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

>Osa04LNT0286200.1

GGTACACGTAGAGCATCCCAAGCCCATATGTGAATGTGACATGAGCAATATATTGCCACTTGAACTTAACCTGTTTTTTGCCTGCTAAGACCTAACTAAAACCATTAAGAAATGCAGTGCAGGCCAATTGAAAAAGCCTAAATTTTACAACTCTGATCAAACTAGCTACAAAAAAAAAAATTAAGCGCGAATCTGTGGATCCCACTCTCTTTCTTAAAATATCTTTTTGAAACTTTCGCCAACTACACGGGCAAAAAATAGCATTGTGCGTATCATACGTCGAAGAACCAGAACAATATTTGTCAAATCAAAGTGCCAAAACACAAAACGCAAAAAAGGCTGTCCTAGCTTATTTTGGACTGGAACCCGGCGTCGTCATAGCCGCTGCCAGCGACGGCCAGCAGCTGCACGTCGACGTCATCGAACGCGTCGTCGTCTCCGTCGCCGGCGGCGAAGGCGACGACGTCGTCCAGCTCCTGCGGTTCCATCACGCTCCTGCTCGCCTTCAGCTGGTCCTCGAACATCTTCTGCAGCCTCTTCCCCTGCTCCTCTATCCTCAGCTGCAGATTTCTCTGAATCTCTAGCTGTTCATGGAGGCGCCTCTGCACGTCGAGCTGAACACGCAGTGCTTCCGTGATTTGCATTCCAGTTTTGGGGTCCAGATTCTGCATGTCATTTCCTGTTGCTCTTTTCTCCAGTTGCTTCCCTTCAGATGACGCTGGCATGTACTTCGCTATGCGATATTTCTGGAGATGGCTCTTGATGTGGTAGATCGTCAGGCCATCCGAATTCATCAGCTTCAGAATCCCCTTCGGAGTTGCCTTGTCTGCGCCGCCGAGCTGATTGACGCAGTCGACGAACCGCTCGTGCAGGTCCTGCGTCCACCTGATCCGCGTCTTGCTCGGCGCACCTGATCCGGCGAGGTTTCCGGTGGGGGTCACCGGAGTTGCCGCGCCGATGCAGTTCCTTGTCAGCTGATTCTCCATCTGGTTCTGCAGGCTCGGCGCATCCATCGCCGGCAGAATCGGCTTCGCCGCCACTTGAGGTGGAAACGAGTGGATTTTGGGTTCGCCGCTGAGAAGCCGAGTGGTGGGAGCGCCGGCGAAGAGCCCGTGGATTCTGTCCTGATGCTGTTGCTGCGACGGCGGCGGCAATGGTGTCCTCTCGCCGGAATCCCGCTTCTGCGGCCGGACGTAGTACGTCCTCACCGAGTGGTCCGCACGGAGGAGCAGCGGGTCGACCGGCCGGTACAGCTCGCTCTCCGACGACCGGAACGGCGCCTTGGCCGCCGCCGCCGCCGCCGTACCGAGAGCTGGGAAGTCGAACTGCGGCAGGTTCTCGGCGGCGTAGAACGCGGTCGCGTTGGAGCCGACGCAGGTCTGCGCGAGAAGCGACGACGGCGGCGACGACCTCGGCGCGTAGTACTCCTCGTGCAGCCAGCCGCCCGCGCCGTGCTGCTGGTGCTGCGCCGCCGAGCTCACGAGCCCCGGGTGGAACGACAGCCCGGCGGCGGCGGCGGAGCTCAGCAGGTGCGGCGCCGGCGAAGGGTCACATAGCGGCGAGCCGAAGTGGCAGTCGTGCAGCTTAATCTTCTTGGTGTTCATGATATCTTGCAACATTTAAGGTTACGTGAAGAGGCCAGATCAAACAGCGAAATTCCCACCAGAAATTAAAACAGAATTAGGATGAGATTAATTTGGAGGAGGAAAGAGGGATTAACGCGGCGGCGAAGCTTAAATAGGCTCTCGATCGAACGAACGGGAAGCTAGTGGCACAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.652221
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0286200.1 4 33973483 C T
Osa04LNT0286200.1 4 33973841 A T
Osa04LNT0286200.1 4 33974910 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
Osa04LNT0286200.1 osa-miR5542 Cleavage 4.5 12.026 1 21
Osa04LNT0286200.1 osa-miR528-5p Translation 4.0 15.501 1 21
Osa04LNT0286200.1 osa-miR528-5p Cleavage 5.0 12.504 1 21
Osa04LNT0286200.1 osa-miR1320-3p Cleavage 5.0 24.856 1 21
Osa04LNT0286200.1 osa-miR2095-3p Cleavage 4.5 11.837 1 20
Osa04LNT0286200.1 osa-miR5509 Cleavage 4.5 10.441 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0286200.1 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0286200.1 4 gpps4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0286200.1 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0286200.1 4 np4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0286200.1 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0286200.1 4 np4 Morphological trait Seed RG143 RG214
Osa04LNT0286200.1 4 nan Morphological trait Panicle/flower RG620 RG214
Osa04LNT0286200.1 4 nan Morphological trait Panicle/flower RG143 RG214
Osa04LNT0286200.1 4 nan Physiological trait Source activity RG143 RG329
Osa04LNT0286200.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0286200.1 4 QGwp4 Physiological trait Source activity RG143 RG214
Osa04LNT0286200.1 4 QGn4 Morphological trait Panicle/flower RG143 RG214
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