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

>Osa11LNT0089600.1

TACTGTAATATTGGGCTTTATCAGCTGCATGAGGGATACTAGGCGCCTGTTTACCAGACGATGTAGGTTTATCGGTACAGAGGACTGCATTGTCAAAAGAGCAAAAACTAAAAAAACGTCGAACAGCAGGTAGAAAGTAACCCGCATTACAAATCCAAAAGTCTGCCCTTTAAGCTACTCGGAGAGAATAAAACACCATGGCATCATCCTTGTGGTCTCAACCTTCTTAATAATCAAAACAGTGGTGCATCAAACATTTTCCTCTTCCACTTCGTCTCCATCTTCATCGTCGTCTTCATCTTCATAAGGGTCTCCATAAGAGTCTTCATTTTCGTCTTCGTCTTCATGAGAGTCCTCATCTTCATCTTCCTCCACTTCGTCCTGGTCATTGTCATATCCTTCCAAAATCTCGATTTCCTTAAAACTAAAAACTGCACAAAGAAACAAATAAGAATAGCACAGTAAGTTTCAAGAGGTCCAACCTGAAAATTCACTCCAAAATAAAAACTTCAAATCCATTGACAACCCTTCAAAATACAAATTGACATAAAGACTTCATTACTTCTCCATAACTAAAATCTGATTATGTCCACTACTTCATTCAAAGAAAGGAAATATAATAAAATGCCCTCACTTGGAGAAGCATTGGTCCTTTATAATATGGTTGCATCCTATGCTGCATAGTTGCTGGTTTCTCTATAGCCTAGCACACGACAAGGAGAAAATTGCATGGTCTAGGGACTATACGGATACTTATGGCACTTCGTAAATAAGATTTTTGGACACCAGGCCACACCAGGCGCTGGACATAACAAATAAAATCTAGTGTCACCGAAAAAGACTACCTTAGGCAAACAAAACTGCTAAGCAATCTTTCCCAATTATTGTTTTCTAGTAGCTGCTATGATATAACCAGGATGGGTAGTGCAGCAAGCTGTCACACTCAGCACCTCTGGTACGGTAAACTGATAGTTACAGCAGAACAAAGTTTTCTCACAATAATAGAGTTTGACAACGAGATAAAATGGTATGCGAGGTAGTACTTGTGTACATGGCAAATGACATGCAAGTTATAAGATGGCAACATCGACTTTCACAAATATACAACTGATGGGAAAGGAAATCAAATCAAATGATTGAAAGATATAATAACATACATCTAACATACATGTTGACATACTAGTTATGTGATGCAAGAAAATTTTAGAAATCTTAATATGTTTTTGTAAGTAATACTAGCCAAAAGAGTAGTCTAGATAATGTCTTCCCAATCATACCAAATACAGTGCATGCTTTCATTTCCCAATTAATCCATGGTCCTAACATCCGTTTCCCAAGAACTTACAGTTTCGATACTGCTTACTACATTTCACGCGTATGAAGGGAAAAGAAAATTTCAGAAATGTACAAAAAATGAAGAATGTTACGTATGTTAAATGTAGACAGATACTTCAAAACTTTGAGTACTCTCTTATCAACCGTTTCGCATTTGATTTCAACTATCTCAAGATGTGCTGATATTACAAGTGAACTATCCATTGAATGGCAGTTTCCTTTGATTTTCATTCTATGTTTAGGTCCCTTGGAACAGATCTGAAGAATGAGATTCTCTAGAACCGGTGCATGTTGAAGAATGCAAGTTAGTGCACTAAAATCATCGGGCACACACCAGTATTCATTGAGTAACAAAGTCTTTAGCTTGGTAAATGTTGGGCGCCATTTCAAATCCCTTTTCAAAATAAACGATCCACGTTCACTTATCAGCCCCAACGTCTTAGCTTCCGATAAACCTTCCAAAAGCACACAATTGTTGTCCTTGATACCGTAACAAGATTCGCAGTTCTCATGACCACAATCCCCAGAGTCAGACCAAATGCAATAGTCTTTAGTCCAGTTGAGGACTCCAACAAATGCATCAACTAATGATGGCATCCTCTCAAGCACTGGAGCCCTGTCATGGAAGCCATCCAGCTGCAGAGAAACAAGACTCGGGATAGCGATACGTACCCGAGATATCTCACTGAAATAGGAATTGGTTATGCTCAAACGTTTTGCAGAGCTAGATGAGATCTTGGCACAGCCAAATTTACATGACTGAAACACTAGATGTTCCAATGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.943999
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0089600.1 11 5168922 C G
Osa11LNT0089600.1 11 5169199 A G
Osa11LNT0089600.1 11 5169660 G A
Osa11LNT0089600.1 11 5169961 A G
Osa11LNT0089600.1 11 5169976 T C
Osa11LNT0089600.1 11 5170070 G A
Osa11LNT0089600.1 11 5170144 A C
Osa11LNT0089600.1 11 5170220 A G
Osa11LNT0089600.1 11 5170299 T C
Osa11LNT0089600.1 11 5170422 T A
Osa11LNT0089600.1 11 5170459 A C
Osa11LNT0089600.1 11 5170690 A 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
Osa11LNT0089600.1 osa-miR6251 Translation 4.5 16.648 1 21
Osa11LNT0089600.1 osa-miR395u Cleavage 4.5 15.386 1 21
Osa11LNT0089600.1 osa-miR1862a Translation 4.0 8.204 1 24
Osa11LNT0089600.1 osa-miR1862b Translation 4.0 8.204 1 24
Osa11LNT0089600.1 osa-miR1862c Translation 4.0 8.204 1 24
Osa11LNT0089600.1 osa-miR1862d Cleavage 5.0 8.204 1 24
Osa11LNT0089600.1 osa-miR2864.2 Cleavage 5.0 12.748 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0089600.1 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0089600.1 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0089600.1 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0089600.1 11 dc11 Resistance or Tolerance Cold tolerance RM552 RM3137
Osa11LNT0089600.1 11 fer11 Resistance or Tolerance Cold tolerance RM3701 RM552
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