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

>Osa04LNT0247800.1

TTCCTAATAATGCAGCTTTCTTGTTATTGTTTTATTATTAGACATGTTATGGAAGAGAAAAAACTCACAACCGAGAAACACAAGCAAATAAACCATACACCAAAATAGGTTGGCACCCACAAAGCACACACATATATCTAGCTTTGGTAATATTTATAAGCGGATCAATTTCTTCCGTGGCCAAGCTGCTGCAGGAGTTGTCCATGCCCCCTCCCATTAGCGTTTCCATGATCGTTGTCCGATATCTTAAGCTTGCGAACGACTTCATGCATGTGTACCTCCTGATGCATATGATTCATCTTCTGATGCACCTCCACGCCGTGATACTCAATTGATGTCCCTCCCTTGTGCTTTTGCTCGAGATCCTTAATTTTTCGCTGCAATTTCTTGTTCTCCTCCTCGAGACGCCTGTTCTCTTTCCTCTTTGTGTCTACCTTTAAATTGAGATTTTCTTTGTCTCTCTTCAATCTTTTCTGCTCTTCCTCGGCAGCTGTTTTGTCGGCCTGGAGAACCTTTTTTTCTTCCCTTTTTTCCCTTAGTTTTATGTCTAGATCTTCCTTCTGTCTCTTCATTCTTTCAAGGTCTTTCTTGTATCTCTCTATTTCTTCCTTTACATCATCCGGAATAACCGATTCAATCTTGACACTGGATGCCATCTTCTTGAGGCGTTCGTACAGCTTCCCCACATCCACAGTCCCTCGCACCTCCACCTTCAAACTGCTGCTCTCTGGATTTTTGCTGTAGTTTCTATACTCGATAGATTCTTTGAATTCTTGACGAAGTACATTCTTGACCTCAGTCTCGCTTGCACCCCGAACCTTTAGCTTCACTTGTTTCTTGTCACCCATTTTGCTTCAGCTATGGAATGAAACAAAAACGAGAAGGAAGTCGGAGACAAGTGCAAGATCGAGCTAGCTAGTTCTGCTTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.703456
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0247800.1 4 3410852 C A
Osa04LNT0247800.1 4 3411075 T C
Osa04LNT0247800.1 4 3411095 C T
Osa04LNT0247800.1 4 3411480 A G
Osa04LNT0247800.1 4 3411618 A C
Osa04LNT0247800.1 4 3411637 C T
Osa04LNT0247800.1 4 3411664 C G
Osa04LNT0247800.1 4 3411729 C T
Osa04LNT0247800.1 4 3412022 A G
Osa04LNT0247800.1 4 3412070 T C
Osa04LNT0247800.1 4 3412270 C A
Osa04LNT0247800.1 4 3412315 A T
Osa04LNT0247800.1 4 3412105 T C
Osa04LNT0247800.1 4 3412323 A 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
Osa04LNT0247800.1 osa-miR5079b Translation 3.5 12.623 1 22
Osa04LNT0247800.1 osa-miR2100-3p Translation 5.0 18.285 1 22
Osa04LNT0247800.1 osa-miR5079a Translation 3.5 12.623 1 22
Osa04LNT0247800.1 osa-miR5824 Translation 4.0 12.872 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0247800.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0247800.1 4 nan Resistance or Tolerance Other soil stress tolerance C946 R1854
Osa04LNT0247800.1 4 qOVA-4 Resistance or Tolerance Insect resistance R1854 C946
Osa04LNT0247800.1 4 qCTS4-1 Resistance or Tolerance Cold tolerance RM335 RM261
Osa04LNT0247800.1 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