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

>Osa04LNT0259300.1

GGTACCAAGTAGCAGCGGTTTCCTTCTCTCTAAATTGCGCGCTAGGAAGAAATCTTACTGATTTCGCTACAGAAATTGGCACATCAGAACATCCTTCAAACACGTATCTGAACTTCCAACACCTAATTTTATTCACTGGTGTTTACAAATCAAGGGACGAAAGACCTAACTCTGTAGTCCAAAATCATTTGCAAACATTATGTAAAACAATCCTTTCTCTGTCAAGCGTTACGACCTACATCACCATCCCTCCATCGATGGTAAGAACCTGTCCCGTGATGTAGTTGGCCGCAGGATTGAGAGCCAAAAACTCAACCAAGCCAGCAACCTCCTCTGGTTTGCCATATCTCCCTAATGGGATGGTTGACAAGATTTTCTTCTCAAGATCCTCTCCAAGTTCAGCAGTCATGTCAGATGCAATGAAACCAGGTGCAATTGCATTCACATTGATATTTCTGCTTGCATATTCCCTAGCTACTGTTTTCGTCAAACCAATAACCCCAGCCTTGGCAGCACTGTAATTAGCTTGGCCAATATTACCAACAAGACCAACAACTGATGCTATGTTGATGATTTTTCCCTTTTTCTTCTTCATCATTATTTTTGTAGCAGCTTGTGTACAGAGGAAAACACCAGTAAGATTCAGGTCAATTACGTCTTGCCATTGTGATTTCTTCATCCTCATTAATAATGTGTCTCGGGTAATTCCTGCATTGTTTACCAGCACATCAATTGTTCCCCATTTATCAAGAGCTGCTTTCATCATAGAATCCACATCGGCTTCTTTTGAAACATCTCCCCCGAAGGTAATAGCCTGACCACCACATGCTTCGATCTCTTTGGAGACTTCTTCAGCCTCTTTTGAGGATCGGGCATAGTTCACCAGGACCTTGCACCCAGCTTTTCCAAGAGCCAATGCAGTCGCCTTTCCAATCCCCCTGGAGGCACCGGTCACAATAACAACTGGAGCTTCCAACTTTGTAGCATCTTGCACAAGTGCTTGCTCAACAGCTGCAACATGGGTCTGCACGCCGGAGAAGCCGCCGGACCGCACCGCGCGCGAGCGCGCGGCCGCCGCCGCGCCGAACGAGACGAACCCTCGCCGCGCCACCGCCGCGACGGCGGCGCCGCGCGGGGCCACCGCCGGGGAGGCCACTGCTGCTGCTGCCCCTGCGGTCGCGGAGGTCGCCATGAGTGCGCGTAGAGAAGACGCGGCGGAGGAGGCGGAGGCGAGGAGGCGGTGGGCCACAGGGAGCGGCGTGGCGGGCGCGCGGGGGGTTGGTACTTGTAGCCGCGGCGGCGTCGGAGTCGGCGGAGGCGGCGGCGGCGGAGGGAAGTTTTTTTTTTTTTCTTCCTGGGTAGCTCAGCGACGAGAGGGCGAGGAAGGGTAGATAAACCCGTCGGTGTCGTTGGGGGGCGGAGCGCACGAGGAGAGGAGAGGAGAGGACGACGGGAAGAATAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.851492
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0259300.1 4 18382857 G A
Osa04LNT0259300.1 4 18383959 A G
Osa04LNT0259300.1 4 18384441 T C
Osa04LNT0259300.1 4 18384731 C T
Osa04LNT0259300.1 4 18385573 G A
Osa04LNT0259300.1 4 18386138 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
Osa04LNT0259300.1 osa-miR1437b-5p Cleavage 5.0 8.249 1 21
Osa04LNT0259300.1 osa-miR1873 Cleavage 5.0 12.782 1 24
Osa04LNT0259300.1 osa-miR2919 Cleavage 4.0 12.456 1 19
Osa04LNT0259300.1 osa-miR5075 Cleavage 4.5 24.601 1 21
Osa04LNT0259300.1 osa-miR5338 Cleavage 5.0 23.951 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0259300.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259300.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259300.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0259300.1 4 qNOT4-2 Resistance or Tolerance Drought tolerance RG449 RG788
Osa04LNT0259300.1 4 qFRP4-1 Physiological trait Source activity RG449 RG788
Osa04LNT0259300.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0259300.1 4 nan Morphological trait Root RG449 RG788
Osa04LNT0259300.1 4 qCCFJ-4 Physiological trait Source activity RM261 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