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

>Osa11LNT0101100.3

ACAGGGGCAAAATCAAAATTGAAGATCAAAATAGGGGTAAAATAGTCGATCCGAAGTAATTGATGCTAAAATGTAAAATAGTTGTTGTACTCTTTTTTCCTTACGGGGAACCCTACAAGCTGATTATTAGAAATCATAGCAAGTGCATACTTCTCACATATTTGAGATGATCCTTAGATGAGGGTACTTGCTACTGTCAATGGCATACATGGATCTAAATTCAGGCCTCAATTTCTTATATAGAACTTCCCGGTCCAAAAAAATCAACCTCAAAACACCCAACCATTGTATCCACTTCTTGCATCATCTCAAAATAAACTGGAAGATATCTTCAAATTCATCTTCAAACTCCCAATTCCATGTACAAATCTTGCCCTTGTGCGCCTGCTGCAATTTAATACATTTTCCAATCTCTCGGATATCCTGTAGCCATTGTCTCATCTCAATTTCTTGGAAACCTTCCTCCTCATCGATCCCAAGTCTTTTAGCTTTTGCAAACTTTTTTGATAGATCATAAGTAATATCTCGATTCCAGAGGGCATGTACACATTGAAGGAACTGAGTATTTATCAGGCATTTGGATTGCATGAGACTCTTCTGCTCTCCTTTTGAGCTGCCCTTCCCATGTCTTCGCCACATCATGAACATTCTTCACAAACTGTCTATTAGAAAATAGACGTGTGAGGCACCATGCATAATGTGTGTATTTGCTTTCCCACTCTGGCTGGGTTCAAATTTTGCTAAGAGGACTGAGTATACAAGAACTTCCTTGTATCGCTGAATCCTAAAAGAGAAAAGAATATGATGCAAGTAATTATTTCTACTACATGAAGCCTACTACGGTTGCACATAGTAGCTCCACCCAATTAATGTTAGATAATAACAAATTACATGATGACACATCTAGACCAGGATGACGCAGTAAGGAATGCTTCAGATATAATATTATGCTCAGCAAGGAGTAGACAGCCCAAGTGGTGGAAAGAGTTTGCTCGTCTAGCTCCATCATTACCCAGGAGATCTAATTCACAATCAGGAGAACTCATTACGACTGCAGTGCTACGTTTGTTTTTGCTGCTGCTGCTGCTTCCACTGCTCAGTCTCTTCTGCACACTAGTTTTCTGGAATATTGTACCAGAGCTATTGCTGTAGCGGCTGGAACTACTACTACTTGTATCCTTTGGATTCGCAGAGATACTCAATGCACCCTGTAAAGCTGGCACATAATGAAATGTGGTATGTGGACAGAATAGATAATCTGCAAAATCATGATCTGCAACGGCAATAGCAACAGGTCTTTTCCTCTGCAATATATGTTTGAAAAACTGCGATGCGTGTACACAGAAATCATTGCAAGAAAGTAGGCATCCACATCCCTTAATTAGACCATGCATCCCCAGATCAATAACATGAGCCCACCTTGCATATGCATTGGCTGCATCTAGGACAGCTTTTACTACAGATGCATGTTCCTCAGCTACTTCCACCTGACGCTTTTCTCACCCAAAGCAGCTCCAACGTGTTTCTCAAGCAAAGAGGAAATGAATGGCAAAATCTGCTGAAGGAACTCAGATAAGGAAAGCGGTTCGCCTCCAGAATGTGAAACATGAGCAATTCGATTATCAGAAATTGACTTCAGAATAAAGCAAACTAATTCGGTCTCAGTAGCACCCTTTGCTGATAGACACACAAGGCATGGGATTAGGTCATGCAAGAGAGAAATTCCATGGCTCCAAACCACCTCTGCAACTAAATCAGCTGCTGCATTCTTCCAAACCAGATCATCGGGAACTCCCAACTCAACTCCTAATAAACTAAAAACATGAGCAAATTTGCTTCAATTTATGATGCTAACTTCCTCCCACCTGAATCTCATCAAATGCTGTAGCAATCTGACGCCATGTCCCCGGACCTCATGAGGGAAATCCTTCCTGATAAAATGAAGCGACGCCCTCACCAACGCATCGACATACCCTTCATCCCTCACCGGCACGGGATTGCAGTCGACGGCGCGGACGGACGTTGTGGCGGCGTCCATGGGCGCTCCCTCCAGGGGCGGCTGATCGAGCGGCGGCTCTGGGAGAAGGAAGGGCTCGATCGGGGCAGGTTAGGTTTTGGGCGGGGGGGGGGGGGGTGTGGGTGGGTGGGTGTGGGAGGCGCGCGGCGACGCTACTCCGCCGTAGTGGGACTGTGGTAGCCCTAGGCGTGGGCATGAAATATTCAATGTCATACCATTGGATCTTTTAGCGTAGCCACAATAAATGCGAATGCATAAGGTTGTAAATGTGGCAAGAAATCCTCCATTTGTGGTATCAATGGCTCAGAATATTCTGTTGCTTTTGCCTTGGCCAACCGCCTGGCTATGTCTAAAAGGAAGTCCTTGTGACCCTCCCGTATTAGAGGATGAAACTGAGGTTCCCAGAAATGTAAGATTTGAAGGAGGACACGGATGGACTTTTTCGCATCATCACGGTCAAAGATCCTGGATGGTATCTCAATTTTTTCTCCAATACGTTCAACAATTTCATAATAATGGTCAGAGCCCTTGATATATGGTTTCAAAGTAATGAGTTCTCCAAGAATTTCACATATTTGTTTGTGATGTTTTGCACTGATCATTGAATAATATTTCCGTTCTCGCATATTTGACATGATCCTTAGATGGGGGTGCTTGCTACTGTCAATAGCATACTTGGATCTAAATTCAGGCCTCAAGTTCTTATATAGAACTTCCAGGTCAAAAAAATCAACCTCCCAATTCCATTCTAGTTGTGTTTGGCCAAAAAATTCCTTTGGAGGAGCAGAACATGCCTTAGCATGGAGATCTTCCTTTTGCTTTACCAACCAACATGTAAAGCTATCTGCAGCATCTTCAATCTCCTTTTGTTCCTTCACTAAATCCTGGCTTTGTGCATAAATATGGCTTGATAAATAGTTATATGCTTCTTCACAAAGGACGACAATATCCTTGATAGCATCATTGCTTGCACTTGAATTTAACTTGTGAACTAGGCATCTAATTGCACATGGAAGTTGATCATCTATAAGCCGTATCAAACAGGGAAGTAGCTCATCCGAAATGAATACCCTAAGCTTATCATCATTTGCAGCACCTGCAAGGTGGATCAAAGCACGACAGAAGGGGATAGCTTTGGTGGCTGCTTCACCATCAACCAAGTACCCAAACAGACTCATCCTTAACCTCCCAAGACAATCATTAAGTAAAAGATATCTGCAAGTCAATCGGGATAATGAAAACTTTCTTTTGATTCTTAATAGAAAAGGACACGAACAAAACAGGGAAGATCAGATACCCAACAAGAGATCTGTTTTGAAATGAGGTCAACCCTTTATTTAGTTCTGGTAGTGCTAAAACTCCAAGAAGATCACATACTTCACGAGTGAATTCAAGTAGAAGGGTCTCTTCCAATTTCCTAACTATTTCCAAAGACCCATGAAGATTACCAAAGTGATATGGAACTCTGGCTCGGCCATGATGCAACATACTGGACCATGCATGTTCAAGTACATTCCCAAAATGCATAAGTAAGGGTTGCAGCAGGTTGACTATCAAAATCTTCCAGGATTTATCTGGGCAATTTTTTACCAAAGGAATAACAACCAGATGGATAAGTTTGCTTAAATGTCAAAATTCCATTGAACCCAGATCTTTCAAGATAGCAGCATAAAAACATGAGCTGTCTGTGCATTCAAATAACATTCCCCCAAGAGATGCATACAGACCAATGACGTTGTACCCACTCTCTCGGATATCCTGTAGCCATTGTCTCATCTCAATTTCTTGGAAACCTTCCTCCTCATCGATCCCAAATCTTTTAGCTTTTGCAAGCTTTTTTGATAGATCAAAAGTAATCTCTCGATTCCAGAGGGCATGTACGCATTGAAGGTACCTTAGGAGCAATGGAAGGATCAACCCTAAGAGACTAACTGAGTATTTATCGGGCATTTGGATAGCATGAGACTCTTCTGCTCTCCTTTTGAGCTGCCCTTCCCATGACTTCACCACATCATGAACATTCTTCACAAACTGTCTGGACCAGGATGACACAATAAGGAATGCTTCAGATATAAGATTCTGCTCTGCAAGGAGTAGACAGCCCACGTGGTGGAAAGAGTTTGATCGTCTAGCTCCATCATTACCCTGGAGATCTAATTCACAATCATTACCCTCCACTTGTGTGCTGAGAGTGATACAGGAATCAGGAGAACTCATTACGACTGCAGTGCTACTTTTGTTGTTGCTGCTGCTTTCACAGCTCAGTCTCTTCTGCACACTAGTATTCTGGGATACTGTACCAGAGATATTGCTGTAGCTGCTTGAACTACTACAATAATCCTTTGGACTAGCAGAGATACTCAATGCACCATGTAAAGCTTGCACATAATGAAATGTAGTATGTGGACATAATAGATAATCTGCAAAATCATGATCTGCAACCGCAATAGAAACAGGTCTTTTCCTCTGCAATATAAGTTTGAAAAACTGCAATGCGTGCACACAGAAATCATTGCAAGAAAGTAGGCATCCACATCCCTTAATAAGACCGTGCTTCCCCAGATCAACAACATGAGCCCACCCTGCATATGTAATGGCTGCATCTAGGACAGCTTTTACTACAGATGCATGTTCCTCAGCTACTTCCACCTGACACTTCTCTTTTTCACCCAAAACAGCTCCAACGTGTTTCTCAAGCAAAGAGGAAATGAATGGCAAAATCTGCGGAAGGAACTCAGATAAGGAAAGCAGTTCGCCTTTATCACCTCCAAAATGTGAAACATGAGCAATTCGATTATCAGAAATTGACTTCAGAATAAAGCAGACTAACTCGGTCTCAGTAGCACGCTTTGCTGATAGACACACAAGGCAGGGGATTAGGTCATGCAACAGAGAAATTCCATGGCTCCAAACCACCTCTGCAACTAAATCAGCTGCTGCATTCTTCCAAACCAGATCATCGAGGACTCCCAACTCAACTCCTAATAAACTAAAAACATCAGCAAATTTGCTCCAATTTATTATGCTGACTTCCTCCCACCTGAATCTCATCAAATGCTGTAGCAATCTGACGCCATGTCCCCGGACCTCATGAGGGAAATCCTTCCTGATAAGATGAAGCGACGCCCTCACCAAGGCATCAACGTACCCTTCATCCCTCACCGGCACGGGATCGCAGTCGACGGCGCGGCCGGACGTCGTGGCGGCGTCCATGGGCGCTCCCCTCCCGTGGCGAAGGATCGATCAAGCGGCCCTGGGCTCGATCGGAGCGGGTTAGGGTTTGGGGCGGAGAGGCGCGCGGCGACGCTACTCCGTTATACTGATACTAGCCTGATGGGGACAAAAACAGGGGGGGGGGGAGAGAGAGAGAGAGAGGAACAAGTCGGCGGCTTCCTT

