGCGATGCCGATGCCTCTTCTTCTTCTTCCTTGCTCGCTCGCTCCCCTCCCCTGTAGAGAATGTACTCTATTCGATTCGATCGTGTCTTTGCTGGGTTGGGTCGCCTCCGTCGGTCGGATTCGATGGAACGAGACCGGTTGTTGGCTCCCTTTGGCTACACTACACACAGTTTCTCTCCCTTCCCTGGATCTCTTCTCCTCTACATACAGTCCTTCATTCATTCACTTGGGTTCAAATCTACATATACATACATGTTATACCAGCAATTCCTTACTATTAGTAAATCCCTCGTGCCTTCGTTTCAGCACGCACGCGACTGACACCCACCAAAAACCGCATTTCGTCTTTGGCTATCGCATTTTGCTAGCACATGATGTGTTTCTAACTCCCATCTCTCTTTCCCCCTACACTACAGGGATGTACTACACCAGGATAGATATAGATATTAACCACACAAGAGAGGGGCAAAACACACACAACCGGAAATATAACCAACTCTTCCGCCGCCCCATCATTCCATTCAACAACCCAGAGCTTTGCTCCATTACCAAACTGAGTGTATCAACAAATTAATTACCAGTGCGCCTGCTTAAACATGATCAAACAAGAATACCTACCCACTCCCACTTCCAGCACACCTATGCCCAAAATTACTTCTACTACTTCCACCAAAACAAATATAATATCCCTTCCCTAATTACACTTCAATGCAGTACCAAACTACACAACACACCCCCCCCCCCCCACCAAGAATTCCATTTAAGTGTCAAAAATAAAATGCCAAAACTACATCACACTATCACAATGAACAAATCCGATCTAATAACGATCAGTTACAAAAATGAATGAATAGGCAGGCAGCGCAGCACATGGAATGTTGACCAATTCCATGTGCTATATGCTATTCCGGACTCATCAAACTCTCAAGTCAATGTTGGAGTGGATTCAATGGGACAGCGCATCTCAGCTTCACCTCCTTTATGCCGCATGCTATATGCTATTCCGGACTCTTCATCTCAAAGCTTTATTACAGCAAAGCAAATTAAAATATCATGTGTCCAGACTCCAGAGCCTGTGCCAATGCCTATGCCTATCCTGTCAGATCGCAACACAAATACTTGTACCATCTCATACTGTCTCCAAGCTGCCTTCCACGTTTCCAGTCACTAGTTAGTGAAGCAGAGTGAGCAATGTACAAATGCTACCAGGGGTTCTTATATTAGTCTACGTTGACGGAATCCTTTGGTGAAATGAGGTTGCATCAACTTGACATACAACCCATTCTTTTGCACCAGTGAATCATGCGTTCCCTGCTCAACTATCTTTCCACCATTCAGAACAACAATGTTATCCACATGCTTCATCATTGCCGCCCTATGTGCAATGAGAACTGTCGTCTTATTCCCCATAATCAATGTGTCGAGGGCCTCCTGCACCACTCTACTGGACTCGGATTCAATTGCAGAACTGGCTTCGTCAAGCAGCAAAATGGGTGCATTCTTCAGCACTACACGGGCAATGGCGATTCGCTGCTTCTGCCCAGGAGTTAAATCCACTCCCCTCATTCCCACATGTGTGTCATAGCCATGTGGCAAACTGCTAATGAAATGGTGAGCGTTCGCAATCCTAGCCGCCTCTTTCATCTCAGACTCTGTTGCATTGTGCCTTGCATAGATTATGTTCTCCCTTATGGTTGTGGAGAATATAACTGGGTCTTGAGGAACTAAACCCATGTGGCTCCGCAACCATCTCAAGTTGAACAGCTTCAGATCACGGCCATCCAATAAAACTTGCCCGGCGGTTGGATCATAGAATCTCTCTATCAAAGAAATTATCGTGCTCTTCCCTGATCCAGATACACCTACCACAGCAACAGTTTGTCCTCCATTGACTCTAAGGCTGAAATTACTCAAAACCATCGTCTCAGGGCGTGTAGGATAGCAAAAATCAACATTCCTGAATTCAATGCTACCATAGACATTGGGGGGTTTTAGCCCACTTGCATCATCTGGATCAATCTTGGGTGCACGATCAATAATTTCAAATACCGACGTCAGAGATTTTCGACGCTTGAGAATATATGGCGCAAGGCCAAATGGCTCCACCAGTGCAAAAGTCGCAAAAGAGAAGACAATGTACTCTTTAAGTGCTGTTACCAGACTAAGGTGCCCATTCTTAACAGCTACGGCTGTATACCACAGCAGAAGTGCATTGCAGGCGAAAAGAAGGAACTGAGATAAGCCAAAGGCAAAACCAATACCCATTCCATGAACCAAGCTTTTCCAAAGAATATTCCCAAGCTGCAGTCTGTAAAGTTCCATTATTTTGTTACCAGCACAAAATGCCACAACAGTATAGATATTCCTGACTGCATCCTCAAGAACCAAAGAAGCCTTCCTGTGCATCTCCTGAATTCCTCTTGAAAAGCCAGAAAGCCACATTTTCTGCGCAACTGCAGAAATTACAAGGATGGGCAAAGTTGCCAGGGCAACCAGAGCAACACGCCATTCTAGCAACATGCCAAGAAGAAGTGCCACAAAAATGGCTGCTGTATCCTGAATGAATATAGAAAGCCTGTTGCTGAAAGCAGCACGAACAAAAGTAGCATCATTTGCGAGTCGCATTGATAATATGTCTGCACTGTTTTCTTCTTCATCAAACCACCCTACTTCATTGCGCAAAATTGCTGAAAACATCATCCTTCTAACACGTTCAGTCATCTTCTCTCCCATTATACCAAAATAGAAGTGCTGTAAGAAGTTAGCTAGCACGGTTATTATACCCATGCCAACAATGAATGAGCAGTACTTATTGACTTCATCATGCACATCACGTACACCAATTCTATAGTATGCCACCACTATTAAAGATATTGTATAAGCAAGAAGAGGATTAAATGAACCAAAGCAAGCAGCACCAGCACTCCCTAATAGAGCATAAAAATACTCAGCAAGACTAAGTTCTACAAGCCTCCAAAACGATGGAGCTTTTGTTTTCTGCTTCTTTGACTCCTCAGCATGAAAATTGTCAAACATATCAAGAGGACGACTGAAAGTTTTTGAGTGCGAGCGCTCATTCTTTGGATCAGAAGTCAATAGTGGTGATATTGGTGATTCTGGATCTGAAGTATTTGAAGATTGTCGGTGTAGTGGGACATCAATTTTGGGAAGATCGGGCAATTTCATTTCAAAACTGTCCTGCCTTTTGATGGATGGAGCTCTCTCAGAAGCAACTGTAGGTAACCTAGTTTCTGCCATTTGTTCGGAAGGAGGGCTTTGAATATTTGGTGATTCGTGTGAGTTATGATTTGCATCTGAATTACGGAATGCAAGAAAACCGTGTGTTTTCTGAAGTGACGGCGACTTTGACATATTAGGAGATGATGACTCTTGGAAGCTGTGACTTGCTGAAGAATCCCTTTCAATTTGGAAGGAGCTAGGCTCTTTGTAGTTTCTTATCGGAGTCCGCTTTGGAAGTTTTGCTGCTTCTTCACACCTAAGTAGTTCTGCATAAAGGCCATCCAGATTTAACAACTCATCATGTGTTCCCATCTCAACAAGCTGACCTTCCTCCATTACAGCTATATAATCAGCATTCCTGATAAGACTGAGGCGTCTAGCTATGATGATGGTAGACCTACCAAGCATCAGAATATCTAGTGCTTCCTGAACAGCTTTCTCAGCCTCAAAATCAAGAGCACCAGTAACCTCATCCAGTAAAAGAATTGATGGATTTGAAAGCACAGCACGAGCAATGGAGAGCTTTATCTTTTGTTCTTCTGTCAGTGAAAGGCCAGCCCGACCAACCTGAGTATCATATCCTTTTTCAAGTGAACTGATGAAAGTATGTGCATGAGCTGTCTTTGCTGCCTCCTCAATCTGGTCAGTTGTGGCAGATCTTCCATATGCAATATTTTCCCTGATGCTCAAGCTCAATAAAGCCGGTTCCTGGGTCACAAGTCCTATCTGGCTTCTTAACCACTCTAACTTCAGGTTCTTTATATTCTCTCCATCCAAAAGCACTTCACCTAAAGTTGGATCATAGAAACGTTCCATGAGAGGAATAATGCTGCTTTTCCCTGAACCATTTCTGCCAACAAGAGCGACAGTCTTTCTAGCAGGTACAGTAAGGTAGAAACCACTTAAAATGGGGATTTCTGGGCGGGATAGATAACTGAAGTAGACATTGCGGAACTCAATGTTGCCTTGCACTGAAGGTAAGGTACGGCCATCCTGGTTTACAACAGAGGTTGAACGGCTAATCATTTCATAGAGCCTGTATGCAGCTATACGTCCTTGTTCAAAAGAATAGAAGTTTGTTGCTGCTTGATTAAGTCCCAGGCCACTCAGGATAATAGAAAACAGGGCTACTACAACTTCACCACCATTAGCTTTTCCATGAGATATAAGGAACCTCCCAACCCAAAGTTGTAAGGCACAAGAACATATGGCAAGGCCATATGTAAATCCAAGACCAAGACCTTGCACCAGACTTATCAGGATTCCATAGCGCAGTGTTGCTTGAAGTGAAGTAGCATAAGAATATTTTGCGAGGGTCTCATTTGTGAATGAGTACAAAGTCCTAATGTATAAGATTGCCTGTTCGGCAACGCTTGCTGCTTCACCATACGCATCCTGAATGTTTTCTGCAAGCCTGTGGAGAAAAATATTTGATATTCCTCCTGCAGCAACAATGAACGGACCAGTAGCCAATGTCAAAAGAGCTATTTGCCAACAGTTGACCAAACCGATGATAAGACCACCAAAAAAGGTAGCCATGTTGTGAATGTAGTTCCCAACTTTCTCACTCAGCGCAGACTGGATGAGTAAGACATCACTCAGCACTTGACTGACAATATCACCATTGTTCCCATAGGTATCAAAGAAACTCATGTCTTGATTTAACAACACTTGTACATACTTTGATCTTATCACTGCTGTCTGCCTTTCCCCAGTAAGAATCCAGCATGAAACCTCTATCCATCCCGCAAAGAAAACGCCAATGGCAATATATAGGAAGTGTAAAGCATGCTGGTTGATGTGGTGGAAAAGGTCGTGGTTGTGGCGGCCATGAAGCGAGTGGATGGCGGTGCCGAAGAGGTGGAGGTAGACGACGAGGGCCACCCCGTGGGCGGCGGCGGCAAGGGCGCCGGCGGACATGAGCGCCCAGTCGAGGCGGTCGGCGCAGGCGAAGAGGCGCTTGAAGGGGACGGCGGCGGGGGGCGGATCGGGCTCGTCGTCCCCATCGTCGAGGGCGGCGGCGGCGTCATCCTCCGGAGGCGGCGCGGCGTCCCCGGCGAGGTCAGCGGCGTAGGGAGAGGGGGATTCCGGCGGCTCGGAGGCCTCGGAGACGGGAGTGAGAGGCTGGACGTGCGGCGGGGACCAGCCGAAGAGGCCCCGCGAAACCATGAGCAGCGGCTAGTACTCGTCGGCGGCGGAGGCAGATTTGAATGGCATCCACACTACCTTAGTAGCTAGCTAGTCAAACAAGGTAGTCCAGTCTAGAAGAAGACCCAAGAAGAAGAAGAAGAAGAAGAATGCTTCATGGGCGGGCGGCGGGCGGCGAGGTGAATCGGTCAGTGGTGGCGGACCTCGATCGCCGGCCGACCCGGATCGGAGCCCAACACCAAGACCAAGAGGGGAATACCACTACTACTCGCCACACTAGCCTACTACT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.174052
