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

>Osa04LNT0283500.2

AATGAAAATGCGGTTGTACATACATTTATACATATTTACCCATGATATTTATATCCAAGTGACCAAGTGCATATATACACACTGCATTTATACAGGAACGTAACATCCTAAACGACCAGATCTTGTGAATATGTAAAACCAAGAGGAAACTCAACTAAGAACAGTTCTATAATTTCTTGAACTTACCCATCCCTTCCTGATATTGATTTTGCCGTCGGCTGTTTGCATGTTAGAGGCATATTTAGGCATATCTTGTAACTTATAGTCAAACTTTTACCTGTGACTTGTACAGGAAAAAAAGTATAGTGCCAAACTCTACAAGAAGGATCTTAGGGCCGTCACAACCTTCTCTGGCCAGTCCTCTTGAGGCATATGACCAGCTCCTTCTATTGGCTCCAATTTTATGGCTGCAGGATTACCTTTCTGGAACTCCTCAGCTATGGGGAGTGGCAAGTACTTATCAGAAATCCCCCATGCAAGCAATATTGGTTTTTCCCAGCTGTTGGATGCAAACCCGGCTGAAATTCTACTTAATACATCTCGGAAGTTAGCTTTCCTGGCAGCTTCAAGCAATGCAAATCCAGGTGCACCACTTGATAGATATGGTAATCTGTATACATCAGCCTTCTCCGACTTTAGCACATAGGGGCTACCTGCTTCAATGAATCTCTCAGCCAAAACAGCATTTTGGCAGGTAAATTCACCAAAAAGTGGCAACCTTAGCTGGTTAAACAATCCAGGCACTGGAGAAGAAACAGTGAGTGGACTGTTAAGAATTGCTACCTTCAGAACTTTGCTTGAGTTCTTTAGTGCCCATGTTAGCCCATATGAACCTACAAGAAATCCCTGGACAACTAAGAAGAATGGCTCAGTGATATTTAAAGTACTAAGAAGCTCATCGAGTGACTTGTGGAACTCCTCTTCTGTGTAGTCGAATCCATATCCGGGCTGTGGCATATCACTGAACCCAAATCCTATCCAATCAGGAGCAAAGCAGTGGTAGCCAGCATCTGCCATCTGAGACATAACCATACGATAGCTAAATGACTGAGATGGAGCACCGTGAATAAACACGACAGTCCCACGTCGTGCACCAGCGGAACCTGTTTCCCTCACAAACCACCGCAGCTTTCCTGATTTCACTCTTGAGCCGAACTCCCTCCCCTTGTCCTCGATCCTGTAGAGCATCTGGCCGACATTGCCGTCCTGGGCGGGCGACTCCGGCAGCTGGATGGCGCCGCGGCTCGACGGGTTGTCCGTCACGAACCCGAACGGGTTGAACTCCGACTCCTCCTCCTGCTTTTTCCCCTCCGCCGTCTCATCCTTGCTGCCGCTCGCCGCGACTACCAAACTCCGCTTCGCTCCTCCTCCACGCGCCCTCCAAGCGGCGGCGTTGGCGCTGCTGCCGCCGCCGCCGGACCACCTGCCTCTGCAAGCGGGGCGTGGCAGGGAGAGAGGAGACGAGGTGGTGGTGGTGCAGGGGCAGCAGGACATGGCGGCGGCGTTCGGGTGGGTGTGCGCGCGCGCGCTCCGGCGAGACGTGGCGGCGCGGCGAGACGCTTTCGGTTGGCGCAGCCGCGTCGAACGGTCGGGAAGAAAGAAGATTCTCCGCGAATTGCGGTGGGGCCGACAAGATCACTTCTCATGTGGCTCCCGTGCACAACCGCAGGTGAGCCACTCTCTCACTCTACTCTAGTCTAGTGGCCACAATTGAATCACTCTGGAAATCCATGAATTTTCTAACAACAAAACTTCACAATTCAGCAACACAAGATGGCTATGTACTGTACAACTTATTGGTAAATTCGCCATAAAGGCAACATCATCTAGAGAAAGTTTGAGGAGCTCTTTGTTGTCCACCAAATGGAGGAGTTGTTCTATGTTTTTTTTTCTCTAGTTGTTCAGAATGCAATTGGGAATGGGTATAATCTGTGCAACCAATCATGCAGAATGTTATCCTTGAGCTTGGTGTTGTGGCCTGCAACCTCCTGGTCCATTTCCATAGCTGGGGTTATGGTAGCCTGGTTTGTTGCCAGAGCCTGATGGACCATTTGATCTTCCAGGATGTCCGTAGTGATGGTGATGGTGTTCTTGCCCTGGATGCAGAACTGGACGCCAAGGGCCAGGGGGAGCAAAATTGCTAGGTGGCCTCACGTGTCCTGGAGTAAATGGAGGACAAGGATGTGGAGGAGCATGACGAGGAAATGGGCCTTGATTTGCATGGAACGGAGGACGCCAAGGATATAAGTCTTGACCTGCAAATGGAGGACAACGCCGAGGAAAGAAGCCTTGATTTGGTAGTACAGGTGGAGGATGCCGAGGAACGAAGCCTTGACCAGCTAATGCAGGAGGAGGACACCGAGGAGCAAGGCCTTGATCTTCTAGTACAGGAGGAGGAAGCCGAGGAACATAACCTTGATCTGCTAGTACAGGAGGATGCCGAGCTGCTAACCGTTGATCCCCTTGTGCAGGTGGAGGATGCCGAGGAAACGAGACTTGATCTCTTGGTATGTTCAGACATCCAGATGGCATATTTGGATCATGACCAGAAGAGATGTCTTCTACTTCAAGTGGAGTATAAGATTTCTGAGTAATTGGAGGAAACACTTGTGATGGTGCTTTAGACCCTGTGGAGTTCTTCAAAGATGGTGATGTATGTTTACTTGAACCGCTTTGATGCAGTTTCTCATTATCCAACCCCTGGAAGTGACACTCTGGCATGTCTTCAGCATCAATGTCATCTTTGCTCTTGAAGTTCTCTATTTCTGCCTTGCGATGAGATACTTGATTCGTTATCTCCCTTGAAATCATGTCTGTGACATTTTCTTTCACCTCAACCTTTTCATGATTCTTGATGCCTTCAACTTGAAATGATGGTTGCGATGATTGCTGGAATGGACTGTTTGACTTCTTATCAGATAACCTAGGGCAAATCAGCACATCAGAAGTTATTGTAGTTTCCCTGTTGATTGGATGCACATCAAATTTCAACTCAACTCTATGGAGATTAGCGAAGTCAACTTTTGGAAGGTCATCTATATCATTAGCTCTATGAGCACCATAAGTATCAGGCTGCAGCAAAAATGGATTAGTCTCCTGTTGTTTTGAAGACTCAACAGCATTTGATGCATATTCTTGAGTTATGCTGCCTGAGAAGGCCTCCGCCATATGATTCTTTTGTGCAGCTAAATCATAGTGGGTAGTTCTCTGCTGAACATGCAAGGATTTCAGAGACAATCCTTGAGAATGTGAAGTAGGATGCCACACTCCAAAAGATCCAGAATGAGAATCTATGATGGACTGAACATGTTGCTGAATTTCTGGGACTTCATGCGATGCCAATTCGAACGGTGAAACTTTTTCTGTAGGATCTCTTTCACCAGTACTCTTAGCATGCCCACACTGAGATAGCAAACCAGTTGCCACAGGATGCGTTTTCACAGAATTGCTCTGAATTTCTTGCATTTGATCAATATCATTCTGAATATTGCCTGTGTTTGTTCTAGAGTCCATGCCAGGATTGTTGGAGCATGATGTTGCCTGATGTCCATCTGAAAATGGCAACGAAGTTGGATGCCTTGCTCCAACATGAGGCACACAAGGAGATCCCTTTCCAATAGTTTCAGACCTGCTATGATCCACAATTTTTGACAGTGGATTTCGGCGCCACACAATGCACCCTATCAACGAGTCTTGGTTTGTATCAGCTGCTGACATGCCTTTAAAGAAACCACATTTCGCTAGGATTGTAATTACAGCATCACTTCTGGGGCAGACATAGAGATTGGAACCATCACATACATCTGCAAAACCAACCTTCTGGCTCGCTTCAAAGTTCTCGGCAACCTCTTTCATTCCCAGTAAGCCAGCTTTTGATGTCCCAAACTTCCAACAAAGAGAAATTACCATCAAAGATCGGGTTTGACATCGACGGAGTTCCTGGACAAACTTTTCAAACACATCTAATTTCACTCTCCCTTTGATTTCTATGATTTTCGGCCAAGTAATGTCGTGATTTTTTTCTCCGCTTTTGAAGAAGGCGATCACAGACACCTTGACAGTGCTACTCAACTGGATTGTACCATCACATAGGCTTTCATAAGCAGAAGGAGATAGCAGGCCAACAACTGACATGATTTCATCATCCAAAGAATGAGGAGACAATATACTAGAACTATCATCTGCTTTTGTAGAACCTTGTACATCATGTTTAGCTTCATAGCTTGATATCCCTTGCTTCTGTTGAATTTTTTCAAGGGAACTCTGAGAAGGGTGAACCATAGCTACAATACTCTGATCACCCTTTTCACAGCTGAAAAGTAACTTATGAGCCACAGCTGTCTGGCTCTGATCTGTTGAATCTGCATACTTAGCACAACTATTACTAGACTCTATTTTAGTGTGCATTAGTTGAAAAGTAATATGTGGATGCATAGGTTTGCTTGGTGTTGTATGATTTGTACACTCCATCAATAGAGAGAACGATTGAGTAGTATCCTGACAGTTTGATGTGCCATTATTTGTTGAAATGGTGTGCAGTATGGTTTCATTTGGTTTGCATGAACTAGTTGTACATCTAATGCCACTCAGTTCTGTGGTTCCTGACAGAATATCTTGAGGAGCAAAACCCTGTGAGTTACTCAAAATAGAGCTCAACCCAGCTGGACCATTTAGAAATGATTCTTCACCTTGATGACTATCTTTAGCACTAGTGACTAACCCAGATCCATGAGAAACGGCCCTATTAGATTCACTGTAGTGAACAGAGTTCAAAAATTTTCTTTTTCTTGGCGTATAAACCTGAAAAATCATGTCGGGGGAATTACTTTGGCCCGACATCCTTTCCTCTGGAACAGAAATATTATATGGTTGTTTGTTCCACGCTGTTGCGAAGGCAGAATTAAAGGAATGAAATCAACTGTAGATTGCAGCACTGCTTCCAACAATAGCAGAATGCCAGAATATGAAGCCTGGGAGAGATGAAGTTGCGAGGGTTTTGGGCGTCGGAACTCGGAACTGTCCGATCGACGCGGCGTCGAGCAGGCGAGCGGCCGCAGCCTACAGGAAGCAACCGTCGGAGTCGGACGACGAAAACACTAGCGCACGCGTTAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.204701
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0283500.2 4 32803339 A G
Osa04LNT0283500.2 4 32803393 G A
Osa04LNT0283500.2 4 32803457 A G
Osa04LNT0283500.2 4 32803801 C A
Osa04LNT0283500.2 4 32803968 T C
Osa04LNT0283500.2 4 32805877 A G
Osa04LNT0283500.2 4 32807357 A G
Osa04LNT0283500.2 4 32807414 A G
Osa04LNT0283500.2 4 32807448 A C
Osa04LNT0283500.2 4 32808370 T C
Osa04LNT0283500.2 4 32809201 A G
Osa04LNT0283500.2 4 32809444 G T
Osa04LNT0283500.2 4 32809478 T A
Osa04LNT0283500.2 4 32809671 T A
Osa04LNT0283500.2 4 32810475 A C
Osa04LNT0283500.2 4 32810698 T G
Osa04LNT0283500.2 4 32811468 T C
Osa04LNT0283500.2 4 32812276 A G
Osa04LNT0283500.2 4 32812892 C G
Osa04LNT0283500.2 4 32807822 G A
Osa04LNT0283500.2 4 32803607 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
Osa04LNT0283500.2 osa-miR5541 Cleavage 4.0 13.474 1 21
Osa04LNT0283500.2 osa-miR5824 Cleavage 2.5 16.583 1 24
Osa04LNT0283500.2 osa-miR6254 Translation 4.5 22.269 1 21
Osa04LNT0283500.2 osa-miR167a-5p Cleavage 4.5 11.001 1 21
Osa04LNT0283500.2 osa-miR167b Cleavage 4.5 11.001 1 21
Osa04LNT0283500.2 osa-miR167c-5p Cleavage 4.5 11.001 1 21
Osa04LNT0283500.2 osa-miR396c-3p Cleavage 5.0 11.648 1 21
Osa04LNT0283500.2 osa-miR160f-3p Cleavage 4.0 21.238 1 21
Osa04LNT0283500.2 osa-miR167h-3p Cleavage 3.5 16.163 1 21
Osa04LNT0283500.2 osa-miR167h-3p Cleavage 5.0 17.152 1 21
Osa04LNT0283500.2 osa-miR437 Cleavage 4.5 14.995 1 21
Osa04LNT0283500.2 osa-miR1428a-5p Translation 3.5 13.358 1 21
Osa04LNT0283500.2 osa-miR810b.2 Cleavage 5.0 14.212 1 21
Osa04LNT0283500.2 osa-miR1874-5p Translation 5.0 24.621 1 24
Osa04LNT0283500.2 osa-miR1874-3p Translation 4.0 11.68 1 24
Osa04LNT0283500.2 osa-miR827 Translation 4.5 22.462 1 21
Osa04LNT0283500.2 osa-miR396f-3p Cleavage 4.5 20.53 1 24
Osa04LNT0283500.2 osa-miR2104 Translation 4.5 12.141 1 22
