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

>Osa04LNT0281100.1

GAGTGGTATATAAAGGAACTAATAAATTTCTAGTGGCATATAAGAGATTCTCTCTAATTTGTATGTCTTGACCGGAAAACCGTGTGAGATAACTCCCTAATTATTAAAACCGGTACAATCTATCTCCCCCCGTGGTTTTGAGCAGCGGTTTTATTTCGAGTCCCTAAAAAACCAACGTATTTTGACGCTATTATCTGCCCGTTTCTTGAGAAGTTTGATCCGAACCAAGCACCGGCGAGCAGCGGCGCGAAGCCGTCACCTGCCTTCGTCGACGACGGAGCTCAAGAACGGCGACGACATCTTCGGCGAGGAGGTGGCCCTCGGCGGCGGCGGCGCCGAGCTCCACTGCCCGTTGGCGGCGCTGCTGCTCGTGGACGAGGAGCCGGTGGTGGTGGTGGTGGTGCCGCCGCCCTTGATCTGCCACTCCGTGATGTAGCTGGGCTTCGCCGCCACCTCGCCCACCTCAGCGTCGCCGGTGAGCATCGCCACGACCCTCGACATGGACGGCCGCCGGTGAGGTGAGCCCTGGGTGCAGAGGAGGGCCACGTGGATGGCGCGGAGCACCTCCTCGCTGTTGAATTCTGTGAGGTTTGGGTCTACGATGTCAAGGGCGCGTTCGCTCTCGTACAGCCTCCAGACCCATTCGAAAATATAAATTTTGTCTTCTTCAAGCACATCATCATAGTTTGGCCGGCCAGCTAAAGTCTCCAATAAGACCACGCCAAATGCAAACACATCAACTTTCTCAGTCATATGTCCTCTCATGGCGTACTCAGGTGCAAGATAACCAAATGTACCAGCAACTTTTGTGCTAACATGAGTCATCTTGTCATCATAAAGTTTGGCTAGCCCGAAATCCGAGATCTTAGGATTGAGATTGGCGTCAAGTAAGACATTGCTGGCCTTGATGTCCCTGTGCACAACACGGATGCTTGACTCTTCATGAAGATAAGCCAGACCTCTTGCAATGCCCAAGCATATTTCAAAGCGTGCTGGCCACCCTATATGTAATTTCTCAGTTCCGAACAGTGCTTTATCAAGGCTCCCATTCTCCATATACTCATAAACCAGCAGTGGATTATTGCCTTCAAGGCAACAACCATACAACTTCACGAGATTACGGTGTTGCACTCGGGATATAGTTTCTATTTCAGTTGCGAATTGTTTTTTCCCTTGATGAGATGTTTGAGATAGCTGCTTCACTGCCACTATCCTTCCATCCATTAGCTTACCCTTATAAACTGCCCCATATCCTCCTTCACCAAGACGGTTGCTGGAACTAAAATTTTCAGTTGCGGACCTTAGTTCACCATAACTGAATATATTAGGTCTTCCAACAATACTGTACAGCTCTTGTTGCTCCAGTGATAGCTTTCTCCTTTTCTTTCTCCAAAGAAAGATTCCAACAAGTGCTACCAAACCTAAAATTGTCACACCAATTGCAACTGCAACAATTACAACTGTTTTACTAGTACTACTGTTTTGTTCTGCCACGTTACCAATTGTAGGGGTGAAATCTAACAAAAAAAGTTCACCTGTTAGAAAAAAAAATGCAATCTTACAATGGAATGCAACAGTTAACCCTAGAAAATACATCGTTTTCATACTGGAACCATGATGATTTGTAGTTAAGGGGAATACTTGGGCTTAAACTCAGAGCTGAGATAGTGGGCCCATAGTATCCTTGAGTAGGAATGCAGCAAGTTCCCTTGCCAGCCCAGAAGAGATGAATCTCAACGAAGTTTCTGGTGACAGAAACGATATAATCCTTCTTAACTGCAGTGTAAGATTTACCACCTGCTTCCTTCTTGATGTCAAAGTCCTTCTCCTTACGTTCACCCTGTACATATATATCGAAAACCCTTCTCCCTCGGCTTTTCCAAGACTCTGTATCTTCAAACCCAAACTCTGCAAATTGAAGTGAGACTGTATAGTTTCCATTCTGAAGTCCAATACCGTAATATCTTAAAGATGATGGCGACATCCTTGCAGTTTGGAACAATTCCGAATCTAGCGTGGCCTGAAACTGGCGCGCGTTGTTGATTATGGTAGTTCCATTTGGTGTGTCCATGAACTTTCCAACGTTGCTAATACCCCATGTCAAAGGTTCTGTAACATGATATGATGCAGCTCCAAGATTGGTAGCATCAGCTTGATAGCTGGAATTACGTGAGCCTGATATGAATCTGGTGCTACCACAGTCCACAGCAAAGGAGGCAGAATGTGGAGAACCAAGAAAGCACGGAGTATTTTGCTGAAGACACTCCAGCCCCGAAGGTAAGGCACTGTTATTGGATATATTGACCATGAAATTGTTTGCCACCAAATTCAATTGCAAATCTTCCTCACTAACCCAAAAAGGGAAATTTCCTGAAAGCTGGTTGTAAGAAAAATCTAAATTTCTCAATGAACGTATTTTTGAGCTTGGAAGGCTTCCTGTAAGATTATTATTTCCAAGAAATAAATAGCTAAGAAAATTCAGATTTAACAAGGTTTGTGGTACTTGGCCAGTGATATTGTTAAAACTCAAATCCAGTAAGGTTAAACTTGCAAACTTCGAAAAGTCTATTAATGCAAGACTATCAGATACCATACAGTTCCTCAAAATCAGGGTATTCAAAGATGTCATGTTACTGATGAATGCCAGTGAAGATGAGCTTCCACTTGCTATATCGCCAATTCGCAAGTTTGTTAATTGGACAAGATTAGAAAGATTAGCTGGAAGTGGACCTTGAAAAGAATTTCCTTGAAACCGCAGGTCTGTTAAATTCCAGCTCCCAATATAATCCGGTATTTGCCCAGTAAAATTATTATCCGATGCCCACAATATTTTCATTCTTGTAAGCTTGGATAATGATGATGGTAGCTCTCCACTTAAGCCAGCACTGTCAATGAACAATTCCTCAAGTTTGAACAGGCTCCCAAGTTCTGAAGGAAGGGAACCACTAAAATTGTTTGAGCTGAAACCCAGGGATACGAGATTTGTAAGGTTACCAAGCTCCTTTGGAATAGATCCAGATAATGCATTGATGCCAAAAGTCATGTACTGCATAGCAGCCAACTCCCCAATGAACGATGGTATAGTCCCTACCAAAAAATTATGTGATAAATTTCTGAAACAAGACCAAATCAGATATCGACAATATTAGTTTTATTGAATATCCAAAAGAGATGTTTTTTGAGTTTTTAGATGATTATTTGAGTTCTAAGTTCCATGGCATTATTGAATTTGGTGTTGAGCTTGGCAACTCTTTTTAAGTTACAACAATAGCCTATAATAAATAGTAGCCATCATAACAAATGATGGTAATCAGTAACCCCAACTGAACTTTGTAGCAATCCTCTACAGCTCTACTGAAATGAGATCTGATGGGGAGACTAAAACAAGAGCGTGCAATCTTTGGCAAAATATAAAGTCGTGTGGAGAATGCACTATCACACAGCAAACTACCCCAAATTCCTGGCAGAAAAAAAAGTCCCAAAAACTAATTAACCATGCTCTATGTTTGAGCAATGCCTTGGAAGTTGGAGCACGGCCACTCCACGTAAGAAATCCGAGAGTTCATACAGATGGGTTAAATGTGTGAGGTTCCGCAGCTCTCCTGGTATCTGGCCAGTTGCATCCTTGTCATATATCTTCAGCCCGGTGATGTGGCACACTGTGTTGTTCTGGTCGGAGCAGTCGCACTTGATGGCCGGGTTGATGCTGGAGTCGTTGATGTCGGTGCTGTCCGTCGCCGCGCCGCTGCACGGATCGCCGGTGGTGTTCCATTCCGCCTTCTGGTCGAGCTTCTCGAACACAGCCTTCAGCGCCTCCGCCTCAATCCGATCAGTCGTCGCCGTCGGTGCTTTCTGAGCCTGAGCAACCGCTGCAAGAAGCAGCAGGAGCACAGAGAGAGCCATGGGAGCCGAATCACTGTGCTCTCATCGATCAACCTCACTCTTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.908479
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0281100.1 4 31321152 T C
Osa04LNT0281100.1 4 31318603 G T
Osa04LNT0281100.1 4 31318609 T C
Osa04LNT0281100.1 4 31318624 G A
Osa04LNT0281100.1 4 31318778 G A
Osa04LNT0281100.1 4 31318790 T C
Osa04LNT0281100.1 4 31324753 A G
Osa04LNT0281100.1 4 31326357 T C
Osa04LNT0281100.1 4 31326891 A G
Osa04LNT0281100.1 4 31327123 G A
Osa04LNT0281100.1 4 31327256 A G
Osa04LNT0281100.1 4 31319142 C T
Osa04LNT0281100.1 4 31327411 T G
Osa04LNT0281100.1 4 31327752 G T
Osa04LNT0281100.1 4 31327888 T C
Osa04LNT0281100.1 4 31318544 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa04LNT0281100.1 DTM_#DNAt_MULE_japo_Os2081 Chr4 - 31321257 31321624 367
