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

>Osa04LNT0252000.4

GTACATAACCGTTATACACCTTAATAGAAACCATTAGTTCTTGAAAACACACAAGAAAGCCATGCTCATCATTAATTTACTACATCCGACATAAGCAAGCAGTTCAATAACACAGGAAGTGTATAGTTTATTTTTCAGCTGGTTAGACTGAGTTCTGGCAGATTCAGGCTGAGAAGATCATTATCCTCAATCAGTTGCTCTCAGTTGCATCCAGGCTCCATAGTGTCCTTAGGAATCACAACCAAGAACGTAGCCCTGTAGGTTGGCCTCCTGCAGGTTGGGCTGCAGTGGCTGAAGCTTTGTACTACTCATGAAGCTGAGGTGAAAGCTGCAGTGCTGTCATGGAAGACTCGGCATCCTGACAGTACATCTGGCTGCTGCACACATCCCACAATGGAAATGGCTTTGGATTGACCATCGAAGCTGCCTGGGTCTGCTCACCAATCAGGTTCTTTTGACAAGCACAAACAAGTTACTCGATAGAGAATCCGTGACATAATTTCACTTGAGGATAAATCCTTGTGCCGAGTTGGAATTGGCACAGATAATTGCTCGTCTCCTGGAATTGGCATCTCCTTTTGGAATGGAGAGAGAGAGATCATAACTTGGTAGTTTAAACTAGTGTAGTAAGGTAGGATAGTACAATACTGAACAAGTGTATCCTTTTGTTAGGTCGTACCCGGTTGCACATCTCAAGAAGCTGCTGATAACGTAGCTGTTGCTTCCTTAGACGAACTTTGTACAGAGAGAACTCAATCTTCTGCTCAAAATTACTCAAATCTGCGGAGATCTCGAGGAATCAGCTTCTTTTCAAGCTTTTTTTGTTATCTCACTGGCCGCAAGCTCCTTTTTCTTCTCATAATCCTTCTTAGACAGACCCTCTCAATCTTCTATCCCTGCAGTTGTAAAAATATGAAGTATACAATGTTCTTCAGGATACTTACAAATATGCTTCCACAAGGCTTCTCCAAATTAGCTCAGTCATCCTTTATTTTGCAGTTATCTCATCAAGCTTCAGAAGGATCCTTTCATTTCCAAAATTTTTTCACCTCCAACTGCAAACTGATGAACACTGCCATTCAGCTCCATCCAACTGCAACCTTTCTTCTTCCACGTCCCCTGGACTTCCATTACTCCCCTTACCTCCTTAACATCATTCCAGTTTCCATATTCTGCATATATATTTGATAAGAGCACTTGTGCTCCACCATGATTAGGGTCCAACTCCAAAATTTTCTTTGCAGCAAACGTGCCGAGCTCAAGATCACCATGCATCCGGCATGCTGCTAACAAAGATCCCCAAATGACCACATTTGGTCTTAAGTGCATGGACTGTATCAGGTCAGCAGCTTGTCCAAGAAGTTTTGCTCTTCCCAAAAGATCCACCATACAACCGTAGTGCTCATGCATGGGCTCAATCCTGTATTGCTGGACCATAATTTTGAACAATAAACGGCCTTCTTCAACTAAACCAGCATGACAGCAAGCATAGAGCAACCCAAGAAATGTCACTCCATTGGGTTGAATCCCTTCACTTTTCATGTTCTCAAAAAGGGTTAAGGCGGATCTTCCATCACCATGCATAGCAGATGCAGTAATTATGCTTGTCCAGGTGACAACATTCTTTTGAGGCATTGCATTGAAGACATCCAAGGCAAGAGTTAAACTCCCACATTTGGAGAACATATCAATAAGAGCATTTCCGATGGGTAATATCTTACACATGCTATGATTCTCCACGAAGGAATGGATACATCTAGCTTTTTCAAGGGCACCAAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.719744
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0252000.4 4 8084882 T C
Osa04LNT0252000.4 4 8085016 A T
Osa04LNT0252000.4 4 8085286 A C
Osa04LNT0252000.4 4 8085466 G A
Osa04LNT0252000.4 4 8083806 A G
Osa04LNT0252000.4 4 8084747 T A
Osa04LNT0252000.4 4 8085071 G C
Osa04LNT0252000.4 4 8085829 A G
Osa04LNT0252000.4 4 8086081 T C
Osa04LNT0252000.4 4 8085138 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
Osa04LNT0252000.4 osa-miR5834 Translation 4.0 9.083 1 21
Osa04LNT0252000.4 osa-miR164a Translation 3.5 17.736 1 21
Osa04LNT0252000.4 osa-miR164b Translation 3.5 17.736 1 21
Osa04LNT0252000.4 osa-miR164d Translation 3.5 17.736 1 21
Osa04LNT0252000.4 osa-miR164e Translation 3.5 17.736 1 21
Osa04LNT0252000.4 osa-miR393b-3p Translation 4.0 14.618 1 21
Osa04LNT0252000.4 osa-miR164f Translation 3.5 17.736 1 21
Osa04LNT0252000.4 osa-miR1847.1 Cleavage 5.0 10.166 1 21
Osa04LNT0252000.4 osa-miR1861n Cleavage 4.5 14.975 1 22
Osa04LNT0252000.4 osa-miR6253 Translation 3.5 6.317 1 22
Osa04LNT0252000.4 osa-miR5497 Translation 4.0 14.208 1 21
Osa04LNT0252000.4 osa-miR6253 Translation 5.0 20.355 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0252000.4 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0252000.4 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0252000.4 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252000.4 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252000.4 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0252000.4 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