Osa04LNT0283500.2 osa-miR2864.1 Cleavage 4.5 24.57 1 21
Osa04LNT0283500.2 osa-miR2920 Cleavage 2.0 18.312 1 23
Osa04LNT0283500.2 osa-miR2923 Translation 5.0 15.338 1 22
Osa04LNT0283500.2 osa-miR2929 Cleavage 4.0 24.513 1 21
Osa04LNT0283500.2 osa-miR2929 Cleavage 4.5 16.5 1 21
Osa04LNT0283500.2 osa-miR5080 Cleavage 5.0 19.278 1 21
Osa04LNT0283500.2 osa-miR5080 Cleavage 5.0 15.926 1 21
Osa04LNT0283500.2 osa-miR5340 Cleavage 4.5 15.624 1 23
Osa04LNT0283500.2 osa-miR5491 Translation 4.5 14.707 1 21
Osa04LNT0283500.2 osa-miR5496 Cleavage 5.0 9.803 1 21
Osa04LNT0283500.2 osa-miR2275c Cleavage 4.0 17.078 1 23
Osa04LNT0283500.2 osa-miR5519 Cleavage 4.0 14.18 1 21
Osa04LNT0283500.2 osa-miR5522 Translation 5.0 17.881 1 21
Osa04LNT0283500.2 osa-miR1857-3p Cleavage 5.0 21.05 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0283500.2 4 QGn4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0283500.2 4 QGwp4 Physiological trait Source activity RG143 RG214
Osa04LNT0283500.2 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0283500.2 4 nan Physiological trait Eating quality RZ590 RG214
Osa04LNT0283500.2 4 nan Physiological trait Eating quality RZ590 RG214
Osa04LNT0283500.2 4 nan Morphological trait Root RG214 C1016
Osa04LNT0283500.2 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0283500.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0283500.2 4 gpps4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0283500.2 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0283500.2 4 qSN-4b Resistance or Tolerance Drought tolerance RM255 RM349
Osa04LNT0283500.2 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
Osa04LNT0283500.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0283500.2 4 np4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0283500.2 4 nan Morphological trait Root RM3276 RM3335
Osa04LNT0283500.2 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0283500.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0283500.2 4 nan Morphological trait Panicle/flower RG143 RG214
Osa04LNT0283500.2 4 nan Physiological trait Source activity RG143 RG329
Osa04LNT0283500.2 4 np4 Morphological trait Seed RG143 RG214
Osa04LNT0283500.2 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0283500.2 4 nan Morphological trait Panicle/flower RG620 RG214
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