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

>Osa04LNT0259600.1

ACAAAGTTCACTATATACCTTTTTTTAATGGAAGTTACATAGTTACTGATACTTTACATATCTCTAAGCTGGAAATGTATTGTAATAATGGGGATGCATTAGCAGATTCAAAAATTCTTTGTTCTCTGTAGAATAATCTGTTACTATTGGTATTGCCTTGGTGAATAGAATATATTTTGAGCATTACTTGTTGCCTTGTACTTGCTGGAGTGGCAACTAGAAGCTACCTTAGTTTCCTTATTGGCAGGGCGCGGCTGAAGACCTTCTCAACCTCAGTTGCTTCCATGTTCATCTGATCCAAAAGCTCCATCTCCTCCTTGCTTAGCCCCTGAAAGAAGTTCATCAAGTCCTGTTTCACCTCCATGAGGCCATCTGTCAACCTCTTGAACAATGTGACCTCCTCCTCCTCCAGCTCCTTCACCTCTCCCTCGATCTCGCCCTCGATCTCCTGCACTTCCCTGATGATGGTCTTCTCTCCTTGCTCGACGGTCTTCTCTATTCTCTCCACAAGAGGTGGCTCAGGACCGCAGGTGTTGTCGGTTCTGATGAATGTGGAGAAGTCACGACCTACGCTTTTTGCCGCCCTTTCTAGCTCAGGTACTATTGATTCAGGCACAACTTTGCTTCTGGTGTACAGAACAGCACCTCCATATCCATCCCACGCATCATTTCTGCCGCGGTAGTACACGAAAATGTAGTCATCTTCCTTGTTCTCTACTTTGGATGAGATAATGTACCAGTCATCTTGATAGTGCAGGAACTCGTTGTCATGGTTATAGAGGATCGCGGGTTGTGCTGGGTCCTGCACAAACCGCTGTATGGCTGTTCTGGTGAAGAAGCCAGAGTCGGGGGTGCGAATTCTCCATGTCAAGTTCGCTATAAGTTTGTCTCCCTCGACACGGAACTCGTGAAGTTGGCAATCGAATGTGTCGAAAGTGGGATTGAGGCCACTTGAAATATACCACTTGCCGTTGAAATCAGCCATGTTGAAGTTCTTGACAAGGGCGGATGGATCAGGGACTGGGAACTCGCCAACGTCGGACTTTTGTGGGACGCATTTCTTGCGCGAAACAGCACACTCGTTGAACTCATCGACCACAGTGTTCTCAAACAGATCTCCACATTTGATCTGGCATTCAGTCTCGTCAGGGCGATTGTTGCATGTATTTAAGCATGCTACATTCGCTGCACAGGATGGGTTTGCTATGCATTTGGCCAGCTCTATTCTGCACTCCTTGAGAAGGCAAGTGCATGTCTTGAGAGCATCCACAGCATCGGCAGAAGGGACTACAAGAACAGCACACGCCACCAGCCCTGTCATGGTGACCAAATGCGACCTGCTCCACTCCCTGATGCTGCTTAGAGCATCTGAACCTTGCAGCACCGTGTGGGCCTTGATCTCGGAACAACGAGCAGAGATCTTGGCATGATGGAGAGGAAGATGATCGCCCTTCCTCCATAGGTGAGCCCTCGGGGGGCAGCACCGGTGGTACCTGACACCGCCATGGCTCCTCCTCCTGCTGGAGGTGACAGTGCTGATACCACCTCTGGTCTTGCGGCCATGGACGACCACCACCGTGCTCGATCCCTCCGCTAGCAACGCGCGATTCCCGCACTGCCGCGGCATCATCTGGGTTGCGGCCGCGGCGGCCGGCGGAGCGAGGAGGAGGGGATCGAGAGCTCGAGCAGCGGCGATAGGGCGGCGGCGAGGGGGAGATGGATAACGCGCGCGCCGCGGAGGGGCTTGGCTTGGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.974933
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0259600.1 4 18553667 G A
Osa04LNT0259600.1 4 18552469 C T
Osa04LNT0259600.1 4 18552512 T C
Osa04LNT0259600.1 4 18553425 A G
Osa04LNT0259600.1 4 18551630 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
Osa04LNT0259600.1 osa-miR5543 Cleavage 4.0 18.187 1 21
Osa04LNT0259600.1 osa-miR166a-5p Cleavage 5.0 15.445 1 21
Osa04LNT0259600.1 osa-miR166c-5p Cleavage 5.0 15.445 1 20
Osa04LNT0259600.1 osa-miR166e-5p Cleavage 5.0 15.445 1 21
Osa04LNT0259600.1 osa-miR1848 Cleavage 4.0 21.866 1 21
Osa04LNT0259600.1 osa-miR1854-3p Cleavage 5.0 20.954 1 22
Osa04LNT0259600.1 osa-miR2928 Translation 4.5 15.181 1 20
Osa04LNT0259600.1 osa-miR3979-3p Cleavage 3.5 10.595 1 20
Osa04LNT0259600.1 osa-miR5147 Cleavage 4.5 24.876 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0259600.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259600.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259600.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0259600.1 4 qNOT4-2 Resistance or Tolerance Drought tolerance RG449 RG788
Osa04LNT0259600.1 4 qFRP4-1 Physiological trait Source activity RG449 RG788
Osa04LNT0259600.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0259600.1 4 nan Morphological trait Root RG449 RG788
Osa04LNT0259600.1 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