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

>Osa04LNT0246500.1

AACAAACAATAGCACTATATTTTATAGCACCTCAAATTTGAGCGTTAATACATTGTACACCATACAACCGGTTTTTTGGTCTCAAAATCCCAGCTTAGCTAGTTCTAATCCTCAGAAACTGCAGTAACAGCAGTATGCCCCTAGTCTGCTAAACGAACACTCCTTTTTGTCTCGAACTAGATCTTTTCATGAACTGATCTAACATGGACAAACCAACCCAGAATATGCAACAATGGCACTATCTGAACTGCAAAAAAGGCTTGATCTGCATCATCTGCTGTATTGGACTATTGGTACGATGACAGCTTTGCGGGCGACCTTTTGTACCTTCTGTTGAAAAATGATAAGCGAAGAATTGTTCATTAGGACTTAACTTCATCTCCTTCCTGGTCCTGCAAACCTCCTCGCCGTACCAAATATGAGAGCCTTTGTTAACAGTCCATGGTCAAACGTGCATGCCAGGGCAACTGCGCCACCTACAAGGATGACTTTGGGTATATTGCCTGTCCAGTGCTTTGGTTTCTCAGCTTCAGCGTTGTTGGTTGAACTGGCCTCTGTCTTGTCCTCTGCAGTGATGAGCTCATCAGGATCAACCTTCGTGTTGACATGTGCCATGGCAGCGCATTTTGAAAGGGGCTCGCCAGCAGTCCTTGCGATTTGGTATGCCCTCAAGCCAGGCTCAATCCTTTTGACGCAGCCCCACATCCCCTGCCGAACACCGAGCTTTGCAATTTCCCTTGGAATCCCCATTTCCTCATGATGGAACAGGAGCACCTCACATGCGGTCATTGAGCCATCACCGTTTCTTGATTCAACTGGACGGATGCACCAACTAGAGTAGTACACGTCCACACGACGAGGTTTGTTGCACCTTGGAACAGAGGGGCGAGGCACACCCTTTGTTACACAGTAATACGTCTTTCCAGATGCCCATATCCTGCGACCGATAATGTACTCCCTGTCACTGCAGAAGAACGGGAACTTCCTGACCCACCGGAGAACCATCGTTCCAGTCTTTGTGCACTCCTCCAACGTATCGTGCTGAAGAAGCATGTCGTCCCAAGTGTTCTTAATCCGGAACTCGTCATCCCAGAAGAAATCCCTGACAACTTCTGGCGATGCATCCTCAAAGATAGTGCTACTGCGGTATTGAGGCGGGCCACCCTCAGGATCTCTCCTCCATGCTTGGTAGCGCATCGTGGGCAGCGTCTTGTCCATCATGTGAATCCACGCCGGCCCGCCGTCCTTCTCCTCGACAAGGCGGCGGAGGTGCATCAAATCTCCGGTGTCGACGGCCAATCCCTCATCCTCCTCCGGCGCGGCGGCGGCCATCGCAGTTCTAGGAACGGCGGCAACTAGCTCGTTCTTGCGGCAGGAGTCCTCGGCGGCGGCACGCGGCGGCGGCGGCGCCGCCGAGGGTCGGCTGGCGGAAGACCCCCATGAGCAGATCGAGCAACGCCGACATCTCGCTTCTATTTTTCTTTTTTGAACTAATCACACACACGCCTCAGGAATTAATCAAGGAGGAAGAAAAGATCCGATTTATCCTCGTCGTCGTCCGCCCAAATTCTGAATCCTGAATACAACTAGTACAAGAGCAGCAGCAGCAATCTGACAATCCTCCTACTGGTGATGCAATCTGAGAAGAATTTTCCAAGACGCGGAAGAGTAGAGGTTTTTGGGCCTAGATGATGATGAAATCAGTGTGTGTCTATTGGCACCAAAATCTCTCTCTGGCGCTCATGGCGTCT

Coding Potentia
Explanation CPC Score
noncoding -1.11634
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0246500.1 4 1151944 C T
Osa04LNT0246500.1 4 1149616 A G
Osa04LNT0246500.1 4 1149796 C T
Osa04LNT0246500.1 4 1150218 A T
Osa04LNT0246500.1 4 1150253 T C
Osa04LNT0246500.1 4 1150290 C T
Osa04LNT0246500.1 4 1150296 A G
Osa04LNT0246500.1 4 1150942 C T
Osa04LNT0246500.1 4 1151136 C A
Osa04LNT0246500.1 4 1151370 G C
Osa04LNT0246500.1 4 1151465 A G
Osa04LNT0246500.1 4 1151587 A G
Osa04LNT0246500.1 4 1151695 G C
Osa04LNT0246500.1 4 1151749 T C
Osa04LNT0246500.1 4 1151768 G C
Osa04LNT0246500.1 4 1151777 G C
Osa04LNT0246500.1 4 1151820 G T
Osa04LNT0246500.1 4 1149764 A G
Osa04LNT0246500.1 4 1151855 T A
Osa04LNT0246500.1 4 1150052 A T
Osa04LNT0246500.1 4 1151780 C G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0246500.1 osa-miR5788 Translation 3.5 20.381 1 21
Osa04LNT0246500.1 osa-miR5793 Cleavage 5.0 20.686 1 21
Osa04LNT0246500.1 osa-miR6246 Translation 5.0 23.377 1 23
Osa04LNT0246500.1 osa-miR6246 Cleavage 5.0 19.265 1 23
Osa04LNT0246500.1 osa-miR5497 Translation 5.0 16.849 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0246500.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0246500.1 4 nan Resistance or Tolerance Other soil stress tolerance C946 R1854
Osa04LNT0246500.1 4 qOVA-4 Resistance or Tolerance Insect resistance R1854 C946
Osa04LNT0246500.1 4 qCTS4-1 Resistance or Tolerance Cold tolerance RM335 RM261
Osa04LNT0246500.1 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