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

>Osa02LNT0165400.1

AGAAATAGCGAATGACAATGTTTCAGACAACAAGGTTTACATACAGCAAGAGCTGACAAATCTTTTCTGACAATTAGCCTCTTTGCCCGCCACAAACACTACAGTTGCATATCAGCCTATCAGCTATTCATCGTCCAGTACAACGACAACAACCATGTGAACTACAACTAGCAGTAAAATACATGAAACAAAGTGCATCCTGGCACAACGCTGCAATCGAATGAATGCAGCATAAGCACCCTGGAGCATTATTTGATATCAAAATACCTGAGCAAACGACACTGGAAATGAGAGTTCAACTCTGATTGTAAGCAGTAAATAGTGGTATCGGATGGCATCCTACAAGGATGATGGTAAGGCGATACAAGCCAGAAAGCATCAGGCTCTGATGGTCACACTGCACAGACATAATCCTGGTGGCTTGAGCTCAGATGTGAACCACTCTGATCCCGTTGGTGCAGCGGGATCATACATCAGTGTCTTATAGCAGGGCTCTTCATCCAGAGAGAACAGCAGCAGCTTCCCATCATGTATGCCGAAACAAAAACGAGTACTAGAACTACCTGTGAGTGGCACTGGGACTTTCTGCCAAGAATTATCAGCCGGGTTGAAGACTGCGAGTGACCTCTGGTTCTTCCACTCGATGCAGAAGAGCTTTTTGTCAAGAACAGCATGGGCTGTGACCATTACACAACCATTCTTCACCTCACCCCAGGAGTTGTCATTAGGATTGTACACGTCAACAAAACGCGTGTTACCAATTGTGAAGCGCGAACGACCGCCCATGACATACAATTTGCCTTCAAAGCTGCACGCAAAGCAGCCCCACCTTGGACGGCGAAGGCTCTCAATCAATGTCCACTTATTCTGTTCTGCGTCATAAACTTCAACACTAGATAAACTATCACCATTGGGACCAAACCCACCAGCAACATATATCATACCGTTGACCTCTGCACAAGCAAAGTCACAACGAGCCACATTCATCTTAGAAAGCTCAACCCACCTACAAATAACACAAATGGGTCAGTCCAATATTTCGAAATATCAAAACCCTGGTTATTATCCTGCATTTGAACATTTCATGGTCTGTAAATAAGTACTGTTTGTATTCAGATTACAAGGAGCATGTTAATATAAGCCTTAAAGTCTTCGCAAATTGCAATGATTGTCTTTAAATTAGCAAAATCTATTGTCTGCGCATAGACTTATTGATGCCTATGAAAAGCCAACAATACCTGTTTAGGCAAGAATCGTATCGGTAAACCTCATCAGAAACACACTCCTTCCCATGATCAGCAGCATAGCCAGCAATAACGAAAAGCTTTCCATCTAGAACAACCACACCAAAACCAGCTTTGGTTGGCCCAGGCATGGGTGGAAGAGGGCTGTGCTTTTGCCCTGAACACCCCAAAACTTCCCAATGGGACCCCTTTGATCCAGCATCAGCAGTCAGGACATACACCCACTCCTCAAGCTTCCCAACCTCTTTCCTTACAGCAATGAATTCCTTACTCTCGAGGAATGACATCCACCTCTTGGACACTGAACCCATAACAGGGAACTGGCTCCGAGGAACAAGAGCAAGACATATCTTTGCGAGATCTTCAGGTAAGCCAGGTATTAGAGCACAGTATGCGTCGGATTCTCCTATGGGCATAAAGCCTTGGGAATATTTCGCCCTTGTTGGAGCCTTGAGCTGCATGCCAGCACAAAGTTGTGCCTGTGACTGAGCAAAAGAATCTCTTGTGCCAACAAGTGTAAGCATTGTACACTCTTGAGAGCGCAACTCAATTTTTGCCTCCCCTTGTTAGCCAACAGAAATGAAAAACTTTGGCTTATCTATAAGACTTTATCTGCTATAAATGACAGTGACCCACAGGAAACAATTCATGGAAACCGTCGCCTATGGGGATGGTAAGAGACAAGGGTTTGAATGATGCTGAAATGAGGTTCTTCAACTTTGATGTCTCTGTTTTAGTAATTCTTGGTGCATCAAATGCCATCCGATACTGAGAGACTTTGGAATGGTTTTTCCTTGAAGGGTCGGAAGTCTCCTTACTGTTGAGGTAGAAACCTTTACCTCCCACACACATCGCACAATTATCTATGGCCATATAAATTTTGACGACTGTTAGCCAGCAGTTCCATCCATTTTCTGTGTTTTTAATCACCTTGGGAGCAGCGGAGGCAGTGTGGGGTGGCGCTCCGGCCTCGTGATGGGGAGGGATCGGACGAGAGGAAATCGGGGGAAAACAAATCGCCCGCAAGTTGGAGTGCGCGTGGGGACGATAGGAGAGGAGAGGAGGGAGGTGGAGAGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.37996
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0165400.1 2 17960678 T C
Osa02LNT0165400.1 2 17960788 T C
Osa02LNT0165400.1 2 17959736 A G
Osa02LNT0165400.1 2 17960992 T G
Osa02LNT0165400.1 2 17961343 T C
Osa02LNT0165400.1 2 17960809 A G
Osa02LNT0165400.1 2 17961386 C A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0165400.1 osa-miR5540 Translation 4.5 10.062 1 21
Osa02LNT0165400.1 osa-miR397a Cleavage 5.0 20.497 1 21
Osa02LNT0165400.1 osa-miR397a Cleavage 5.0 18.803 1 21
Osa02LNT0165400.1 osa-miR435 Translation 4.5 10.052 1 20
Osa02LNT0165400.1 osa-miR812g Translation 5.0 15.473 1 24
Osa02LNT0165400.1 osa-miR812h Translation 5.0 15.473 1 24
Osa02LNT0165400.1 osa-miR812i Translation 5.0 15.473 1 24
Osa02LNT0165400.1 osa-miR812j Translation 5.0 15.473 1 24
Osa02LNT0165400.1 osa-miR2093-5p Translation 3.5 22.069 1 20
Osa02LNT0165400.1 osa-miR1863b Cleavage 5.0 17.893 1 24
Osa02LNT0165400.1 osa-miR5487 Translation 5.0 16.231 1 21
Osa02LNT0165400.1 osa-miR5499 Cleavage 5.0 20.186 1 21
Osa02LNT0165400.1 osa-miR817 Translation 4.5 19.411 1 21
Osa02LNT0165400.1 osa-miR2275a Cleavage 4.0 19.911 1 22
Osa02LNT0165400.1 osa-miR2275b Cleavage 4.0 19.911 1 22
Osa02LNT0165400.1 osa-miR2275d Cleavage 4.0 19.911 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0165400.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0165400.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0165400.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0165400.1 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
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