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

>Osa04LNT0265600.2

ATTCCCATCAGTTTCCATTTTATTCCCCCCTTTGATCCCTGTGACCTGATCCTGCAGAGATAAGCATGGTTGGTTAAGCAGCCCAGAAGAAAGAACACAAAAAGCCAAACCACACCCTTCATTCCGGTGTATGACAGGTCGAGGTCTACATGCCAAAGCTCTGCCCTTTACACAACATTTTTTCTTGCTGGGAGAAGCTTCATCTTTGTCTCAAGGGTATATGTCCTGATTCTGCAGCCATTGCATGGCTTCCCAATTATTAAGGTCATGTCGTCTTCAGGACGGGATGTGTGTCTCTGACAGCAGATGGCCTTTTTTCTGGGTCAAGCCGCCGGGTCGTTCTCCGACTAACTGTCATGGAACCCACTTGGCAATCCACCAGTAATCCCATATTGTCGCGGACCCAGCAGCAGCATAACTTCTGGTTTGCACGAATGAGCTGAATGGCTGATGGTATGTATACAGCAGAACACTGGAGCGACCTTATCCTGTAATCTAATTCTAATTGTTCTATTAACAATTTGTCTATGGAACAAAACCAGATGTAGTGCTTCTAGCAAAGACTACAGAGCGCAAGATTGTTGTCAAGTGAAATCCTTGGACCTCCGTGTTTCACATTCAGAAGCTTGATTTCTTCTGATTTGGTGGCAGTTTTCTCCTCCAAGCACCTAAATTTGCAGCCCCAAAACTCAGAAGAGTGCAGTATCCTTCACATGTACAGTAGAGACGCATATTTGCTCCTACACGACTATAACCGACATGTTCCCATGTACGTTGGCAATTCAAACACCATTTTGATTGCAGCTTAACTTCTTTCTTCCTTGCAAAGCCTCCAGTTAGCTTAATGTATGATATCCCATAACTCCTCCAATATCATCTGGGTTTGTTGGTCTATTTCCAGGTTTAGGTAACCATGGAAACAATTTAGTGAGGCCTTGCCTTTCAGAATCAGCATTCTCTTGTCTACCATTGACCCCATATTTCTCCCTCTCAATTGCATCCATAATATCCTCCCGAGCCACAGTATTGCCACCCCTTCGAGCAGCTAGTAACGCAGCCTCATTCACAATGTTTGCTAGATCCGCACCAACCAATCCTGGTGTTAAACTAGCAACCAGATCACAAATTATTTCAGGATCCTCTTCCAAAGGAACGTCCCTTAAATGAACAGCCAAAATATTCCTTCGCCCCTCCAAATCAGGCACACCAACCAAAACTTTTCTTGAGAACCGACCAGGGCGACACAGAGCAGGGTCCAGTGCTTTAGGCCTATTAGTAGCAGCCATGACAATAACTTTCATGTCCGAGTCAAAACCATCCATCTCAGTAAGCAGCTGGTTTAAAGTTTGGTCCCTCTCATCATTAAAACTTCTACCTCGACTTCCACCCACAGCATCAAGTTCATCAATGAAAATTATAGATGGGGCAGCTTCTTTGGCCTCCTTGAATAAATCCCTTACACGGGCTGCTCCTCTTCCAACGAAAACTTCAACAAATTCACTAGCAGAAACAGAGAAAAAGGGAATTCCAGCCTCTCCTGCAACTGCCCTTGCCAGAAGAGTTTTCCCAGTTCCTGGAGGCCCAACAAGCAGAACACCCCTGGGTAATTTAGCTCCGAGCTTCTTGTAGTTCAGTGAACCATGCAAGCAACTCACTACCTCGACGAGTTCCTCCTTGGCCTCATCGACGCCCTGGACATCGTCGAACCCCACTCGCTGCTTCCTCGGCCGGCGCCGCTTCTCTGCGCCGCCACCGGCGGACATCTGCCGCTGTATGAACCACATCATCGGCAGCAGCGACACCCACAGCGTGAGCAGCGTGCTCAGCATGTCCACCAGCAGCCTCCCCGCCGGCCGCGGCGCCGACCGGTAGTCCACCCCGCCGTCCCGCATCAGCCCCAGCAAGAACCCCTCGTCGTGCGGCACCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.09923
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0265600.2 4 23307330 T A
Osa04LNT0265600.2 4 23308099 A G
Osa04LNT0265600.2 4 23308109 T C
Osa04LNT0265600.2 4 23308257 C A
Osa04LNT0265600.2 4 23308608 A C
Osa04LNT0265600.2 4 23309770 C T
Osa04LNT0265600.2 4 23306727 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0265600.2 osa-miR5533 Cleavage 4.5 20.626 1 21
Osa04LNT0265600.2 osa-miR5798 Cleavage 4.5 17.787 1 21
Osa04LNT0265600.2 osa-miR812v Translation 4.5 14.299 1 24
Osa04LNT0265600.2 osa-miR6250 Cleavage 4.5 15.97 1 22
Osa04LNT0265600.2 osa-miR159c Translation 4.0 17.687 1 21
Osa04LNT0265600.2 osa-miR159d Translation 4.0 17.687 1 21
Osa04LNT0265600.2 osa-miR159e Translation 4.0 17.687 1 21
Osa04LNT0265600.2 osa-miR164d Cleavage 5.0 22.584 1 21
Osa04LNT0265600.2 osa-miR171f-5p Cleavage 4.0 17.647 1 21
Osa04LNT0265600.2 osa-miR1427 Cleavage 5.0 21.357 1 21
Osa04LNT0265600.2 osa-miR1427 Translation 5.0 18.343 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0265600.2 4 nan Morphological trait Culm/leaf RM3337 RM3785
Osa04LNT0265600.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0265600.2 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0265600.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0265600.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0265600.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0265600.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0265600.2 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0265600.2 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0265600.2 4 d11 Morphological trait Dwarf nan nan
Osa04LNT0265600.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
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