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

>Osa04LNT0259200.1

CTTTTCTTGTTTTCTTTTGTCAACGAGGACACAACATTCACATTCTCAGAAAGAGATAACAAATAAAGCTCGTCTCGCAACACAGCAAGACCAATACATGCATTATTATGCCATAGTTCACATTTGCCACTTCCAAAGCGGCAATCATATCCATCAAAATCCAACTTTGATACACTTATTAAGTTTCTTTGCAAAGAAGGAACATAAAAGACATCTCGAAGTAAAAGTATGAAGCCATTCGCGAGCTCTAGAGGAAGATCTCCAACAGCTTCAACTTTTTCTTCAACTCCATTGGCAACTCTAATGGTGCTTTCTCTTCTTTGCGTAGTCCTCGTCGAACGGAATGCCTTTAAACAATTACAAGCATGAATAGTTGCTCCAGAATCAATCCACCATGTGGATCTAGAGTAACCAACATAATGAGATTCATTTACAAATGTAATAATGTTCTCACCTTTCTTTGCCATGATCATTTTCAAAAAGTCAGGACAATCTCTCTTGTAGTGTCCTGTCTTCTTGCAGTGGAGACATTGATCTTTCTCAACAGCGAACTGTTGTTGCTGAGGCAGATGCTGAGACTGTTTACCTTTTGAGGTGGGAGACTTGTGGTTTTTTTTCTTATCTTTAACATAGTTTATTGAACCACCATTTGATTCGTTGATTCTCTCCTCCTCTTGCACACAATTAGCAATGAGCTTCTCAAAGTTCCATTTCTCTGGACTTATGTTGTAGTTGACAATAAAATTGTCAAACTGCTTTGGCAATGAGGCCATAACCAGATGGACCAGAAAGTCATCTGTTATGCCCAAATCCATTGGCTTCAACTTGGAAGCCATGTTGCTTATTCTAAGTATGTGGTCTCTAACACCACCTCCATGGTACCTTTCTGTCACAAGCTGCTTGATCAGCTGTGTAGCATAAGTCTTTGAAGAGCCAGTAAACTGACTCTTTATTCTTTCAAGGTACTCTGAGACAGCGTCACACTCTGGGATCGAGCCCAATATGGTAGGCTCAATCGTATTCTTTACCACAGCCAAACATTTCTTGTTGGCTAAGGACCATTTCTTTTGTTCAATGTCATACGACATGACGAGAGGAGCATTGTCCCTCTGTCTCTTTTGCCAGTCAGCATCTGACTCATTTTCACCTCTGATAAGTTCAGCAAGTTCTATAGGACATGGGGTAGTCAACACCCAGTCCACCTCTCCCAAGATAAAAGCAAGGTCGAGTTTTCTTTTCCATTCTGCGTAGTTATCTCCTTTTAGGGTCGGAATATCTTTAATGCAACCCATCAAGGAGTAGCCACCTGAAATAATCATGTGCGGTGAGAACAAAATTAACATTAAAATAGTATGCATTAAGCCTACATCACCGTTGGGCAGAATTAGACATAACACATAGCCATAACTATAACATTGCAATTATCAACGTTGGTCAGAAAATTACAACATCATAGCACATAATTAATGTTCCTAAAATTAAATTCTCCCGTTGGTTCGAAATTTAATTTTAGAAACACTAATTTTCATCAATTTCATCTATTTGCAGCGGAAAAACTATATAAAATTTATATGAACAGTAGCAAAACACTGTAATTTACTCTCTGCAAAATTCTCCCGTTGGTTCAAATTTAAACAGAGGTAAAACATGCAAAAATCTATTCAAAATTCTATTGAAATTTGCATGAAAAATCGACAAAATAAATTGGAAAAAATGCTACTGTTCTCTTTTCTTTGTTTTCGGCCCCGAGGGACCTCAAACAGACTTTTCCCGGTCGGCCCGCGGCCTTTTGGCACGGGCGGGCGCCCCCCTTCCCCAGGCCGCAACC

Coding Potentia
Explanation CPC Score
noncoding -1.25427
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0259200.1 osa-miR5827 Cleavage 4.0 16.081 1 21
Osa04LNT0259200.1 osa-miR156a Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156b-5p Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156c-5p Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156d Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156e Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156f-5p Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156g-5p Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156h-5p Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156i Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156j-5p Cleavage 3.5 11.14 1 20
Osa04LNT0259200.1 osa-miR156k Cleavage 4.0 11.14 1 21
Osa04LNT0259200.1 osa-miR156k Cleavage 4.5 15.585 1 21
Osa04LNT0259200.1 osa-miR156k Cleavage 5.0 20.816 1 21
Osa04LNT0259200.1 osa-miR156l-5p Cleavage 4.5 11.14 1 21
Osa04LNT0259200.1 osa-miR1873 Translation 5.0 17.161 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0259200.1 4 qFRP4-1 Physiological trait Source activity RG449 RG788
Osa04LNT0259200.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0259200.1 4 nan Morphological trait Root RG449 RG788
Osa04LNT0259200.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0259200.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0259200.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259200.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259200.1 4 qNOT4-2 Resistance or Tolerance Drought tolerance RG449 RG788
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