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0058300.1 1 43120822 A T
Osa01LNT0058300.1 1 43124654 T C
Osa01LNT0058300.1 1 43128514 G C
Osa01LNT0058300.1 1 43121224 T C
Osa01LNT0058300.1 1 43121381 T C
Osa01LNT0058300.1 1 43121576 T A
Osa01LNT0058300.1 1 43121788 T C
Osa01LNT0058300.1 1 43122621 T C
Osa01LNT0058300.1 1 43123304 T C
Osa01LNT0058300.1 1 43124443 A C
Osa01LNT0058300.1 1 43124639 G T
Osa01LNT0058300.1 1 43125020 T G
Osa01LNT0058300.1 1 43125161 A G
Osa01LNT0058300.1 1 43125572 C T
Osa01LNT0058300.1 1 43125686 C T
Osa01LNT0058300.1 1 43132842 A T
Osa01LNT0058300.1 1 43133355 A G
Osa01LNT0058300.1 1 43133621 A C
Osa01LNT0058300.1 1 43134254 G T
Osa01LNT0058300.1 1 43125967 G A
Osa01LNT0058300.1 1 43126086 G A
Osa01LNT0058300.1 1 43127769 C T
Osa01LNT0058300.1 1 43127957 T C
Osa01LNT0058300.1 1 43130983 T C
Osa01LNT0058300.1 1 43131145 A G
Osa01LNT0058300.1 1 43131147 C T
Osa01LNT0058300.1 1 43132126 A G
Osa01LNT0058300.1 1 43134409 C T
Osa01LNT0058300.1 1 43128124 T A
Osa01LNT0058300.1 1 43128403 A G
Osa01LNT0058300.1 1 43128927 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
Osa01LNT0058300.1 osa-miR5536 Cleavage 5.0 8.852 1 22
Osa01LNT0058300.1 osa-miR5796 Translation 4.5 14.511 1 21
Osa01LNT0058300.1 osa-miR5796 Translation 5.0 18.427 1 21
Osa01LNT0058300.1 osa-miR5820 Translation 4.0 16.355 1 21
Osa01LNT0058300.1 osa-miR156a Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR156b-5p Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR156c-5p Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR156d Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR156e Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR156f-5p Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR156g-5p Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR156h-5p Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR156i Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR156j-5p Cleavage 4.0 12.59 1 20
Osa01LNT0058300.1 osa-miR169a Cleavage 5.0 10.382 1 21
Osa01LNT0058300.1 osa-miR396a-5p Translation 5.0 19.762 1 21
Osa01LNT0058300.1 osa-miR156k Cleavage 4.5 16.7 1 21
Osa01LNT0058300.1 osa-miR156l-5p Cleavage 3.5 12.59 1 21
Osa01LNT0058300.1 osa-miR169d Cleavage 3.0 10.382 1 21
