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

>Osa04LNT0252400.1

GAAAATGTGGTCTACCATTCTATTACTTTTTAGAAAGAGTAATCTTCCGTGGTACATCCATCGATCTACATCATGCCGATGAGATGTTATTTCACCACAAATCAGATAGAAGTAATAAAGTGCACAAAAGGACAACTGAGAACATTTTAGGACCCCAGCCCTCTTGCACCGAATTATTCTTGCACTAGCCTGATTGTCTAAGTTTCATACTTTGCTTTTATTGTATGACTCACGCTTATTCACAGAAATTATGTTTCACTCATTGACCATTATGTTTGCCATCCCTGAATTGTGCATTCTTGGATGACTTGAATGTTTCCAGGAAATCTTTACCCTTTTGTAGTTCAAGCTTCTGCCTTGCCTTGTCCCACTTGCGTTCCAGAGCTAAAATCTCGATGATCCGAGGCAATGCTCTCCCAGCAGCATCTGTGTCAAGAAATGCAAGACGGCATCTCCTTGCAATGAAGTCCACAGCAGATTCACAGTACTCGTGGCGAGCACAGTATGCTACTTCAGCCTCCAAAAATGGGTATCCATGAGCAAGTCGCTTCCCCAAGCCTTCATTCTGGGCAATTGAAGCCACTTGTGTAGCCAAAGTTCCATATGCATGTGACAGATGCTTCGATACAGCACTGTCCATTGCACCTGGAATGATCTTCCCACCATATGTCCTTTTCATCCGTTTATAGTTCTGTGCAAGGACAGTAAACGAAGCAGGATCCCAACCATATCCACCAAGAATATGCAGATGATCAGTCACACAGCCATTGGCAGGCTTCAAATTACCTGACCTTATGGCTGCATTAACAGCATCTTCAGCCATGCTTCTATAAGTTGTCCATTTTCCACCAGTGATAGTTATTAGTCCTGGGTAGTCTTCAAATACAACATGATCTCTGGAAATGCTCTCAGTATTTTTTGCCGATGGATCCATAGCCAGTGGACGTATACCACTCCAGGCAGAAAGAACATCTGAACGCCTTACCTGAACGTTAAGATAATCACAGATAGCATCTAATATGAACTGTATCTCATCCTCATGTGGTTCAGGAAGCATTGTTATTGCTGTACTAGAGTCGGTTGTACCAGCTACTGTCCTTCCTAACCATGGCAGCATAAATACAACTCTACCATCCTTGGTTTTAGGGACAATTAGCCCCATCCCATCAGGGGAATAATAATCAGGAAGTACAATGTGCACTCCACTGCTTGGACTGATCATGGGCACTACGTCATTGTTAGCCATCTTCCTCACAGAGTCACAGAACGGTCCTGCTGCGTTAACAACCACCTTTGCAAATGCATCGAATTCTTTACCTGATAGCGTATCACGGATCCGTGCACCAATAATCCTTTCTCCAGATTCATCCTTAATGAGGGATACCACTTCAGCATAATTAAGAATAGCTGCACCAACAACCGCTGCAGTGCATGCCAAGCCCACATTCAGCCGACTGTCATTCATTTGACCGTCATAGTATACCACTGTCCCTCTTAGGCTACGATCATGGCTGTTTTTTGCAAGGGTTGGGAAAAGTTCAACTGATTCATCTACAGAATAATATCGTGACAAATGTAGCAGCCTTCTTCCAGCAACGATATCATAGAATTTCAGGCCGAACCAATAGTATACAACCTCAAACCAATTAAAGCAAGGAGTCATGCATGGCAAAGCATGGCATAAGTGGGGAGCATTTTCAATAACCTGCTTTCTTTCTTTCAAAGCATGAAAAACGAGTTTCAGCTGCCCATAATCAAGATTGAATACTGCCTTCTCCAAATAGCGCACACCGCCATGGATGAGTTTGGTGGATCGGGAGGATGTCCCAGAGGAGAAGTCCTCGCGCTCCACGAGGCCGACGCGGAGCCCGCGGGTTGCGGCATCGAGCGCGACGCCGCACCCGGTGGCCCCGCCGCCGACGACGAGCACGTCGAGGGGATCCGCGGGGGTGGACCCGGCCAGCGCCGCCCTCTGCGCGGCGCGTGGCGGCGGGGCCGCGCCCGGCTGGGCCACGCG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.940474
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0252400.1 4 8307423 A T
Osa04LNT0252400.1 4 8307941 A C
Osa04LNT0252400.1 4 8308823 C A
Osa04LNT0252400.1 4 8308964 A T
Osa04LNT0252400.1 4 8309100 A G
Osa04LNT0252400.1 4 8309783 G A
Osa04LNT0252400.1 4 8309790 A C
Osa04LNT0252400.1 4 8310082 C A
Osa04LNT0252400.1 4 8310979 A G
Osa04LNT0252400.1 4 8312087 A G
Osa04LNT0252400.1 4 8312093 T C
Osa04LNT0252400.1 4 8312870 T C
Osa04LNT0252400.1 4 8313062 A T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0252400.1 osa-miR5793 Cleavage 3.5 15.221 1 21
Osa04LNT0252400.1 osa-miR390-5p Cleavage 5.0 21.055 1 21
Osa04LNT0252400.1 osa-miR2106 Cleavage 5.0 14.78 1 21
Osa04LNT0252400.1 osa-miR812n-5p Cleavage 4.5 23.78 1 24
Osa04LNT0252400.1 osa-miR5502 Translation 4.5 12.57 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0252400.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0252400.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0252400.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0252400.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252400.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252400.1 4 An8-glum Morphological trait Panicle/flower nan nan
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