Coding Potentia
Explanation CPC Score
noncoding -1.21449
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0101100.3 11 18557501 T A
Osa11LNT0101100.3 11 18555388 A T
Osa11LNT0101100.3 11 18553659 T C
Osa11LNT0101100.3 11 18554159 A T
Osa11LNT0101100.3 11 18557591 T C
Osa11LNT0101100.3 11 18558458 T G
Osa11LNT0101100.3 11 18553616 T A
Osa11LNT0101100.3 11 18553734 A T
Osa11LNT0101100.3 11 18553742 T C
Osa11LNT0101100.3 11 18553778 A G
Osa11LNT0101100.3 11 18553785 T C
Osa11LNT0101100.3 11 18554078 C T
Osa11LNT0101100.3 11 18558663 T C
Osa11LNT0101100.3 11 18558809 A G
Osa11LNT0101100.3 11 18559439 C A
Osa11LNT0101100.3 11 18559718 T C
Osa11LNT0101100.3 11 18559831 G A
Osa11LNT0101100.3 11 18560214 A G
Osa11LNT0101100.3 11 18561464 C T
Osa11LNT0101100.3 11 18558316 G T
Osa11LNT0101100.3 11 18562137 T A
Osa11LNT0101100.3 11 18562144 A G
Osa11LNT0101100.3 11 18562160 G A
Osa11LNT0101100.3 11 18562193 A G
Osa11LNT0101100.3 11 18563328 A C
Osa11LNT0101100.3 11 18563395 A G
Osa11LNT0101100.3 11 18563822 T G
Osa11LNT0101100.3 11 18563861 A C
Osa11LNT0101100.3 11 18563945 C T
Osa11LNT0101100.3 11 18564289 C T
Osa11LNT0101100.3 11 18564679 G A
Osa11LNT0101100.3 11 18562038 A G
Osa11LNT0101100.3 11 18565687 A T
Osa11LNT0101100.3 11 18565688 A T
Osa11LNT0101100.3 11 18565705 A T
Osa11LNT0101100.3 11 18565863 G A
Osa11LNT0101100.3 11 18566175 C A
Osa11LNT0101100.3 11 18566558 C T
Osa11LNT0101100.3 11 18566721 G A
Osa11LNT0101100.3 11 18567378 T A
Osa11LNT0101100.3 11 18567455 T G
Osa11LNT0101100.3 11 18567552 T C
Osa11LNT0101100.3 11 18568048 C T
Osa11LNT0101100.3 11 18568059 G A
Osa11LNT0101100.3 11 18568342 A G
Osa11LNT0101100.3 11 18568553 T C
Osa11LNT0101100.3 11 18569033 G T
Osa11LNT0101100.3 11 18569133 T G
Osa11LNT0101100.3 11 18569632 T C
Osa11LNT0101100.3 11 18569892 A G
Osa11LNT0101100.3 11 18570114 G A
Osa11LNT0101100.3 11 18561806 C T
Osa11LNT0101100.3 11 18565615 G A
Osa11LNT0101100.3 11 18568481 T A
Osa11LNT0101100.3 11 18555272 C T
Osa11LNT0101100.3 11 18555475 T A
Osa11LNT0101100.3 11 18557717 T C
Osa11LNT0101100.3 11 18569710 G A
Osa11LNT0101100.3 11 18564095 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa11LNT0101100.3 osa-miR5528 Cleavage 4.5 11.696 1 21
Osa11LNT0101100.3 osa-miR2873c Translation 3.5 20.513 1 21
Osa11LNT0101100.3 osa-miR1440b Cleavage 5.0 17.418 1 21
