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

>Osa04LNT0281300.2

TGACCAGAAGTTAAAAGATTAATTAATTGACACATTCACTGGATTTTTGAAGAGAACACTAGCATTGGCACAAGACCATCAAAATTTCAATTTTCAGGTACAATGCTAATAAGATTTTGCACAACAGACGATGTCCTTGAGGACGGCAGTACAACAAGAATATGGTCATGCTGTTGCAAAAAAGAACAGAAAAACTCCCCTGTTATTCACCTTTAGGGAGGGAGTCAGGACGGTAAATCTACTTACGACATGCACGCCAATGTGCTGGTGACAATTTACATGTCTCCAGGAATTAACACCTGCTGGAAAAGCCTACAGCTCCAAATCTACTCTGCAACAGGGCTTCAGGGATCAGTCATGCTTGCACATCTACATTTGGTCCCAGTCAATAGAACTGTTGTTTTCAAAATTATAACTTGGTTGCTGTAGACGGTTGCGACCCAATCGGCTCATCATGGCAAGTCCTTCCATGACTTTGTATAGCGATGACCACCACCTATCAGATGGAACCTCATACTGAGCGAGTGTATCATCAATTTCGGTGTTGTGCTTCCCTTCGAGGACATTCTGTAGAGTGATTACTGCATCCTTTGTTTTCCTGAGGATGTTGTTTCCCTCAGCAGCCTCCAGTGCAAGAAGGTCACTGTGTGAAGAGGCAAGGCTAGCGGCAAGCGCAAACTGCGCAGCAACAGCCCATCGGTTAGATGCTACCCACTTCCTCTGGATATCTTGCATCTTGCTTTCTTCCTTTCGCAACCTCTCCTCACCATCCCCAAATACAAGAGTCTTCAGGTACTCTGCATTGCTAGGTCCTGTACTCTGAACCATCTTGGAGAAAGCACTGTGCTCATTGCTCAAAAGATTCTCAGGAGAGTCGAACTCCAAAACCTTCCCAGCACTTAGAATAAGCAACCTGTCACAGTCAATAACAGTGTTCAGGCGGTGAGCAATTATAAGCATTGTACAACTCTTGAATTCTTCCCTGATTGTCTTCTGTATAAGAGCATCTGTTCGAACATCAACAGCTGCTGTTGCCTCATCAAGAACAAGTATCTTTGCCCTCCGCAGCAATGCACGAGCTAAACTCAGTAGCTGCCGCTGTCCAACGCTAAAATTTTCACCAGCCTCAGAGACCTCAGCATCTAGTCCCAGAGCATTCCTCCTTATGACATCTTTTAGATGAGCCCTTTCAAGCGCTTCCCAGAGATCCGCATCATTGTGCTCATTAAAAGGATCCAGATTAAATCGAACAGAACCTGAAAATAGGACAGGTGCCTGTGGTATTATTCCTAGTACTTTTCGTAGGTCCCAAATTCCAAATTTAGAAGTGTCACAATCATCAACCAATATTCTCCCTCGTTCCAGTTCCACAATACGGAACAGAGCATTCAGCATGCTAGATTTACCAGCTCCTGTTCTGCCAACTATTCCTACCTTTTCGCTGCCATTAATGATGAAAGATATGCCATGAAGAACAGGAGGAAGTTCTGGTCGGTACCGAAGCACGACGTCTTCAAACTTGACAACACCAGATGATGGCCAACCAGGAGGTGGCCTGCTATCCTCAATGACAGGAGGAGCCTCAGAAGGCAACTCAATGTATGTTCCTACCCGCTCAACAGCATTTAAACTGTTTTCAGCCAGACTAGCAAGACGAAGAACAGCCGTGAGCAAATTGGTGATATTGAGGGTGTAAGTAAGAAGAAGACCCATTGTGGAGGCAAAAGCCTTTTGATTTTCTGCTCGTTGGTTTTGCATGACAGCAAATGTTGCTGTGAACCATATCATGATGCCACCCAATGTTTCCAGACGGATGGCTAGCCATCTGTTTGAACTCATGTTCACAAGAGTGAATCTGATGTTGTTGTCCATTGATTTCCCATTGATGTTTGCCATTCTATCATAGGCTTTGTAGGCACGGATTGTAGACAGACCATTCAATGCCTCTGAAAATTGAGCATACACAGGAGACCTTGTAATGGAATCCAGGCGCTTTACCTCACGAGACGTAGTCTGGTAATAGAGGTAAGCTGCATAAAATAAAATCAGAAGTGGCATGATAGCCCACAGAGACATAGTGCTAACAATGCCAATGAGAACAAATGTTGAGAGCAACTGAGATATTTGTGCCATAAACATATTCACAAAGATGGCTACATTCCTGTCAATGTCACCCAAATCCTTTGAAAATCTGTTGATGATTCGTCCAAGTGGATTGGTGTGAAAAAATACCATGGGAGCTCTTAATATAGACCGGAGCATGGCATCATGCAACCTCTTGGCTGCTCGAAGACTTGATGTGATCAGCCAATAAGAATTCGTTAGAGTGACTAGAACCTGCCCAAAAGAAAGAAGGCCGTAGATTAAATTGTAGTAACCAGGGCCATGGATTTTCGTAGAACCTTGATCTGTCCAAACGCTCAACCATGTGCTACTTGAAATGCGAAGAACTTCAGTGAGTGCATAGCAAAAAAAGAGAACAGATACCACCCAGATCCCTCCCAATGCATTTTTGTAGCGTGAAAGGACCTTTGCACTTATAACTCCAGTTTCCCTTTCTTCTTGTTTAATCAGAACAGATTTCCCCTGTTTTGTTTTATTAGAAGTGTCCTGACTCTTCTGCATATCACCATCAGCTATTACACTGCCCCCATTTTCAGGGTGTTTTATGTCATCCTGTCTTTTGCTTTCGTCCTGTTTCTCTTCCATCTGTTCTTCCATCTTTCCAGCATTTTCCATGAGCTTCTTAAAGAGTTCCCCAGAGTTGCTAAGTTCATCAAAGGTACCTTCTTCTTTAATTACACCATCATGGACTACCAGTATTTTATCCACATATGGTAGAAAATGCAGCTGATTGGTAACAAGAACCCTAGTTTTGTGCTGTAGCTCTTCTTTAATACATTTGTCAAATACCTGTCGACCAACATGGGCATCTAATGCACTCAGTGGATCATCAAATATGTAGACATCTGAATCAGAATAAACAGCTCTTGCCATTGAGACTCTCTGTTTTTGTCCCCCACTAATGTTAACTCCTCTTTCTCCAATCTCTGTTAGGTCACCACCTGGGAGTAAGTCAAGGTCATGCCGTAATGAAGTGACATCTATTGCTTTCTCGTAGCGTGGAGGTTGGAAGGGAGACCCAAACAATATATTGTCCCGGACAGTTGCATTGAAGATCCATGAAACTTGAGGAACATAAGCCACTGTTCCACGAAGGACCACCGATGTATTCGATCCTGACACTGGTGGTATTTCACCAAGCATTGCAGAAATAAGAGAAGTCTTCCCCTCCCCAGTGCTTCCTACTATTGCAACCAAACTGCCCATAGGTACATCCAGATTGACGTTTGATAATGTTGGTCTCTCAGCCTGCGATTCCCATGAAAAATATCCATTCTTAATAGAAATTGCTGGAAGCTCAGGATCAAGAGGTGGATTGGGCAGAAGTAATCTCTCTTCAGCCAAGAGGAGATCTTCCAGACGTTTCAATGACACTTTACAATTAACCACCTGAGTTATCAGATTTGGCAGCATAAAAAGTGGAAATCTTAAGACAGCAAACAGTGAAAGTGATGTGAACGCCTTTGCTGGTGTCAAGTCACCTCCCAGCAGAGAGTATACACCAAATGAAACCACAGTGACAATAACGGGGATACTGTTTAGGATGAAGCTATTCAGCGCAGCAAGCAATTGAGCGCTGCGGAACCATGAAATTTCATCATCACGGATGTCCTGCACTTTTGACTGGAAACTTTGCTCCCAAGCATAACATTTGACCGTATCCATTGCAGCTAATATTTCATTCATTAGACTGATTCTCCTGTCAGTCCTTTGCAACCCTTCCTTGGTAAGTTTTTGCATTTTGCTTATGATAACAGTCTGAATTGGGAACAAAAGAACCAACATGGCTGCACCGACCAATGCAGCAGGGCCTAGTTGTGCGTATAGAAGGACCATGGCAATAACAATGCGGAAAGGAGCAGACCATAGACTGTGAAGTTGCTGGCACACTTGCTGAAGAGATTCTGCGTCAGTTGAAATCAAATTGGTTATCCTCCCAGAGGCAAACTTCTTTCGACTATCATTAGTTAGTCGCAAAGACTTACGGAAAACAGCTGCGATCAATGTTGACCTCAACCTGAAACCCGTTCGCATGACATTCTGAAAGTACTGTGCTTCAGAAAGAACACCCAGTGACACTCCAGCGAAGATTGAGAAAGCATAGATGTAACCGCTCCAAGATGGATCACCTTTTTGCATAGACTCCAACAAGAGGTTCAATATGAGTGGGCCAACAAACTGAGAAGCATCATTGCCAATCTTAAAAAATCCTCCTAGCCAAAACCTTCCACCAAGGCTGCTATGCAGAGCCCGTAACAGCCAAGGCTTTGGTTTTTGAAGCTCATTGTTCCAGCATTTTTGGAACCGGTTGTACAATGTTTCAGTCTCATCCCAACTGTCTAATTTCCAAATATCCTTATCGGTGATGGGCCTTTTAAATCCTTGTTGCATTAGAGGAGTCATCCATGAAAAGAATATCCTGGAAAATATATTAGCATGCCTCTCAGGGCAAATCTGCTCCCCACCAGGCAGAGGTTCGTAATCAGTATTATCAACAAGTGCCTCATGCCTGACTGGAGTATAACCCGGATAGGAATCCAAGCTAGGCAGATAAACCACCATGAGAATTCCAAACAAGAGCTTGAATATTATCTCACTGCAGTACAAGTAAAATATTGAACTCGAACTATAATACTGCCTTACTGAAAGCACAAGATTGAACATAGCAGCTTCCCCAACCAAGATGTAAATGACCACAAACCGGATGTACCATCTAAACTCATAGATGTAAATTCTTGTCTCAAGTGCAATCATTACAAGCATACAACACCAAGCAGCAATCTCAATGATAGATGAGGTAACCTCAAATGGAGCAAGGCTAGTCTCCCCATCCAAGTTCATTATGGAGGTGCCAGTAGCGATCCGATACAGTGATTCAGCTATGCACAACACCACAAGCAGGCCGAGCATATAGTTGTAGTATGGCGACCGCAATTTGTAGCGCTGCACCGTGTAGTCCCTCGTCGTCCTCCATATCCGATAGAAGCAAACACCGAAGAGTGCAAAGTATGAGATGCACACCACCAAGGTTTCAGTGCCACATGGTGTGTATGCACCAAAAGCATTCTCTACATCTGACCACACCCCGCCATTGACCGGCTGGCAGTACCATTCCAGTGGATCAAAACCCATGTCAAACCGTCCCCTTAGCAACCCTCACTCAGTTTTGATCTTCCCCTCCTGAATCTATGAATATTGAAAAGGCAGGCACGAATCATGGAACATGTCTTCTGCAAAGGAGTTCAAGAAAGGCTATTATCTATTCAACAAGGATTTTATCTTCCCAAGAGAATCAGCACCCCGCATGGTCCAAACTCCAAACCCCAACTATTCTTCCCAAAGTTTGAAGCTTTTTAACAATGAAAGGCCTGAAAAAAGGGCACCTTTCTGCGCTTTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.833673
