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

>Osa04LNT0252600.1

CCTGTCATCCCTAAGAAAGTAACCACGCACCAAGAAAAATAGAAAAAAAAGCGCGCCGCTAACCTCCGCCATCCCCACGTCGCGCCGCGCCGCCCTCCCCACGTCGTACCTCCGCCGCCCGCCTCACCCGCCGCACTCCCCTCTCCCCTCTCCCTCGCGTCGCCCACCTCCCCTCGCCGCACTCCCCTCTCCCTCGCATCGCCCACCTCCCCTCTCCCCGCTGCCTCAGGATCTCCTCCGCGCCGCCGCCGTTCAGTCGTCGTCGCCGATTCTCCTTCGCCGCGCACAGCCGTCGTGGCCTCAGGTTGCTTGCACCTTCTCCCATGCTGACTAACGGCGTCGTGGCCGCCGCCGCCATCATCACCGGCACCGACCTCTCCTCTCAGATAACCGAAAACATCATGTTGAGTTTTGAGTGGTCTCTCCGAGAAATGGAGCCTGAAGAAGCAGTAGACAATTGATTTTGTTACCAAATTTGGAGCCTCCAGACAAGCAGGCTGATGCGCAACTTGCTCTGTGGTGGTTAGCACCGAATCATGTAGTACTAATGAAGCTAATTAGGCGCAAGAGCTGCTCTCCACCCTGATTGCCATAGACCTTCCTTCCAGGTGAGAGGTGGGGCAGAGGCGGATCATGCCTGATGTCGGGATGTGCGAGTAAATTAGAGGGTTGAAAAGGGCGGCGAAGTTGTGAAGAGCTGATTCCAATCCTCGGTCTGACTTTGGGATCAATTGACATATCTCTAAAGTGCTGCAGTTGTAGTAGGGGTCTCTGTATAAACCACTCTTGAGCTTTCTCAACTCCAAGTGGATCTATTGCAACCAACACAGTGGCTCTCCCTGCTGACCATCATTGCAGGGACCATCACAAGTACCTGGACATTTTCTCATCTACTTACAAACTAAAACAGAACTTGATGCTTGAGCATACTTGATTTGATTTTTAATTTTCTGCTGGCATTGCAGGGACATCACAAGTGCCTGGACATTTTCTTCTCTACTAACATGCAAGCCACAACATGTTATTGATACAAAATGGTTTGATTTGACTCTTTCCTGCCACACATTAGAGGACGACCTGCCATGGTCGATGTTACAAACTTAACTGCTGCCAAGGATAGGAGAAAGCGTGACAGAGAGGTATGCTGCACTCCCTCTACAATCGTCACAGGAAGGGTGCCCATAAGAGATATCACAAATTATGCTGGCTTTGGTGCTACCAAGCCTATTCAGGAAGGGTGCCCATAAGAGATATCACAAATTATGCTGGCTTTGGTGCTACCCAAACCTATTCAGGAACCGTGATACTGAAAGGTCTTCTATGGGTCTTGGAAGTGCTCATCCACTGTTTTGATCAGTGAAGGGGATGCTGTTAGTGATGGAGTTAGAACAAGACATAAAGGCAAGCATCTATGGTGCTTGAGACCTACTTTCTTATTACGTCACCCAATTTTGCTTGAACAAGAGGCATGCAAAACATTTGAAGGATGGATCATGATCAACGGCAGAGGGTGAGCTGCGCCATGGGTCGTGAATCACCGTTGCTATTGCCTCCAACTTGTCGCTGGAGCCACGCGCCCAACAGCTAGAGCCAAGATGAATTCCTGAGAGAGTCTCTATCCCCTTATTCTCTCTCTTCTCTCTCTAAACCTCACACCACATACATGAAAAGGTTGCGGTGATGATGGTATTGTTGTTTCCATGGCCGCCTGGTGGCGATAGTGACGGGGAGAACGACTGTTGTGGCGGGCAGAGTAAGAAGACATCTAGGAGGTCACCAGTGGAGAGGAGGAGGGGGATGACCCCATCGTGGCGAACCAGCAATGAAGGAGATGGCCGTTGCTGTGGACTCCGACAATGAGGAAGGCAAGATCATCGAAGGTAAGGAGCACTGGGTCGTCATAGGCACGAGTTCATCGAAGGAATCTTAGATCCAGCCATCGGAGAGTAAGAAGGACCTAGATTTGGATTGGCATATTTTTTTGTCATTTTTTCCATGTTTCATCCCATATATGTTTTACATGTTTCTTTGTATTATATCAAAATATTTATGTATAAATTCTTTTGATGTTACATATTTTTTCTTACTTCGATTTGTAGGGATATGTTGATGTTTCATCAGTTGAAGCTTGATGTTTCATTTACA

Coding Potentia
Explanation CPC Score
noncoding -1.0383
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0252600.1 4 8588688 A G
Osa04LNT0252600.1 4 8588703 T G
Osa04LNT0252600.1 4 8588995 C T
Osa04LNT0252600.1 4 8590224 T C
Osa04LNT0252600.1 4 8591005 T A
Osa04LNT0252600.1 4 8591278 A T
Osa04LNT0252600.1 4 8592344 A G
Osa04LNT0252600.1 4 8593341 A C
Osa04LNT0252600.1 4 8590165 A 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
Osa04LNT0252600.1 osa-miR5526 Cleavage 4.0 13.505 1 21
Osa04LNT0252600.1 osa-miR5532 Translation 3.5 13.534 1 22
Osa04LNT0252600.1 osa-miR5804 Cleavage 5.0 22.175 1 21
Osa04LNT0252600.1 osa-miR156k Cleavage 4.0 19.812 1 21
Osa04LNT0252600.1 osa-miR408-3p Cleavage 4.0 23.246 1 21
Osa04LNT0252600.1 osa-miR529b Cleavage 4.5 18.803 1 21
Osa04LNT0252600.1 osa-miR1431 Cleavage 5.0 20.826 1 21
Osa04LNT0252600.1 osa-miR2104 Cleavage 3.0 5.466 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0252600.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0252600.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0252600.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0252600.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252600.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252600.1 4 qCCFJ-4 Physiological trait Source activity RM261 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