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

>Osa04LNT0246100.2

AATTTTTGGGATCCCCCCACTACATGGCCCTGTGGGTCTATTTATAGCCTTAGCACAGGCTTACACCTTCTAGGTTTAGGTTTACAGGGGATTTTACATGGTTGCCCTTATAAAAGGGACATTTACATGGGTACGCAGTGTCATTTGCATATATGGGCCTCTTGGCGAAGGGGCCTTAAAGGTCGGGGGCCGCCTGTTGGGCCTCCTTGATGCCGAACTCGTCATGGCAAAGTCTTTGTGGTTCGTCATACGCCCTTCGCCCGAGATGCCTTCGCCCGAGAAGCCTTTACTTGCGGGGTACCGACGCGGCTTTCCATCTTCGCTTATGGCTTTCGCCATAGGGCTTCGCCCAACTGGTCTTGACGGCTTTACAGTCTTCGCCACCTTCGCTTATGGCTTTCGCCATAGGGTTTCGCCCAAGTGGTCTTGACGGCTTTGGCTTGAATCCTTGATGGTACTATGGTTTCGGCAGGTCCGGCCGAAGGGCTTCATGGCATGCCTCCAACATTGAGTATGGGACTTATCGCCCATCATGAATGGGACGTTCTTCTTCATGAGACTGACCATAATTGTTGATTTGTAACATCTAAACTTCCATTGTAGCAAGCATACGGAAGCAGAAAATGGCAGGAGCTCATGCAACAGTAACAGCAGACAGGTCCCATGTCCTGTAGTCTAACATCAAATAATTTCTTACTGGATAGAATGAACAACTTGAGAAACTCAGCTGGTACGAACTCTCAAGTTGCACCTCACAGCTTGTCCTGAGCACCAATGCTTCATATGCAATACATCGTAATCTTCCAGATGAAATTAATTGTCTTCTGGAAACCGTCCCATCCAAGGTGAGTATGGAAAAAACTTTTGTATAAATGGCTGAATGCCCACCTCTGTTCCATAATTTGTTGGACGGAGGCTGCCCAAGTCTTGAATCTTTGAGCTATTTAAGTGGTAGGCCAATCCTCTTCTCAACGAATCACTCAAGAAGATAACCTCCTTGTAAGGGTGAAATCCAAGAAAATCAATATAACCACCAGAGTTATATCTGCCCCTCCTTGTAGTGTCAACAAGAAAATTAATATAACCACCAGATCCCCTGCTGTTGGTCTCAATAACATTATCATTGTCTGAGTCCCATTCAAACCTGTCCTCTACCACTGCCTCATTGTTACCGTCTTCATACTCAAATCCCCGCTCCTGATTGTTAATATCTTGTAAAGTCCAGGGTCCAGGCCCGTCAATTATTTGACATGGCTGAATACTACACGAATCCTTGCATACCCACTCCATTCTGTCACTCGATTCATCAAGAATATAGATCAAAAAACGGGATGCCAAGTGACGCACAGCACAGTACACCCCTTTCATTGATTTTCCCAAATAAAGATTTGTGTATGCCATCCCCTCACAATCTGAAGGTGGCTTGATTACTTGATATTTCCCATTGGATAATGATATTCTCATAACATACTTGTTTTGGCAATATACATAAAGTACTCCCCGGCAATAAACAGAAGTGTCTGGAACATAAACAGAAGTGTCTGGAACATATGGGTGATCCAACCGCATGTCAGAAACATTCCCTGCAGCCTCCCCTTCTCGAACAAATGACCTCTCCTCCCACACCTTTGTCCTTGATGAGAACACATGCAGGATGCAAGGCGACGGTGGCCATTCTAATTCCTCTATTGCAGGGTCTAACTTGTCATCTGAATTCAACATGTTATACCACACATTGGATCGTCGGATCTCAGGGATCATGAATACCTCAAAATGCGGTGACAACGTGGGGTCGAAGACAAGGTACTCCCTGTGGAAAATGTGCTCTACGACCATATATGGGCATGGGGGCAGTGGCGCCGACTGTCGTGTGGCTGGGTTAACCACATACTTGTGAAACAAGAGAAGCCCATTGCAGTGGTCTATAATGCAGGAGCTGCAAGGCAAATAGTCAAAGTTGCCAGATACCGTTGGGCCTTTTGAGGGGCGGGAGAAGAACTCTGACATGCTTAACTCATTAAAGTTAATGAAGATTCCACACAACGGCCGTGGGAGGAGGTCCACATGCAGCAGGTTGTGGGCCTCGATGATGGTACACCAGGTCTTGCAGACGCAGCGGGATATGGCAAGGTAGCGTGGTGCAAGACGGTGGATGATGTTGCTGAGCACATCTTCAGGTAGCAGGTTTTCCATGCCCTCTATCGTTCCAAATTCTCTTAAGATGGCCATTTATTCCTTCATATCCACACAAACCCCACTTCTATGTTGCCAGCATGAGTGGTTTTCTCCTGGATTGGGCGGGGGCATCAGGTGATTGCCCCAAATGCGTAGCAAGCGGAGGGCAATGCACATATGGCGACGGCCTGCGATTCGCCTGGTTGCAAGAAACAGGATGCAGTAGCAGATGCAACCGATTGTCTCGTGGCAGGCGAGGCGCGGATCCAAATCCTAACCCGCCGCGCCGCGCGAAATTTATGCGCAGAGGAACCCGCGGATCCAAATCCTAACCCAACGCGCCGCGCGCGGTGTCCTCGTCTCTCCACGCCGACGAGGCCGCGGCGGCTCGACCGCTCCGGCTAAATTTCACCTCCGTTTTGGGGTGGGTTGGGATTGCCGGCCAACTCCCCCGCGGCGCGTGCCCTAGTCCCTGAGCCGGTGCGCGGCGTGGCGTCGCGACGACGCGGTGGCTCACT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.426986
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0246100.2 4 794758 T C
Osa04LNT0246100.2 4 793581 A C
Osa04LNT0246100.2 4 793747 A G
Osa04LNT0246100.2 4 793861 A G
Osa04LNT0246100.2 4 793929 G A
Osa04LNT0246100.2 4 793998 A G
Osa04LNT0246100.2 4 794036 T C
Osa04LNT0246100.2 4 795123 A G
Osa04LNT0246100.2 4 795261 T C
Osa04LNT0246100.2 4 795819 A G
Osa04LNT0246100.2 4 797110 A G
Osa04LNT0246100.2 4 797915 A G
Osa04LNT0246100.2 4 798726 A G
Osa04LNT0246100.2 4 795513 T G
Osa04LNT0246100.2 4 795660 A G
Osa04LNT0246100.2 4 795754 A C
Osa04LNT0246100.2 4 795813 T C
Osa04LNT0246100.2 4 795166 C 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
Osa04LNT0246100.2 osa-miR5796 Cleavage 4.0 17.865 1 21
Osa04LNT0246100.2 osa-miR5143b Translation 4.5 16.103 1 24
Osa04LNT0246100.2 osa-miR5835 Cleavage 5.0 14.686 1 24
Osa04LNT0246100.2 osa-miR6248 Translation 4.5 5.999 1 21
Osa04LNT0246100.2 osa-miR6248 Translation 5.0 22.581 1 21
Osa04LNT0246100.2 osa-miR1436 Cleavage 4.5 21.711 1 21
Osa04LNT0246100.2 osa-miR5143a Translation 4.5 16.103 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0246100.2 4 qOVA-4 Resistance or Tolerance Insect resistance R1854 C946
Osa04LNT0246100.2 4 qCTS4-1 Resistance or Tolerance Cold tolerance RM335 RM261
Osa04LNT0246100.2 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0246100.2 4 nan Resistance or Tolerance Other soil stress tolerance C946 R1854
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