Osa01LNT0058300.1 osa-miR169e Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR169f.1 Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR169g Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR169h Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR169i-5p.1 Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR169j Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR169k Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR169l Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR169m Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR413 Cleavage 5.0 21.52 1 21
Osa01LNT0058300.1 osa-miR416 Cleavage 4.5 14.311 1 21
Osa01LNT0058300.1 osa-miR816 Cleavage 4.0 14.615 1 20
Osa01LNT0058300.1 osa-miR169r-5p Cleavage 4.0 10.382 1 21
Osa01LNT0058300.1 osa-miR444d.3 Cleavage 4.0 11.612 1 21
Osa01LNT0058300.1 osa-miR2095-3p Cleavage 4.0 16.055 1 20
Osa01LNT0058300.1 osa-miR396f-5p Cleavage 3.5 13.564 1 22
Osa01LNT0058300.1 osa-miR2105 Cleavage 3.5 16.135 1 20
Osa01LNT0058300.1 osa-miR395x Cleavage 3.5 12.64 1 21
Osa01LNT0058300.1 osa-miR3979-3p Translation 5.0 8.353 1 20
Osa01LNT0058300.1 osa-miR5490 Cleavage 4.5 15.524 1 21
Osa01LNT0058300.1 osa-miR5490 Cleavage 5.0 6.522 1 21
Osa01LNT0058300.1 osa-miR5492 Translation 4.0 16.684 1 21
Osa01LNT0058300.1 osa-miR5492 Translation 4.0 23.931 1 21
Osa01LNT0058300.1 osa-miR5509 Translation 4.5 18.261 1 21
Osa01LNT0058300.1 osa-miR5517 Cleavage 5.0 22.309 1 21
Osa01LNT0058300.1 osa-miR396b-5p Translation 5.0 19.762 1 21
Osa01LNT0058300.1 osa-miR396c-5p Translation 5.0 19.762 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0058300.1 1 rrw1b Resistance or Tolerance Other soil stress tolerance C86 RG236
Osa01LNT0058300.1 1 nan Morphological trait Root RM1387 RM1067
Osa01LNT0058300.1 1 qRNd1 Resistance or Tolerance Other soil stress tolerance RG236 C86
Osa01LNT0058300.1 1 ph1 Morphological trait Dwarf RG236 C547
Osa01LNT0058300.1 1 nan Resistance or Tolerance Other soil stress tolerance RG810 RG331
Osa01LNT0058300.1 1 nan Resistance or Tolerance Other soil stress tolerance RG810 RG331
Osa01LNT0058300.1 1 fla1 Morphological trait Culm/leaf RG810 RG331
Osa01LNT0058300.1 1 qHID-1 Morphological trait Seed RG810 RG331
Osa01LNT0058300.1 1 qTGW-1 Morphological trait Seed RG810 RG331
Osa01LNT0058300.1 1 nan Physiological trait Eating quality RG331 RG810
Osa01LNT0058300.1 1 nan Resistance or Tolerance Drought tolerance RZ14 R117
Osa01LNT0058300.1 1 qPH1-1 Morphological trait Shoot/Seedling C86 RG236
Osa01LNT0058300.1 1 qBMS1-2 Physiological trait Source activity RZ801 RG331
Osa01LNT0058300.1 1 qHID1-2 Morphological trait Seed RZ801 RG331
Osa01LNT0058300.1 1 qTGW1-3 Morphological trait Seed RZ801 RG331
Osa01LNT0058300.1 1 nan Resistance or Tolerance Other soil stress tolerance RG810 RG331
Osa01LNT0058300.1 1 nan Resistance or Tolerance Other disease resistance RG109 RG236
Osa01LNT0058300.1 1 nan Resistance or Tolerance Drought tolerance RZ14 R117
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