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

>Osa04LNT0265800.2

TGAGATCAGAAAGTTTTTTTTTTCCCTTTCATCAGTAAAAGGTTCTGTAGCCTACAGTGCACCATGTGCACACAATAAACAGCAATCTTGGCATCCTGCCAAGTAGATTAATGAAATAAGATACCCATCAAAACAATTGTTATTCAGAGCAGACAGGCCCAAGGAGAAGGCAAAAATGTAAGTCATGCGTTACTCATTCGTTTGCCAACTGATGTTTTGCCATCCTGTAGCGCATCTAAGATATCCTGGTATGAAAAATCATCGTCGCCTTTATTCTTGGAGCCAGACTTCGCTCCTCCTGACTGCTGCACCGAGGCAGGCACAGTTCCATCAAGAGCACTCCCGTATGCTCCGGATCCATCAGCAGCATTGCACTCCTTGAACTTGGACTCGCTGTTTGAAGTTGAACAAACCGCTTCAGCTTGATCCGCGAAGGAGAACTTTGATACAGAGGAGCGGCAAATATCTCTGTAGGTATCATATTTTGCCGCTCGTGTTTTGCCTCCTTCCAGTATAGTTGACAAAGGGTGCAAGACTGAAATAGCACTATCTGCACTCTCTAAGGTAGCCTTCAGATCCAAGAAATCGTTTACAGACTCTTGTTTGCTGAATTGAACAAGAACCGCAGTGGAATCAATCGGGAAGACTGATGTAACAGAAGCTCGACCAAACACTTTGCAGATGCAGTCCTTTATATCCTTTGGTCTCACCTTAGACTGGAATCCCCAGATAAGAATGACGTTGTCATACACGGCAGCAGGATATCTACGCTTATAACCTGCATCTGGTCTCTCCGTGCCAGTACTCAAATCAAGCACTGTTCCACTGTTCCAGCATGGGGGCAGCAGATTGATGTGTTTCTTCAGATTAATGTTTGTTGCTAGGTCCTCCAGGGGAGAGAGTTGCTCAAATTTAATGCCATGATAAGCACAGAGCTGAACAAAAACACATCCAGTCATGAATGCATCATAACCTGCTTCATGCTTAGCACCTGAAGTGAAGCAAGATAACACTGTTTCATCTGCCTCGACTTCAATTCTCACAGAAGGAAGGGTGGATGACTTCTCATCAGGTGCATGAAGTGCAGGGCACAACAATGAAAAGGCTGACGAAAGTGATTTGCTTTTGTGCCTCATACGATACTGAACCGCGTCATTAACAGACATAAGATGCCTGGTATCTGCCATATGTGGGAACATTCTGTTGATACTCAAGGCAAATTCCTCCATGGATGAAGGAAGAGGACCAACAAATTTGCTGTAGATTTGTGCAATATCTAGGAAACAACTATGACCAACAATCAATTTCCTTTCTGAGGCAAGAAGATCAATGACATGACGGATCCCTACTGCTGATTTGACTTTTGCTTCCCTGCTTTTTAGTAGATCTTCCCGAACATTTTTCATCAAGGATATCTTGTCTTCATTGGTGTCTGTATAAACTACTCTCTTCTCTGATACGCCATCCTCCAAAAATGTACACACATACACAAGGTCCCTAAAATGTGTTCTTAAAATCTGTCGGATTAACTTTAACTGATGTGACGTGAATCCATTAAGCATGATAGCAGGACGCATTTTGAAGAAAACAGTCTGGAACTGGTCTGCGAATTTGAAGTTTTCTGACCTATGGTCATCGACTCTTTGATTGCTGACTATTGAATTGCGCCACTCATTGAATTTGATCTTCATTCTTTCTGTGAAAAGAACATCCGCAGCACTCTTTAATGGCGCATCTTCTTCCTCCTCGGAAGTGTTTGGATATGCAGATGTTTCATTATTATGCAATGTATATAATTTCTGAAGTGCCTCTTCTTCTTGTGTTCTGGATAAATAATATATTCCTTCACGGAAGCATGTGTTGAAATCAAACTGGTACTTTGCAAGGAAGTCAATCGATGTGGTCTGACACAGAAATTCATGTGTTGAACAATCATTCAGGGGCTCATTCCGAGAAAAGATAAAGAAGTTATGCGGGTGGGCGACGAAGGCGGACTTGGCGGGGTCCCAGCGGAAGGGGCAGACGCCGAGCTGCAGGGCCGCGAACCGCTCCGCGGAGTCGCGGAGCTTGAGGTAGCGGACGTCGGCGCGGTCGAGTCCGAGGGTGTCCCTCCACGGCGCGCTCGTCACGCCGCTCATCTCCAGGTCGATCCCCACGAACGCCGCGCCCCGCACCCGCGCGCGGAGCTCCTCCAGCGCCTCCGCCAGGTTCCCCCGCGTCACCTGCTTCACCGCCACCCCTCCTCCTCCCCCGCCGCCGCCGCCGCCGCTGGCGGGCGGCGAGGAGGAGAGCAGGCGGGAGAGTAGGGTTCTGGACGGCGGGCGGCGGCGGGGGAGGAGGAGGAGGGGGTGGCGGCGGCGCTGCATGGCCGCCGGCGCCGTAGGGTGGAGGCGGGGCAAAGTGGGTTGGGCTCGGTTTCGTTGCCGTGGAT

Coding Potentia
Explanation CPC Score
noncoding -1.18992
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0265800.2 4 23357681 T C
Osa04LNT0265800.2 4 23357040 C T
Osa04LNT0265800.2 4 23357058 T G
Osa04LNT0265800.2 4 23357236 A G
Osa04LNT0265800.2 4 23357256 T A
Osa04LNT0265800.2 4 23357356 G A
Osa04LNT0265800.2 4 23358116 C T
Osa04LNT0265800.2 4 23358565 C A
Osa04LNT0265800.2 4 23358567 C A
Osa04LNT0265800.2 4 23359131 A T
Osa04LNT0265800.2 4 23359403 A C
Osa04LNT0265800.2 4 23359590 T A
Osa04LNT0265800.2 4 23360490 A T
Osa04LNT0265800.2 4 23360512 G A
Osa04LNT0265800.2 4 23360816 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
Osa04LNT0265800.2 osa-miR408-5p Cleavage 5.0 20.176 1 21
Osa04LNT0265800.2 osa-miR5488 Translation 2.5 18.162 1 21
Osa04LNT0265800.2 osa-miR395x Cleavage 4.0 11.901 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0265800.2 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0265800.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0265800.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0265800.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0265800.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0265800.2 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0265800.2 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0265800.2 4 d11 Morphological trait Dwarf nan nan
Osa04LNT0265800.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0265800.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0265800.2 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