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

>Osa04LNT0264800.1

GACGGACGGAGCAAAAGACATGGTGCATTCATTATGGGATACCATCCACACCGTCACATGGTTACTTTATATCTAATACAATGGTCATTGACTTCTACCGATTACAGTAAACTTTGTAGAGAACGGGGAGCAAGGGAGAAAAGAAACTTTTCCTCGAAATAATTACACATTCTTTTACCTAGCATGTGAAAGCTACAGGTAAGTAAAAGAATATGATGTATAAAACACGGAGTCAGGAAAATTTTCTGTTCTACAAAGAAGCAAGAGCTCATTAACACGGAGTCACCGATTTACAACAAAAGAAAAAAAAATGCAGCTTACACAAAATGTTTCCTGGTATGGTGTACAAAATTGAGCATCTCTGAAATGCTCCGTTTGCCCCAGGGCAGTATAACCAGATGAACCATTTCCTTTACAGGTAGCTTCTGCTGGAAGCAAGCAGCCAAGTCACTTGTACTTTGATGACCAGTTGGTTATAAACTATGCACGGGAATCAATAGTTTCAGAGCAGAAAGCATATGAGAAATATTAGTGGGTTGGTTCACTGGCGTTTTTTGAACTTGGAGCGGCCTCGCCCCCTACTGTGACAATAGTTCTTCAAAAGTAAGTCCTGAAAATGGAATGAGTTGTGGGTAGTACCAACAGGAAGGCTACATTCAATATTCAGTTGAATTTTCCGATTTCCATCTTCTTCTTGATTGCTCTCTGGCCATGGTATACAAATGAATCTATGATTCCAGAAACAGTGAAGACGCCTCCAACTATAGCGCAAACATTAGTTAAGAAGTGCAAAAATGACACATGCTGTTCCGTGAATGTGACCTTAATTGGCGAAAGGTCGTAAAAGAAAAATACTCCAGGAACAGCCTGTATCCGACCGCTCTCACTACTTCTAAAATGTTCCGTCACAGAAAACTGATTCGAAAGAATAATGTGTTCATTTATGTCTGTGTAGACAGTGGGAACAACCTTGATGAAGTATTGGTACATTCCATATGATGAATGTTGCATCCATTGTGCCCCGTCAAGAGGATTAACCACACCAGGAAAGCGTTGTCCAAAACTTAACTTATTTATTTTATGGCTGACATTGAAGCTGTCCTTTTGGAATGGAAGCAAGTCGTGGACATGAACATTTGCCTTCTGGAAGCTTTTCCCTGGAGCAAAGTGGAAATTTCCAGCAACCTTGTTAACTTCCAGGAAACCATAAATATTGCATCCTTCTCCTTCTTCATCCTTTATACTCTGAAGGAAGCCTTCCCTTTTGCACTGGTCGATCAAATCTGGATTTGATACACCCCAACCTTTTTTCCTGTATGCTTCTCGAACATCTTCACACGAGTTACAACACTGCTCATCAGATTCTTCCGCACCATAACAAGAGCCACAATAGGTCTCATTGTGTTCAAGCCTGCCGCCATGCCGCTGTAGGGGCTGTTCCACCTTCATCCCACCAACTGCATCTTGCTTAGTTGCAATAACATTACCATGGACATCAATTCTCTGCTTGAATATATCATGTTTCACATCAAGGTGCTCTTGTCCACTGATGTCCATTGCATCAAGGCTTATTATAGAACACTGAAGGGCTGGAAAGGTGACATCAAAATTTATGCGAAGTGTTTCTCCCCTTGAGGTATCAACCCTTAGTGTTGTTTCTGTGACCGCATGAAGATATAATCGGAGCTCGGAGACGAAGAGGAGGAGCATGACGACGGAGGAGGCGAGCGTGATGATGCCGCCGGAGAGCGTGCGGCTGTAGAAGTCCTCGTTCACCTTGGGGTAGGCGTCCAGGCTCCGGAGCTTGGACAGGAGCCCCTCCATGGCCGGGGCCCGGGGGATCTCGCCGCTCCTCGCCGACGAGGAATGTTTCCGGTTCGGGGTCGAGCTCGAGCTTGGAGGCCTTTGGGGGAGTTTGGGAACGGAGGCTTACTATTACCTTTTTCTCTTTTATTTTCTGGTCTTTTGTTTGATCGAAACGGGAGGAGACCA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.681065
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0264800.1 4 22807704 C T
Osa04LNT0264800.1 4 22808578 A G
Osa04LNT0264800.1 4 22810059 T C
Osa04LNT0264800.1 4 22810213 A C
Osa04LNT0264800.1 4 22810693 T C
Osa04LNT0264800.1 4 22811292 G A
Osa04LNT0264800.1 4 22812157 C A
Osa04LNT0264800.1 4 22807595 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
Osa04LNT0264800.1 osa-miR5815 Translation 5.0 9.459 1 24
Osa04LNT0264800.1 osa-miR393a Cleavage 4.0 16.735 1 21
Osa04LNT0264800.1 osa-miR393b-5p Cleavage 4.0 16.735 1 22
Osa04LNT0264800.1 osa-miR1430 Cleavage 5.0 19.627 1 21
Osa04LNT0264800.1 osa-miR444d.3 Cleavage 5.0 13.944 1 21
Osa04LNT0264800.1 osa-miR1854-3p Translation 4.0 14.655 1 22
Osa04LNT0264800.1 osa-miR5513 Cleavage 5.0 13.727 1 21
Osa04LNT0264800.1 osa-miR5513 Translation 5.0 24.356 1 21
Osa04LNT0264800.1 osa-miR5518 Translation 4.0 10.993 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0264800.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0264800.1 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0264800.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0264800.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0264800.1 4 nan Morphological trait Culm/leaf RM3337 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