Osa04LNT0281100.1 DTM_#DNAt_MULE_japo_Os0372 Chr4 - 31317679 31318591 53
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0281100.1 osa-miR5527 Cleavage 5.0 19.137 1 21
Osa04LNT0281100.1 osa-miR5528 Translation 3.5 10.901 1 21
Osa04LNT0281100.1 osa-miR5815 Cleavage 5.0 17.056 1 24
Osa04LNT0281100.1 osa-miR5821 Translation 4.5 15.508 1 21
Osa04LNT0281100.1 osa-miR1319b Cleavage 4.5 13.698 1 24
Osa04LNT0281100.1 osa-miR5179 Cleavage 5.0 18.328 1 21
Osa04LNT0281100.1 osa-miR6253 Translation 5.0 10.965 1 22
Osa04LNT0281100.1 osa-miR1437b-5p Cleavage 4.5 16.65 1 21
Osa04LNT0281100.1 osa-miR396a-3p Translation 3.0 18.811 1 20
Osa04LNT0281100.1 osa-miR396b-3p Translation 3.0 18.811 1 20
Osa04LNT0281100.1 osa-miR169i-5p.2 Cleavage 5.0 21.83 1 22
Osa04LNT0281100.1 osa-miR426 Cleavage 4.0 11.154 1 21
Osa04LNT0281100.1 osa-miR1854-3p Translation 5.0 13.18 1 22
Osa04LNT0281100.1 osa-miR1854-3p Cleavage 4.5 16.333 1 22
Osa04LNT0281100.1 osa-miR1855 Cleavage 4.5 12.575 1 21
Osa04LNT0281100.1 osa-miR1861g Translation 4.5 17.679 1 22
Osa04LNT0281100.1 osa-miR1877 Cleavage 4.5 9.864 1 24
Osa04LNT0281100.1 osa-miR1320-5p Cleavage 4.0 14.042 1 21
Osa04LNT0281100.1 osa-miR827 Translation 5.0 15.937 1 21
Osa04LNT0281100.1 osa-miR396g Cleavage 5.0 14.329 1 21
Osa04LNT0281100.1 osa-miR396h Cleavage 5.0 14.329 1 21
Osa04LNT0281100.1 osa-miR396d Cleavage 5.0 14.329 1 21
Osa04LNT0281100.1 osa-miR2928 Translation 4.0 9.69 1 20
Osa04LNT0281100.1 osa-miR5071 Translation 4.5 21.313 1 21
Osa04LNT0281100.1 osa-miR5484 Cleavage 5.0 23.07 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0281100.1 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0281100.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0281100.1 4 nan Morphological trait Root RZ23 RM255
Osa04LNT0281100.1 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0281100.1 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0281100.1 4 qPN-4b Resistance or Tolerance Drought tolerance RM317 RM255
Osa04LNT0281100.1 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
Osa04LNT0281100.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0281100.1 4 nan Morphological trait Root RM3276 RM3335
Osa04LNT0281100.1 4 gpp4 Morphological trait Seed RZ569 RZ565
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