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

>Osa03LNT0243100.1

ACATTCAAGGTAATCCTAGATCACCAGGAGATCCAATTTATTTCTTTCTAGCTACATTTCTTCTCTGCAACGTGTGCCTGTGATGCATTACTACTCTGGATGAGAACACTGGAGACAAAGTACACTATACTAATTTAGAATAACACATCGACACTGCAGTAACAACTAACAAATTTAAAGTTTCCGGATCTACTGTCTATGAAAACAGCGGCCATTTCGCGTCGCCCATTGCATACGAGATTATGTTCTTCTTCAGTGGTGATATGTACTGGGCACCGTGAAACGCTGCAGCCCTAAGCACATTGAGGGGTCCAAAATCAACAGAGTACATCTTCTGGAAACCATCTAGCAGCGCTGCCATTGCAACATTGGCTGCTTTGCGATTATTCTCATACCTTTTGAGCAAGGAAATATCCCCAAAATCAGCACCCACAGAAACTCCTTCAGCGATAACTTTTGCTAAAGCAGCTGCATCTCCAAAACCTAAGTTGACACCTTGGCCAGCTAAGGGATGGACTGTATGAGCTGCATCACCGACTAGTGCTAACCTTTTTGAAATATAATCATGTGAATGCTTCAGCGACAATGGAAATGCCATTCTCTCACAGACTACCCCGATTGCTTTTGGAGGTACTTCAAAGCATTCCTTTGTAGATGCAGCAGTACTTCCAATGTCAGAAAATAACTTTTCCATGTAATAGTCAAGACTACCAGAGTGTGGATGTGGACCGTAACCAAAATCCAATGCATTGTTCACAGACTTCACAAAATCTTCAGGACTCATTGACTTATGGCGCAATGACTCCTCTGGGCTCATTGTCCACACAATATTGCTGTAGTTGTCACCTATTGGAAGTAGAGCAATTGGCCCAGAAGGGAGAAACCTCTGCCATGCACAATCGTTTTCGGTAATATGCTCCACTGTACAAATAATTGCACTTTGAGGATAATTCCACCCTGTTGTTTTTATGCCTGCTGTTTGCCTTACATTGGACTTGGAACCGTCAGCTCCCACCACTAGTTTTGAATATAAAGTTTGTCCATCACTTAGCTCAAGTTTAACTAAATTGCTGCGATTTAATTCTTCTGGAGGGTAACCACTGGATATTGCTTCCCTTGTTGGTGCTTGTCTGCTCTTTGATGGCAAAGCAAGAGAAATCAGTCTAGTAGGGTAGATCATCTTTTCAATGTCTCCATTTTCCTCCTGTAATCGTAACAACAGTGAGTTGCAAAGCACCTTGTTCTCCACCACGCATCCGAGATATTCTTTTCCCACATCCCTTGCACTATACCTTGTGTAACCCAGTCCAGTGTAATCCCATACCTGCATTTTACCAAAGAAAGCGTGTCTTTGCTGTTGAACATGATCCCATGCACCAATATCTCTGAAGAAGGATATGGTCGCGGGAGTAATAGTACTGACCCTTGAATCAGGTACACCATCTTTCTTCAGATAATTTCTTGACTTCAATGCAGGATTGCTATCAATGATGCCAACCCTCAGATGTTTAGTCAATGGCATATTGGACAATGCACAAGCAACAGCCAATCCCACCATGCCTCCACCAACGATAGCAATGTCGAGCTCGTCGGGTCTAGCTTTCACATCATCAACCTTCTCTGTGTGATCCTGCGAGCTGGGCACCCCGGCGGCCGCATCCTGGAGCGAAGGCGGCACGTCGCAGAAGGCCCTGACCAGCGGCCGGATCCGACTCGCCGCCGGGAAACATCTTCCTCTGGAGAGCATGCCGGAGATGGCGGCGGCGGCGGCGGCGGCGGCGTCGTCGGCGACGGCGGAGAGCTCCCGTCCGGTGCTAAAACCTGTGTGCCGTCGCCGGGTTTGGTTTGCGAGTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.997938
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0243100.1 3 35259655 T C
Osa03LNT0243100.1 3 35260584 A G
Osa03LNT0243100.1 3 35262056 C T
Osa03LNT0243100.1 3 35262057 A G
Osa03LNT0243100.1 3 35262383 C T
Osa03LNT0243100.1 3 35263431 A G
Osa03LNT0243100.1 3 35261236 A G
Osa03LNT0243100.1 3 35261466 T G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa03LNT0243100.1 DTM_#DNAt_MULE_japo_Os0314 Chr3 - 35261212 35261690 478
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0243100.1 osa-miR5527 Cleavage 4.0 18.457 1 21
Osa03LNT0243100.1 osa-miR171i-3p Translation 5.0 15.627 1 21
Osa03LNT0243100.1 osa-miR444a-5p Cleavage 5.0 14.563 1 21
Osa03LNT0243100.1 osa-miR5517 Translation 3.5 15.197 1 21
Osa03LNT0243100.1 osa-miR5523 Cleavage 3.5 20.169 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0243100.1 3 Qbp1 Resistance or Tolerance Insect resistance R1925 R2443
Osa03LNT0243100.1 3 nan Morphological trait Panicle/flower G249 RG418
Osa03LNT0243100.1 3 spp3.1 Morphological trait Panicle/flower RM130 RG1356
Osa03LNT0243100.1 3 yld3.2 Morphological trait Seed RM130 RG1356
Osa03LNT0243100.1 3 QFll3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0243100.1 3 QSn3 Morphological trait Culm/leaf G249 RG418
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