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

>Osa11LNT0100700.2

TCTCAAATGAGTAATGAATGTTTACAGTTGGTTACATAGTATAGGCTTTGACAATAATTATGTCACATTCATAATTAGCTTGGGTCATGTTACACAGTATTTGTATTGGTAAATCCCACGAGCTACCTCTAGGAGCCGATACAAAGAACAAATGGAAAGGGTGTTCTCAACATATTTCATCGAGCTATTTGTTTTCTTTAATGCAAGGGACAGTCAGTACTTTTGTCATTGAAGGAAAGGAAAATGGCTAGAAAGCTTGTGATGATCAGATGAATTAGATAATATCCTTCAAGAAAGTACTCCCTCCGTCCAAAAAAAAAAAAGACAAACCCTGGGTTTTCGTATCCAACGTTTAACCGTCCGTCTTATTTGAAAAAATTAAAAAGACAAGTCACGCATAAAGTATTAATCATGTTTTATCATCTAACAACAATGAAAATAGTAATTATAAAAAAAAATTCATATAAGACGGACAATCAAACGTTGGACACAGAAACCTAGGGTTTGTCTTTTTTTGGGACGGAGGGAGTAATAGATTAACAAATTTCTGAATAAGGTCCAGACAGCATGAAACAAATTTGTATCTTATGGCTCATTACAGATGAGCAAGTATGCCTCGCCGCAAGCTCAGCTCTCAATGAAAGCCACGATCATGATACCTTTGCTTGGACACTTCTTTTGCATTAGTCCCTAGCCAAAACATCAAGCTCGCCATAACCGTGACTGCTTAGCCTCCTTGCACTGCAATGCGCTACACTCTCAATATTCAATATCCAGTTCAAGAACAAAATTTTGAGCTTGGAGAAAAATCTTTTCCAAATTTAAACGAAGCTGACATTCCAGATCTGGATCCCGACCAACTAATTGGATTTTCGATTGGGATTGTTTAACCTTTTCTGGAATATACTCGTTTTCATGCTCAAATAGGTCTCTTAGTCCATCAATGAAAGATAAACCAGTTTCTGTGGTTGGTGCTTGATAATTAGAACTTTGAGTTATCCAGTGAGGCATAGCCTTCGCCCATTGTAAACTAGCATTCATGAATTTCACCAGTTCGCTAATGATCTTGTCCTTTTCAGGATCTCCAGATGGAACCTGTGGTTGACTTTTTACATGTACCAAGATGAATAAATTGAGGGCAATTATGTTCTCAAATTTTTCTCGTACATTCAACAATGCACTGTGTTTAAGAACTTTCATCCCTCTCAGAGTTTTGTTCTTTAACTTCTTACACAGATCTTCAATCTCAGCAGTGTACGAATCATTTCTTTTCGCTGCAAGCTCAAGCAATTTGCCAAGGTCTACCCAATCTTCAGACTTTTTTGCCTCATTTCCCCCTGCAAAGCAAAAACTCCAAATCTTTGCATCAGTACACTTCTCCATTTTGTAGATGCATATGTGTTTCCCTTTCAAACCAGAACACCAGTAACCTTGGCAATGAAGGGTGATAATTGCTCGAACAATATCCCCAGTTATCTTGATGAATTCTTCAGTGAATCTCTTCATACTGACAGTTTTATCATTGAATCCATCAGTGTAGTTAGACAGCAAACAACTTGGCGGTGGAACAGCTAAGAAGGTGTATTCCCTGTACCTTCGAATACCTCTGCCATATGACAATGGTTTGACTGTGAATGGGCTATTAACTGCAACAAGTCGCACATACAAGGCATCTGCAGCTTCTCCATCACATGAGGTAAATGCAAGCACAGATGCTTTGGTTTGTATTCTAAGTCCTTTACCAAACTTAACAGTACCCTTATAATATTTCACATAGTTTGCTGAACTCCCAAGTTTTTGGACCTTGCTGTCTGTTATGACTATTTGAGAACTTCCATTGACCTGGGACAAAATGTTGTGGCTTGTATTATCTGACATCGTGTCCATGTTGTATCCTTGGGGCAAAAGGAGGAGGAGTCGCAGACAGGCCGCGGCGTCGCGTCGACGGAGGCGCTCGGTGTCGGCGACCCGCCTCCGCAGGTACGGGCGAAACGAACGCCGGCGAAGGTGATGCAGCGCGCGCTCTGGGGGGGCTCCGGCTGCGCCGCGTCAACCGGCGGCGCGAGGTGGGGAGGGAGTGGAGGGGCCCGACGAGGCGATGGATGCCCGCGTCCGTCCCTGCCTGGTCGCCGCGCACGGCGCCCCCGCTACCTTCCTGCTCGCTCGGTGCGAGGAGGCGACGACTCTCCGGAATGGCTGCGCTCCAGCCCTCCCTACCTGGTCGGTGACGGTGAGGGGGGCCGCGGCCGGGCTGGCCAAGCGCGGCGCGCACGGTGGGGTAGCGGGCGGTGCGTGGGGCCGCGGCCGCCGCCGGAGGCGACGACGATGAGGGCGAGGGTTTTGTAGCGGGTTGGCGGCGGCTTAGCTCCCCGAGGCGAAA

