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

>Osa04LNT0268900.1

GGCAGGCACGAAAGATGAAATAGACCCACCCAATCAAACACATTTCTGATAGCCACAAATGATTTGGTAGGGTGAAATGGAACACGGATACAGAAACCTACGTCTAGTGCTAACACCGCTATGCCAAACAAGCTCAACAAAGAGAAACAAGGCACCCCAGCACTTCTGTTACTTGCTGACGAGTGTTTCTACTACAGGAAATGAATTAGCAACAGAGTGATTTTCACTGGTAATATTCGTCGCATAGGCCAAGCGTGAAATGTAGTGAAGATCACACCACATAACGGTACGTCACATATCTTCCAGCGGTCTCACTAGCACGGATGATCTTTACAACTTGCCCACGCTTCATGCCGTAATATCTTGCTATTGGGTCCGTAATTTGAATCCGGGGGAGCTGAGTCTCTTTCACGGTATACCGCTCCAGCAGCGTCTTCTTCTGCTCAGGCGTCAGGAGCTCGTGCTCTGGCACAAGGGTATGATCCTTAATGTTCACAAGCAGTTCCGCTTCCTGGAAGACCTCGAGGTGGAACTTCTGGGAGACCTCCTGCACGGCGCTGCGGGCGAACGCGCTGAGCGCCTGCTGCACGACGAGGATGCCGTTGAACACGCTCTCCTGCTTCATCCTCTCCACGTAGCTCCTGATCGTCTTCACCCCGGGCTTCGCGTCCTTGGGGAAGAAGACGTAGATCTGGTCGGCGCCGTTGTCCTTCTTGTGGCGGCTGAAGACGAGATGGTCGCGGTCGACGGGATCCCCGAAGCGTGCGACGAAGTCGCCCCTCGGGAGGTCGATGTCCAACTCCGTCACGAGGTAGCCCCTGTCCCGCAGCATCTGCATCACCGTGCGGCGGATGCGGAAAAGCCGGCTCGTCTCCTCCTCCGACGCCATCTATCTCCTCTCCCTTCCGCCGCCGCCGCGGGGTTTCGCTAGGGTTTTGTGGGGGGAGCGTCCGCGCCGACAAGGGGGAAGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.597714
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0268900.1 4 24353240 G A
Osa04LNT0268900.1 4 24353373 A G
Osa04LNT0268900.1 4 24355067 A G
Osa04LNT0268900.1 4 24355171 A G
Osa04LNT0268900.1 4 24355172 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
Osa04LNT0268900.1 osa-miR5808 Cleavage 5.0 18.974 1 24
Osa04LNT0268900.1 osa-miR1427 Translation 3.5 22.702 1 21
Osa04LNT0268900.1 osa-miR2868 Translation 3.5 19.434 1 20
Osa04LNT0268900.1 osa-miR3979-3p Cleavage 4.0 23.209 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0268900.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0268900.1 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0268900.1 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0268900.1 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0268900.1 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0268900.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0268900.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0268900.1 4 nan Morphological trait Culm/leaf RM3337 RM3785
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