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0281300.2 4 31504109 C A
Osa04LNT0281300.2 4 31503376 C T
Osa04LNT0281300.2 4 31502980 T C
Osa04LNT0281300.2 4 31503164 T G
Osa04LNT0281300.2 4 31503484 A G
Osa04LNT0281300.2 4 31503579 G C
Osa04LNT0281300.2 4 31503624 C T
Osa04LNT0281300.2 4 31503629 T A
Osa04LNT0281300.2 4 31503893 G A
Osa04LNT0281300.2 4 31504466 A G
Osa04LNT0281300.2 4 31504469 G A
Osa04LNT0281300.2 4 31505186 G A
Osa04LNT0281300.2 4 31505191 A G
Osa04LNT0281300.2 4 31505231 G T
Osa04LNT0281300.2 4 31505690 A T
Osa04LNT0281300.2 4 31505846 A G
Osa04LNT0281300.2 4 31505970 A T
Osa04LNT0281300.2 4 31505981 G A
Osa04LNT0281300.2 4 31506434 C T
Osa04LNT0281300.2 4 31506495 T A
Osa04LNT0281300.2 4 31506890 T C
Osa04LNT0281300.2 4 31507345 C T
Osa04LNT0281300.2 4 31507536 C T
Osa04LNT0281300.2 4 31507580 G C
Osa04LNT0281300.2 4 31507819 T G
Osa04LNT0281300.2 4 31507877 G A
Osa04LNT0281300.2 4 31508050 A G
Osa04LNT0281300.2 4 31508190 A T
Osa04LNT0281300.2 4 31508274 T C
Osa04LNT0281300.2 4 31509168 C T
Osa04LNT0281300.2 4 31509177 C T
Osa04LNT0281300.2 4 31509224 A G
Osa04LNT0281300.2 4 31509228 G A
Osa04LNT0281300.2 4 31509265 G C
Osa04LNT0281300.2 4 31509277 A C
Osa04LNT0281300.2 4 31509323 T A
Osa04LNT0281300.2 4 31509863 G A
Osa04LNT0281300.2 4 31509873 C T
Osa04LNT0281300.2 4 31509878 A C
Osa04LNT0281300.2 4 31510233 C G
Osa04LNT0281300.2 4 31510264 C A
Osa04LNT0281300.2 4 31510712 A C
Osa04LNT0281300.2 4 31511242 A G
Osa04LNT0281300.2 4 31511390 A G
Osa04LNT0281300.2 4 31511938 A G
Osa04LNT0281300.2 4 31511979 A T
Osa04LNT0281300.2 4 31512173 T G
Osa04LNT0281300.2 4 31512216 G T
Osa04LNT0281300.2 4 31512238 C G
Osa04LNT0281300.2 4 31512307 A G
Osa04LNT0281300.2 4 31512410 C T
Osa04LNT0281300.2 4 31512504 C G
Osa04LNT0281300.2 4 31512553 C T
Osa04LNT0281300.2 4 31512833 A C
Osa04LNT0281300.2 4 31513227 G A
Osa04LNT0281300.2 4 31513260 A C
Osa04LNT0281300.2 4 31513719 A C
Osa04LNT0281300.2 4 31514034 A G
Osa04LNT0281300.2 4 31514065 G A
Osa04LNT0281300.2 4 31514486 A G
Osa04LNT0281300.2 4 31514488 A C
Osa04LNT0281300.2 4 31514654 T A
Osa04LNT0281300.2 4 31514802 G A
Osa04LNT0281300.2 4 31511892 G A
Osa04LNT0281300.2 4 31510915 C A
Osa04LNT0281300.2 4 31511493 G T
Osa04LNT0281300.2 4 31514248 A C
Osa04LNT0281300.2 4 31505861 A G
Osa04LNT0281300.2 4 31512412 C G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0281300.2 osa-miR5827 Cleavage 4.5 15.425 1 21
Osa04LNT0281300.2 osa-miR6253 Cleavage 4.5 12.028 1 22