Coding Potentia
Explanation CPC Score
noncoding -1.09623
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0100700.2 11 18544175 C T
Osa11LNT0100700.2 11 18544415 T A
Osa11LNT0100700.2 11 18544422 G A
Osa11LNT0100700.2 11 18544448 C A
Osa11LNT0100700.2 11 18544483 A C
Osa11LNT0100700.2 11 18544503 A G
Osa11LNT0100700.2 11 18544511 A G
Osa11LNT0100700.2 11 18544608 A G
Osa11LNT0100700.2 11 18546364 G A
Osa11LNT0100700.2 11 18546504 T C
Osa11LNT0100700.2 11 18546799 G C
Osa11LNT0100700.2 11 18546819 A C
Osa11LNT0100700.2 11 18547685 T C
Osa11LNT0100700.2 11 18547775 A G
Osa11LNT0100700.2 11 18547808 A T
Osa11LNT0100700.2 11 18547831 A C
Osa11LNT0100700.2 11 18548137 T C
Osa11LNT0100700.2 11 18548212 T C
Osa11LNT0100700.2 11 18548436 T C
Osa11LNT0100700.2 11 18548728 A C
Osa11LNT0100700.2 11 18549073 T C
Osa11LNT0100700.2 11 18549336 A 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
Osa11LNT0100700.2 osa-miR812p Translation 3.0 14.337 1 24
Osa11LNT0100700.2 osa-miR812q Cleavage 2.5 13.196 1 24
Osa11LNT0100700.2 osa-miR5797 Cleavage 4.0 19.966 1 21
Osa11LNT0100700.2 osa-miR812s Translation 3.0 14.347 1 24
Osa11LNT0100700.2 osa-miR5799 Translation 5.0 14.347 1 24
Osa11LNT0100700.2 osa-miR6251 Translation 4.0 10.219 1 21
Osa11LNT0100700.2 osa-miR166a-5p Cleavage 5.0 7.468 1 21
Osa11LNT0100700.2 osa-miR812a Cleavage 0.0 14.337 1 22
Osa11LNT0100700.2 osa-miR812b Cleavage 0.0 14.337 1 22
Osa11LNT0100700.2 osa-miR812c Cleavage 0.0 14.337 1 22
Osa11LNT0100700.2 osa-miR812d Cleavage 0.0 14.337 1 22
Osa11LNT0100700.2 osa-miR812e Cleavage 0.0 14.337 1 22
Osa11LNT0100700.2 osa-miR444d.3 Translation 5.0 15.125 1 21
Osa11LNT0100700.2 osa-miR1439 Cleavage 4.0 14.079 1 21
Osa11LNT0100700.2 osa-miR1850.1 Translation 4.0 10.638 1 21
Osa11LNT0100700.2 osa-miR1850.1 Cleavage 5.0 17.624 1 21
Osa11LNT0100700.2 osa-miR812f Cleavage 3.5 14.336 1 24
Osa11LNT0100700.2 osa-miR1862d Cleavage 5.0 21.141 1 24
Osa11LNT0100700.2 osa-miR1862e Cleavage 3.5 21.779 1 24
Osa11LNT0100700.2 osa-miR812g Translation 3.5 14.347 1 24
Osa11LNT0100700.2 osa-miR812h Translation 3.5 14.347 1 24
Osa11LNT0100700.2 osa-miR812i Translation 3.5 14.347 1 24
Osa11LNT0100700.2 osa-miR812j Translation 3.5 14.347 1 24
Osa11LNT0100700.2 osa-miR812k Cleavage 3.5 14.336 1 24
Osa11LNT0100700.2 osa-miR812l Cleavage 3.5 14.336 1 24
Osa11LNT0100700.2 osa-miR812m Cleavage 3.5 14.336 1 24
Osa11LNT0100700.2 osa-miR812o-5p Cleavage 2.5 11.392 1 21
Osa11LNT0100700.2 osa-miR812o-3p Cleavage 5.0 16.297 1 24
Osa11LNT0100700.2 osa-miR166e-5p Cleavage 5.0 7.468 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0100700.2 11 gpl11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0100700.2 11 gw11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0100700.2 11 yld11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0100700.2 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0100700.2 11 hbd3 Physiological trait Lethality nan nan
Osa11LNT0100700.2 11 Hbd3 Physiological trait Lethality nan nan
Osa11LNT0100700.2 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0100700.2 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
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