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

>Osa05LNT0310800.2

TAAAAAGTGCTTCCGAGATATATTGACGATCTAGATTGTACAGAGCTAGGTTTTTCTCAATTTATAGTCTAAGAGGGGAAGAAAAATGGCAATCTAAAGATGAAATTATCTACGTTGCAGGCTATCAGAGTGAAGTGCAGAATATAACAGCAACAGTAAAAACGAAACCGGCTAGACATTGTGTTACAGAGGGTTCTTATAAATACACCTTATTTTTAGTATCAAACAAGATCTTCAAGAATTAGTGGTTGCTCAGAAGCCAACAAATAGGCTCCGAGAGCATCCCAGTAGCAATCACCTAGCTAGTGTGTTCTACTATATTGGTTATCAACGACCTTTGCCGATGATTTATTTTGTTCTCCAAAGCTATGCCAGCACGATCAGGACGTTAGCTGCTGCTGGGGCGACTGTCGCTGCTTGGAATGGCAAGCAGCGTCTGGGGAAGGTTACTGACCTTTGTTGCCTCATCTGCACGCTTTGCCGGCTTCTGTATTTCAATACCATGATGATGAAGTTCAGCAGTAGCCTTCGGTGGGTTAACTTGCCTATCTTCAGAGTCTATTTTTCGTTTCTTCATGCTGGTAGAACTCCTGTTGCCATCCGATCCTGCACCGACGCTCATTTCATTAACTTTGTCGACACTTCTGCTACTCTGACTATTTCCATTGTTAACCACAGGATACATGGTATGGGTGCTTGTCATATTTTGCAGGGACTGTGCAGATTGTGGGGCGGCAGGGTCGCTGTCACGCAACTTGGCAGCAGCAGCCAGCCTTCTCCTCTTCATCCTCTGGTCATTGCGGACCTTCCTCTGCCTATATAATAAATTCCTTCGCTCCTTAGATCTAGAAATGGCATCTCGAATTCCAACTTTATCCATGTCGCCATGTGGCCATAAGTTAGCAAGCTCTAGATACAACTTACGACTCTGAGGGCCCTTATCTTCATCCATACCCTCAACATACAGATCATACAGGTCGCAGATCCTGTCCTCCAATACAGCATCCATGACAGATTTTCCTCTCAAGGCCATTCTGTCATCATGAGTAACAGGATCCTGAAAGCCATCTATAGATTCAACCTTATGTTCAGCACCCTTAGGTTTGGTGGCTAGACGTGCTTTGACCATTTCATAGATTTCCATTTTCACTTGTTGCAATTTCCCAGCCTTCTCTTGTTTAGCACATAAACCTGATTGCACCATTTCTTTCATGTTTCTCTTCAGTGTCCTACGGTGCACAAGGTGGCCAACTATGCCCATGAGGCGATTGATCAGCTCATGTTCTGGTATTTTTCCTTGATTTGCCGATAACCTTGCGACCTTAGCAAGTTTTTGTTTTACTTCTTGTGGCAATCTTCTTTTAACTGCTACCTGGCAATTTGCCTCAGCCTCATGTACATCAAGAATCTGTGGTTTGTATTCAGTGACAATGTTTTGGAGGTCACGGATAGCTCGCTCAAGTCTGGTACCCTTGGTCTTGGTACCTGAACCTTCTGTATGGATTTTTGTGGCCAAGTGCTGAAAATGCAAATATAGAATATTGAGCAATTGTCCCATAAATTAGGGCATAATTGTCTCGACAGAATTATAGCAGTTGACAGACAACACATTTCATGACACTTACTAAACATGCTGCATATGCGTGTGGCAGTTTTTCTCTGTTTACTTCCATGTCTTATGTTGTAATGCTTTTGTGCTGAATAAATTAGTGCTATGTACTTTGGGGATGAAAAGATAACTATGGTTTGCACCATGCTCACAAGTCACAATACCAGTTTCCTTGATTCTTACCATTGTTTCTGTTGAATAGATGTTACTGGAAGCATGCAAACCAGAAAATTGACCAGCATTATATTTCTCTTTGTGGTGCATGTTCTTTGACAAATCTTGGTTCGCCCCATTAGAAGTTATTTTCTGTTGGAGGCCAAGATGTCCTGGAGCATCCTTGTCTCGGTATGCTGAATAAGGGTACTCAAATGTTCCATTAGCTCCAGATTTGTGACCATTACTAGTACTCTTCCCCGTTTGGAGAGTGCTTCTTTTAGAGTCTCTTAAAGGCGTGCCCATGTATGAGGAAGAGCCTGGAGAAAATTCCTTGTTATTCTCAATATAAGAACTTGATGAGTCTTTTCGTCTTCGTTTCTTTGGTTCAACAGTCTGTACTGAATCAAAGTCAATTTGTTCCAATTTTCCTTTGTTCACAAAATAACCATTGTGCTTGGTTGCAAAATTGTCAACTTCAAAATATTCATCATTTGGTTTGCATATAAATTAGTGTCGGTAGTTAAGTTCTTCCAGCCATATAGATCATTCTGGTTTTGCACAAAGTAGCAGTTTTTCTTGTTGCAACTTGAGTGAAGTACCATATTGAATTCAAGATAATAAACCCTCATTCTTCCTAACACTAGAAAAATAGCTCAATGAAAAAAGAAAGATTATAAGAGCATGCCATTCTCAGCTGTTCTTCAAATTTGGCATATGGAATGGTAGCCAAGAAGTCAAGGCTGTTATTTATGATACATATAACAGGATAGTAGCAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.926238
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0310800.2 5 20729756 A G
Osa05LNT0310800.2 5 20729780 A G
Osa05LNT0310800.2 5 20731602 G T
Osa05LNT0310800.2 5 20732125 T C
Osa05LNT0310800.2 5 20732318 A G
Osa05LNT0310800.2 5 20732680 A C
Osa05LNT0310800.2 5 20728260 T 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
Osa05LNT0310800.2 osa-miR5816 Cleavage 4.5 10.798 1 24
Osa05LNT0310800.2 osa-miR167a-3p Cleavage 4.5 15.504 1 22
Osa05LNT0310800.2 osa-miR437 Translation 5.0 14.607 1 21
Osa05LNT0310800.2 osa-miR818a Translation 5.0 19.376 1 22
Osa05LNT0310800.2 osa-miR818b Translation 5.0 19.376 1 22
Osa05LNT0310800.2 osa-miR818c Translation 5.0 19.376 1 22
Osa05LNT0310800.2 osa-miR818d Translation 5.0 19.376 1 22
Osa05LNT0310800.2 osa-miR818e Translation 5.0 19.376 1 22
Osa05LNT0310800.2 osa-miR1850.2 Cleavage 4.5 8.655 1 21
Osa05LNT0310800.2 osa-miR5158 Translation 4.5 17.647 1 24
Osa05LNT0310800.2 osa-miR5160 Translation 4.5 12.463 1 22
Osa05LNT0310800.2 osa-miR5340 Cleavage 4.0 12.835 1 23
Osa05LNT0310800.2 osa-miR5484 Cleavage 4.5 11.921 1 21
Osa05LNT0310800.2 osa-miR5488 Cleavage 5.0 22.047 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0310800.2 5 nan Morphological trait Seed RG13 RG573
Osa05LNT0310800.2 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0310800.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0310800.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0310800.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0310800.2 5 nan Physiological trait Eating quality RM163 RM31
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