Osa04LNT0281300.2 osa-miR395b Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395d Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395e Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395g Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395h Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395i Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395j Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395k Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395l Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395s Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395c Cleavage 4.0 17.249 1 21
Osa04LNT0281300.2 osa-miR395u Cleavage 5.0 17.249 1 21
Osa04LNT0281300.2 osa-miR171f-5p Cleavage 5.0 15.023 1 21
Osa04LNT0281300.2 osa-miR172d-5p Cleavage 4.5 17.416 1 20
Osa04LNT0281300.2 osa-miR395m Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395n Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395o Cleavage 4.0 17.249 1 21
Osa04LNT0281300.2 osa-miR395p Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395q Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR395w Cleavage 4.0 17.249 1 22
Osa04LNT0281300.2 osa-miR395r Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR814a Cleavage 5.0 17.773 1 22
Osa04LNT0281300.2 osa-miR814b Cleavage 5.0 17.773 1 22
Osa04LNT0281300.2 osa-miR814c Cleavage 5.0 17.773 1 22
Osa04LNT0281300.2 osa-miR1424 Cleavage 5.0 16.688 1 21
Osa04LNT0281300.2 osa-miR1850.1 Cleavage 3.5 6.951 1 21
Osa04LNT0281300.2 osa-miR1862e Cleavage 4.5 13.625 1 24
Osa04LNT0281300.2 osa-miR395x Cleavage 5.0 17.249 1 21
Osa04LNT0281300.2 osa-miR395y Cleavage 4.5 17.249 1 21
Osa04LNT0281300.2 osa-miR3981-3p Translation 5.0 22.096 1 21
Osa04LNT0281300.2 osa-miR3981-3p Translation 5.0 17.956 1 21
Osa04LNT0281300.2 osa-miR5083 Cleavage 4.0 14.688 1 20
Osa04LNT0281300.2 osa-miR5160 Cleavage 4.0 16.149 1 22
Osa04LNT0281300.2 osa-miR5160 Cleavage 5.0 11.881 1 22
Osa04LNT0281300.2 osa-miR5522 Cleavage 4.0 8.026 1 21
Osa04LNT0281300.2 osa-miR5521 Cleavage 4.5 13.487 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0281300.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0281300.2 4 nan Morphological trait Root RM3276 RM3335
Osa04LNT0281300.2 4 nan Physiological trait Source activity RG143 RG329
Osa04LNT0281300.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0281300.2 4 Gm7 Resistance or Tolerance Insect resistance nan nan
Osa04LNT0281300.2 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0281300.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0281300.2 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0281300.2 4 qSN-4b Resistance or Tolerance Drought tolerance RM255 RM349
Osa04LNT0281300.2 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
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