Osa11LNT0101100.3 osa-miR6248 Cleavage 5.0 11.727 1 21
Osa11LNT0101100.3 osa-miR156g-5p Cleavage 5.0 20.191 1 20
Osa11LNT0101100.3 osa-miR156i Cleavage 5.0 20.191 1 20
Osa11LNT0101100.3 osa-miR393a Translation 4.0 20.048 1 21
Osa11LNT0101100.3 osa-miR395b Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395b Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395d Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395d Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395e Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395e Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395g Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395g Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395h Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395h Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395i Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395i Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395j Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395j Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395k Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395k Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395l Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395l Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395s Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395s Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395t Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395c Cleavage 4.0 14.556 1 21
Osa11LNT0101100.3 osa-miR395c Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395a Cleavage 4.0 14.556 1 21
Osa11LNT0101100.3 osa-miR166l-5p Translation 4.0 21.146 1 21
Osa11LNT0101100.3 osa-miR169i-3p Cleavage 5.0 16.968 1 22
Osa11LNT0101100.3 osa-miR393b-5p Translation 4.0 20.048 1 22
Osa11LNT0101100.3 osa-miR395m Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395m Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395n Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395n Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395p Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395p Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395q Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395q Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR395v Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395w Cleavage 3.5 14.556 1 22
Osa11LNT0101100.3 osa-miR395r Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395r Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR169r-3p Translation 3.5 23.861 1 21
Osa11LNT0101100.3 osa-miR169r-3p Translation 4.5 16.676 1 21
