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

>Osa04LNT0252300.2

TATGTATCCCTCTAATTAAGAAAATTGTCAGATCTCTTGTCCCATGGGTTCAGATTTAGTCGGCTCGTGCTATTACAACTTGAAGTTTATTGTGGTCATGATTCATTTTGTATTCTAGTATTGCAGATTTTCTAGTGCCACGGATCACAGCTGGCGAACTGTGAGCTCAACACAACTTCATGAACAAAGCTATCTTTGAGATATTTTCTTTCTTGCGGGAATTTTATCTGGTGCCAACACAGCGCATATGTATCCATCATCAGGTGTACCTGGGAATATCTTGCATGAACCTTGTGGATCTGTCTGTATATGTACTATGCATTTTCAACGCTACAATCGGGTAACCAGTTTCTTATTGTCCAATAATACCGTGCTGATATATACTCCGTATATTTTATCTGCCATGCATGTCTAAGCATTGACGGTGACTTTTTTTCTGTGATTATCATGGGTCCAGCTCCACCGAAACCTTGAAACCTTGTTCAGTTAATCCCCTAAGAAACTTGAAAAGAATTAAGAGAAAAGACGTGGACTTAATCCCCTCGATCTTGTCCGATCTCTTTCTTGTGAGGATTAACCGAAAAATCCTGAAACGGTGAAAATCTCCTAACGGTAGGAAGCAATGAAGAAAAACGCAAGCACCCGCACAAAGGCTTCATTTATAGGAACCATAGGTGACTGAGATTTCTAAAAGTTTTTGGAAATATAGTCATAATTCCAAATATTTTAATCCATAAATATAATCATAATAAACATGACTTGTGATAAACATGACATGTGAAAAAGAGAGTGATTCTACCATGGTGGTACACATGAATATGCTACCAGTAACAATAGCATCTAAGAACACATTTAACACCGAGATGAGAAGAATATACCTAGAGAACGCTCCGAATCCGGAGGCGACAGTGTTGTTGGTTTTGTCGCCGTGTTGCCATTGTAGTTTTCTCTCCTCTATTGCCGTTGTTCCCTTCGTTGCCGGTGACGAAGAGGAAGAATAGCCTATTATTGATGGAGATCGATCTGACCGGAGTAGATCTGTCGGTCTGACCGGTGTAGTTGTTCCGGTCTAACCGCCTGATGTACTGTTGTTGCTTGTCGCCACCACCGGTCTGACCGCCATGGAGCCGCCGATCTAACCGGGTCGATGCCATCGGTCTGACCGCTGATATCTCGCCGATTGGACCACCGCACCTCATCAAGGGAAGAAGGGTTCTCCTTTGTTTCTTTGAGTACTGCTTGAAAGATCTGTAGTGGGTCCCCATGACTGACAATAAGAATTGCAGAGCCATGAAGCTCCATTTCTGCAGCAGACAGGAATTGAGAGAATCTAGTAGCAACATCTGCAACGCTCTCGCCACCATCTGGTGCCATTAAGGGATCTACTTCATCTACTGCCCATACTTCTGCATACTTCTCATGTGAAAGCAATTCATGCGATGGCCCAAAATAGCGTTCCCGAAGTTCAACAGCTGGAATGCAGCTGGGAGTATCAAAGGGGACACCAAGCACTCTAGCAACCTCTCTGGCAGTCTCCATGGTCCGTGAGAATGGGGAATATCGGATCTGAACAGAATCCAGTGGCACACCCAATTCCTCAAGCTCCTTACGGAGCGATTCGCCGGCCAAGCGCGCCTGCTCGACGCCCTGCGGCGCCAGCCCAAACTCCGGCTTCGTGCCGTTCTCCAGGGAGGAGACGATGATGCCGCGCTCGTTGGGGACGCTGCGGCCATGGCGGAGGATCCAGTACCTGTTGCGGAAGGAGGGCGCCGGCGCCGGCGGCGAGCTGCTGCCGGAGTCATCCATTCCCCCCCAAATCAAAGCACGTAGTGACACCCGCTCCAATCAAAGAGCGGAGTTT

Coding Potentia
Explanation CPC Score
noncoding -1.20153
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0252300.2 4 8277494 C T
Osa04LNT0252300.2 4 8277772 A G
Osa04LNT0252300.2 4 8278234 A G
Osa04LNT0252300.2 4 8278283 T C
Osa04LNT0252300.2 4 8278762 A G
Osa04LNT0252300.2 4 8279394 A G
Osa04LNT0252300.2 4 8280319 T A
Osa04LNT0252300.2 4 8280820 T C
Osa04LNT0252300.2 4 8280900 T A
Osa04LNT0252300.2 4 8281002 A G
Osa04LNT0252300.2 4 8281091 C A
Osa04LNT0252300.2 4 8281527 C T
Osa04LNT0252300.2 4 8281687 A G
Osa04LNT0252300.2 4 8282136 A T
Osa04LNT0252300.2 4 8282442 G C
Osa04LNT0252300.2 4 8282448 T A
Osa04LNT0252300.2 4 8282614 C G
Osa04LNT0252300.2 4 8282700 A G
Osa04LNT0252300.2 4 8282845 A G
Osa04LNT0252300.2 4 8283916 T C
Osa04LNT0252300.2 4 8284019 G A
Osa04LNT0252300.2 4 8284140 A C
Osa04LNT0252300.2 4 8279238 G T
Osa04LNT0252300.2 4 8285044 C G
Osa04LNT0252300.2 4 8278448 A C
Osa04LNT0252300.2 4 8278950 T C
Osa04LNT0252300.2 4 8284083 A T
Osa04LNT0252300.2 4 8278425 A G
Osa04LNT0252300.2 4 8278574 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0252300.2 osa-miR5540 Cleavage 5.0 17.152 1 21
Osa04LNT0252300.2 osa-miR435 Translation 4.5 10.382 1 20
Osa04LNT0252300.2 osa-miR2099-5p Cleavage 5.0 17.323 1 22
Osa04LNT0252300.2 osa-miR5144-5p Cleavage 4.0 19.526 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0252300.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0252300.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0252300.2 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252300.2 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252300.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0252300.2 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
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