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

>Osa05LNT0299000.1

CCAATATAATCACAGATTCATTAATGAACACAAACATCACAAGTTCAGTAACCAAAACAGGTTCAATTACATCGATACAACATCAGTACATTGAGCATATCATCGCCGACCAAAATCCAGCCAACGTCATTGTGACCAAAATGACGTCACTTGTCCAAATAGTCGTTTACATTCACCAACAAAAACAAAGTCACATGTCCAGATCACACCAACCACAAAACTAGTCATCTCAGCATGAATCAGCATGAGGCTAACCACAAGAGTGTTAAGGCCAATCAGCCGACGAAGGTCATTTGTCTCCTTCGGTGACTTCTTTAAAATTTCAATATCTTCCAGCTGTTGCTTCCTTGCTTCGTGTGATTCTTCTACCTCTTTCTTGATGGTAAAATAGTATTTATTGGTTAATACAGAAGAAACCAACTACATGAACAAAACAGATGGGTGAATATCTATTCATGCAAACAGTGGGTTAAGTTCAATTACTCAGAAATGTACTGTAACGCATATATAACTTGTATCGTGCATGTATTAGAACAATAGTGTGGAATATAAGCAACAATACCTCCCTGACTACTATATCTTATCTAGAGAATCCAAATGTTTGGATGCAAATGTGGTATGAATATATATTGAACAATTAAGCAAATGCGTAAAAAGTAATCCCATCTAAACCCTAAACATGTATACAACTACAAGAAAGCTTGCGGCAAAAAACTACAAGAAAGCTGTATAGTTTTGTACTAGTCCTCAACTAAATGTCATACAACTCTTAGCTTGTTTCATTCATGTTGAGAGCCCGCAAAATACAAGGTTTAAACCAATCAATACATAAATGAATTACGATAATGATATGAATGCATTACTGAGCAAATCTGAGAATCTAGACCAGCTTATAACTGATCCTGGAGGAAACATTGGAAATAGCACATCTGGACACACAAAGCAAGTGTCTTTGCACAATAGCCATGTCAAGCTGGAATCTCTGTCCATTTTAACAAGAAGGAGCTCTGATATGAGAAGTTAAAACACATTAATAAATCCAAATGGTAGCAAGTGTGCTCAGCTTCTGATACTTACATTGTGCAAAAAACGATAATGGAATATTCATCTCCTTGCTTAAGAAGGTGTGACGGAATTCAATAAGTTGAATATGTTAGAGAAAATATCAAGTGTCTGCAAGAAACCATCATGATAGTAGGGATAGATAAATGATGGATTGAAAATGAAATTACCATTTTGTCAGTAGTATAAGGGTCATCCTATCTTGTCAACTTGCTCGTTCTTGCCGAGGCCCTTGCCCTTCCACCCCATCTTCTGGAGCAGCCTGAATCCGATGTTGGAGGAGGTGAGCTGCGTGTCGACGGACGCCTGCTCCAGCCCCTCCGTGTCGAGATTCTCTGTGGGGCGGTGGTTCATCGGGCTGGTGCTGCTGCTGCGGCCAGGCGAGGAGGGTCGCCGCCGCCGTCCAGATCCACCGCCGTGCCTACCGCACGCCGAGCTCCTCCGTAGGGCGGCGGATCCGGCCCTCCCGAGGACGGTGCCGCCGGATCCGCCGTTGCAGGCCGTCGCCGTGGCCGCCGCCCGCTGCCCGCCGCCATCGGGGAAGGGAGGTCGCCGCCGCGCATGGGAGGTCGGGGAAGGGAGGCCGCCGCTGGTGCCGAGCCCGCCGCTTCCGCGCCGGATGGGAGGTCGGGGAAGGGAGGCCGCCGCCGCCGGTGCCGAGCCCGCCGCTCCCGCTCGCCGCGCCGCGCATCTCCCGTGCTCGCCGTCGGTGAGAGAAGAAGGAAAGGAGGAAAGAGTAAGAGGCTGAAAGGAGGATAAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.889705
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0299000.1 5 7848213 A T
Osa05LNT0299000.1 5 7848360 G C
Osa05LNT0299000.1 5 7848942 T C
Osa05LNT0299000.1 5 7849720 C G
Osa05LNT0299000.1 5 7850214 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa05LNT0299000.1 DTM_#DNAt_MULE_japo_Os1404 Chr5 - 7846386 7851931 2499
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa05LNT0299000.1 osa-miR396e-5p Cleavage 5.0 11.412 1 21
Osa05LNT0299000.1 osa-miR396g Cleavage 5.0 11.412 1 21
Osa05LNT0299000.1 osa-miR396h Cleavage 5.0 11.412 1 21
Osa05LNT0299000.1 osa-miR396d Cleavage 5.0 11.412 1 21
Osa05LNT0299000.1 osa-miR1862f Cleavage 3.5 16.464 1 20
Osa05LNT0299000.1 osa-miR1862f Cleavage 5.0 13.947 1 20
Osa05LNT0299000.1 osa-miR1862g Cleavage 3.5 16.464 1 20
Osa05LNT0299000.1 osa-miR1862g Cleavage 5.0 13.947 1 20
Osa05LNT0299000.1 osa-miR5144-5p Cleavage 4.5 12.443 1 21
Osa05LNT0299000.1 osa-miR5488 Translation 4.5 17.545 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0299000.1 5 yl(t) Morphological trait Shoot/Seedling nan nan
Osa05LNT0299000.1 5 qTHJ-5 Morphological trait Seed RM289 RM249
Osa05LNT0299000.1 5 gnp5.1 Morphological trait Panicle/flower RM194 RM249
Osa05LNT0299000.1 5 nt5.1 Morphological trait Culm/leaf RM169 RM249
Osa05LNT0299000.1 5 snp5.1 Morphological trait Panicle/flower RM194 RM249
Osa05LNT0299000.1 5 QKw5 Morphological trait Seed RG182 RG13
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