Osa11LNT0101100.3 osa-miR1850.2 Translation 5.0 15.87 1 21
Osa11LNT0101100.3 osa-miR1857-5p Cleavage 3.5 6.155 1 21
Osa11LNT0101100.3 osa-miR1857-5p Cleavage 4.5 16.809 1 21
Osa11LNT0101100.3 osa-miR1862a Cleavage 5.0 6.421 1 24
Osa11LNT0101100.3 osa-miR1862a Cleavage 5.0 16.513 1 24
Osa11LNT0101100.3 osa-miR1862b Cleavage 5.0 6.421 1 24
Osa11LNT0101100.3 osa-miR1862b Cleavage 5.0 16.513 1 24
Osa11LNT0101100.3 osa-miR1862c Cleavage 5.0 6.421 1 24
Osa11LNT0101100.3 osa-miR1862c Cleavage 5.0 16.513 1 24
Osa11LNT0101100.3 osa-miR1866-3p Translation 3.5 14.971 1 22
Osa11LNT0101100.3 osa-miR2122 Translation 4.5 15.532 1 22
Osa11LNT0101100.3 osa-miR2868 Cleavage 3.0 15.775 1 20
Osa11LNT0101100.3 osa-miR2863b Translation 4.5 10.914 1 21
Osa11LNT0101100.3 osa-miR2863b Translation 4.5 10.977 1 21
Osa11LNT0101100.3 osa-miR2920 Translation 4.0 13.646 1 23
Osa11LNT0101100.3 osa-miR2929 Translation 4.5 10.98 1 21
Osa11LNT0101100.3 osa-miR2929 Translation 5.0 12.839 1 21
Osa11LNT0101100.3 osa-miR395x Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395y Cleavage 4.5 14.556 1 21
Osa11LNT0101100.3 osa-miR395y Translation 5.0 10.071 1 21
Osa11LNT0101100.3 osa-miR1862f Cleavage 3.5 6.421 1 20
Osa11LNT0101100.3 osa-miR1862f Translation 4.5 12.86 1 20
Osa11LNT0101100.3 osa-miR1862f Cleavage 5.0 16.513 1 20
Osa11LNT0101100.3 osa-miR1862g Cleavage 3.5 6.421 1 20
Osa11LNT0101100.3 osa-miR1862g Translation 4.5 12.86 1 20
Osa11LNT0101100.3 osa-miR1862g Cleavage 5.0 16.513 1 20
Osa11LNT0101100.3 osa-miR156a Cleavage 5.0 20.191 1 20
Osa11LNT0101100.3 osa-miR156b-5p Cleavage 5.0 20.191 1 20
Osa11LNT0101100.3 osa-miR156c-5p Cleavage 5.0 20.191 1 20
Osa11LNT0101100.3 osa-miR156e Cleavage 5.0 20.191 1 20
Osa11LNT0101100.3 osa-miR156f-5p Cleavage 5.0 20.191 1 20
Osa11LNT0101100.3 osa-miR156h-5p Cleavage 5.0 20.191 1 20
Osa11LNT0101100.3 osa-miR156j-5p Cleavage 5.0 20.191 1 20
Osa11LNT0101100.3 osa-miR156l-5p Cleavage 5.0 20.191 1 21
Osa11LNT0101100.3 osa-miR156d Cleavage 5.0 20.191 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0101100.3 11 hbd3 Physiological trait Lethality nan nan
Osa11LNT0101100.3 11 Hbd3 Physiological trait Lethality nan nan
Osa11LNT0101100.3 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0101100.3 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0101100.3 11 gw11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0101100.3 11 gpl11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0101100.3 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0101100.3 11 yld11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
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