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

>Osa04LNT0264700.1

AAGAGGAAATGGTATTGTAGATACCTTCGTTATCTTTTGCATAACTCACAAATAAGTTAATTTGATACAAGACAGACATTATTTCCTGATGATACCATGAGCTCACAAAAATGAACCAATAAAACTTATTTCAGTCTCAGTCCAAGGAGATTAATACATAAGTACCATAAGACAGATGAGATTAAGTCAAGTTTACAACACATAAGCTGAGTCAGATTCTGCTGACTCTAGATGATATCAGGGCCAAGATATCAGCTCTCAACCATGATCAAGAACCAGGGTCCAGGAAGAGCACATGCCACGGACTTCAGCGATGAGGGTAAAAGTAGCCAGTCCAGATTAGGGCAGCCTGCGGCGATTAGATCAGTGCAATGCTGCTCTCGCCACCAGGGGGCTTGCGGACACCGCCGAGATAGTCTCGGGGAGCTGCCGCTCCATCAGCAAAGATGTCACTGCCGCTCATCTCCTTCAGCTTTGCTGAGCTCAGAGATTTCTCAGCTGATGCAGGGGTAGCGTCCTCTTTGAAGATGTTGTTGCCTGTCAACTCTTGGAACTTCTGGTTATGGATTTTCTTTGACGTCTTGACTACAGGCTCCTCACTGAACGTGATGTTGCTTGGACCTCCAGCAGGATTGGATACTTTCACTGATGTGTGGACGCTTCTCGGTTGTGGAAGTGCAAAATCTAGATTTCCTTGCAGCTCCATATTGCGAGCAGCCAATGGCCTTGCAGGGATCTCTGGAGGAGGACCAAAAATATCACTCCCACTGAGCTCCTTGCTCTTGGCTTCAGAATGCTGCTTATTCATTTTAGCCTCAGCATCAGTCTCCAGTGTACCACTAAGCTCTCGCTGCTTAGCCACCTCAGGTAATGACGATGGCTTCTTTGGAGAAACACTTCCATCAGCACTGAATGAGATTTGGCTTATTCCAGTTACAGTTTGCTGATACATCCTTACAGAAGTTTTGTTTGCAGGATTTGAAGCCTCTGAATCATCATTTTCACTATTCTCAGCGAATATCCCACTTCCAGTCATTTCTTTTAACTTTGAGCCCGAGCAAAATTTTCGTTCACATAATTCGGCCACCACAGAAAGTGGTCCATCAAGAAATTTTCATGGACTGTTTTCCATAAATTATACAAATATAAACAGCCAACACTCCACAAAATTCTATGACAGGCGAAGTAATAACATAGTGTATGCAATGACATGGTCACAACTGCAGGTCAGAACAAACAGTCAGGCTCCACATGACTTGACTTATTAAGCTATAATTTCTGGTCTCTTTGTGGCACCCACGACAGAAATATCCAAATTTTGAACCAGGCATTTGCCGTTTGCCTCAGCCCAAATCACTTTCAAGCATCATTGCCTGTACTGCTAAAACTTGGATTCTAGCACTAAAAATTTGGACATTAGCAAACATCTCATGTTTGCACTGTACCACACATACACGGACACGGTTGATCGTCACATGAACCAACCAACCAACCACCTGCAAGCGACTATTCTCCCTCCAGCAAACCACCCTGAAATTAAAGGCGTCGAGAGCGCAATTTTTTCTTCAGCTGCTACTTCTTCCTAAACCCAGAGCAACAACCCCAACCAACCTTCCTAAGTTCGAAATGTTGATGCACTAAACCACACGCCCAAACAGAGAACACACGTTCGTAGATCAAAATGCCAGATCAGGCTAATTAATCGAATGAGAAGCACAGCACAACGAAATCATAGATCGATCAGATCAGGGACGAAACAATGAATGCGGCAGGATGGGGTACCCCCCCCCCCCCCCCCAGATCTCACCTCTTGCTCAGATCCTCCGCCTCCTTCTCGCTCACCGGCGCGCCGAACATCGCCGGCGTGATCCCCCCGGCCGGCTTGAGGCTGGGGCGGGAGGAGGCGACCGGCGAGGCCGCGGCGGCGGCGGCGTCGGGCCCCGTCGCCGACCACGTGAGCAGGTCCGCCGTCGAGGTGTGCGGCTTCCTCACCGGCACCGCCCTCTCCATTGCTCCTCTCCTCCTCCGCCGCCGCCGCTTTTGCCTCGCTTGGGTTGGGTTTCGTTCCTTCCGCGGAGCTGAAAAAAAAATGCGAGCGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.542033
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0264700.1 4 22796862 A T
Osa04LNT0264700.1 4 22795512 C T
Osa04LNT0264700.1 4 22796078 T G
Osa04LNT0264700.1 4 22796747 A G
Osa04LNT0264700.1 4 22796844 C A
Osa04LNT0264700.1 4 22797020 C T
Osa04LNT0264700.1 4 22797697 G C
Osa04LNT0264700.1 4 22798487 T C
Osa04LNT0264700.1 4 22797077 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
Osa04LNT0264700.1 osa-miR7694-3p Translation 4.0 19.843 1 22
Osa04LNT0264700.1 osa-miR396a-3p Cleavage 4.0 18.174 1 20
Osa04LNT0264700.1 osa-miR396b-3p Cleavage 4.0 18.174 1 20
Osa04LNT0264700.1 osa-miR1851 Cleavage 4.5 6.096 1 21
Osa04LNT0264700.1 osa-miR3979-3p Cleavage 4.5 20.422 1 20
Osa04LNT0264700.1 osa-miR5507 Cleavage 4.5 15.109 1 21
Osa04LNT0264700.1 osa-miR1851 Translation 4.0 15.066 1 21
Osa04LNT0264700.1 osa-miR1871 Cleavage 3.5 19.755 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0264700.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0264700.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0264700.1 4 nan Morphological trait Culm/leaf RM3337 RM3785
Osa04LNT0264700.1 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0264700.1 4 gpp4 Morphological trait Seed RZ569 RZ565
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