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

>Osa03LNT0243700.4

GCAGCTGCATTAACAATGCGGGAAAAAACAAACTTCATGTAGCCCTGCGTGTGTTATCAAGTTCATCGTTCATCAGAACTATGGAGTGTACAGGATCATGCAGGTTTTTTCTTTAAGAAAAACTTCTGTACATAACCGTGGTTCTCATGTACTAGTTGTAAACGACAATCGGGTCACAGAAAATAACTCAAAATTATCCAATGTAAAATTCCTGCTTATCCATATGTTTCTTGTAGTATCTACTGTATGTTGTAATGTAGTCATATACTGTTATCCACAGATCTGCCTGCCTACCTCTGCATGTGGGGAGGATGAACTTAGCTTTTAATCTTCATAGATTAATATTGATCTCTGTCAAAAGCTCCACACAGTAGTATTCTTGCAAAACAAAGTCATTTGTTCCAGTTTCAGTAGCCAAAATTTGTTCCAGTTTCCAGATTCTTCAGAATGAAACGGTTATGTGAAAGGAAGTAGATACTGACCTGCACGTCTGCATGTCAAATTCCAACAGCATCAAGAAGCTCTGAATGTTGTGACACGGAGACTAGCGTGTTTGCGACAATTGCACCACTTGCAGCGACGGCCGGTACACCGATGCCTGGAAAAGTCGAGTCACCACAGCAGAATAGCTGGGGTATAGGTGTTGCCTGCCCAGGGAAAGTGGCCTCCCCAGCTTTTATGGCTGGACCATAGGTTCCTCTATTTCTTCGGAGGAACCTCTTGTGTGTTAATGGTGATCCAACCAGCTTCACATCGCATTTTTCTCTGCTAAATCTTGGACCAAGGGCAAGCTCCACGGCTTTCCACATCACCTCAGAGCGTTCTTCTTTCAGCCTTCGATACTCGGCGCTTTTCCTATCTAGTCCTTCCCACAAACTGAAAGGTTCTGTTCCTGGTGTATAAGCATGTAGGACGTGCTTTCCAGGCGGTGCTAAGCCATTTCCAAGAACAGTAGGAACTGATATCAATACAACGTTCTGGTCAGCATCAACTCCTTTGTTCCAATCATTAACCACAATATGATGGATTCCAAGGTCCTCTCTGGCATTCTCGACATCAAAACCCAAGTGGAGATGCATAAATGATTCACATTGTGGAGTTGCTTTCACTTTGTCTTGATATGATCTTGGGACAGCATCTGGTGGCAGCAAATCCAAAGTATCCCACATAGATGCATTGCTAACAACTGCTTTCCTTGCGCGCACAATTTGTCCACTTTGTAGCTTGACACCAACTGCTCGACCATTCTCAATTAAAATCTTTTCAACATGCGAACGAAGAGCAAGCCTGCCACCAAATTTTTTTATTCCTCGCACAAGAGCATCTATTATTGCTCCGCTTCCCTCAAGAGGATACTCAAGCGAGCATCCTGGTTTATACCATTCTGCAAACATATAAACCATTTCTGCAGAAAGAGCACCATCAGATTTGACTCCAGCAAGTAGAAAACACAAGAGATCGATCCAATTACGAACAAAGGGGTTTTTCAGGCCCAATGAATCAACGATCTCTGAGAAAGGTCTTAGAAGTTTTGTAGCACCAAGAGCCCCTTGAGGTCCCATTTGCAGGATTGATTTCAACAGAGAAGGAGCATATCTACCAGCAGATGTGGAGAGAACACCTAAATCACCTCGAATGGAAAGTGGAGGCAAAGCCATTGCAGCTGCAGAGATAGGAATAACTGCATCAAGAAGCTTTTTCCACTCCTGGACTGCATCAGCACCAACAAATTCATCAAGGTCCTTGAGGAAATCAGTTGGACCTATCCGCGAAAGGAACTGGCCTTCAGGTACATAAACCATCCAGGAATCATATGAGGCACATGGAACTGATTCGCCTAGCGCATCAAGGACCTGGGCGAGGGGATTGGCCTGGGGGCCTCTGGACTGGAAGCCGGAGAACAGGGAAGGGCCCGAGTCGAAGTTGAAGCCCTTGATGTCAAACGAGTGCGCGGCGCCTCCGGGGCGGTCATGGCTCTCGAGCACGAGCACGTCCTGGTTATACCTCGCCAGGAGCCCCGCGCAGCACAGCCCGCCGATCCCGCTCCCGATGACGACGACGTCCGCCTCCGGCCTCTCCGCCTCCCGGGGTCCGCGGGGCGCTCGTCGGCGGCCACCGCCCTGCAGCGCGCGGGACGAGCGGCGGCCGCGCATCCGCGTCGTGGCCGTGGGGCGGTGGTCGGTGGAGCGCGCGGGCGGCGAGCGCAGTGGCGGGGCGGAGGCGGCAGCGCGCGGGAGGCCAAGGCGGCGGAAGCCATGTCGGAGGCGGAGAATAGCGCGCGTCTCGCCGGCTACGCCACATAGCTTCGGGATCAGGCCGCGGTTGGAGTGAGGCGGCCGTCGTGGACACGTGGCACTTCGCCGGCCTTTCTCCTTCCGCGGCAGCCGACCCGATCTCTCCCGTGAGACATGGAGAAGATGGGAAGCGAGGCCCAT

Coding Potentia
Explanation CPC Score
noncoding -1.02753
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0243700.4 3 35393089 A G
Osa03LNT0243700.4 3 35393757 A G
Osa03LNT0243700.4 3 35394171 T G
Osa03LNT0243700.4 3 35394566 A G
Osa03LNT0243700.4 3 35395539 T C
Osa03LNT0243700.4 3 35395556 A G
Osa03LNT0243700.4 3 35395641 T C
Osa03LNT0243700.4 3 35395851 G A
Osa03LNT0243700.4 3 35395944 G A
Osa03LNT0243700.4 3 35396043 A G
Osa03LNT0243700.4 3 35396169 G A
Osa03LNT0243700.4 3 35396205 A G
Osa03LNT0243700.4 3 35397023 C A
Osa03LNT0243700.4 3 35397543 G T
Osa03LNT0243700.4 3 35397883 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
Osa03LNT0243700.4 osa-miR5791 Translation 5.0 15.782 1 21
Osa03LNT0243700.4 osa-miR5837.1 Translation 4.0 18.002 1 21
Osa03LNT0243700.4 osa-miR1853-3p Cleavage 4.0 8.815 1 22
Osa03LNT0243700.4 osa-miR2105 Cleavage 4.5 16.743 1 20
Osa03LNT0243700.4 osa-miR5511 Cleavage 4.5 23.216 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0243700.4 3 nan Morphological trait Panicle/flower G249 RG418
Osa03LNT0243700.4 3 spp3.1 Morphological trait Panicle/flower RM130 RG1356
Osa03LNT0243700.4 3 yld3.2 Morphological trait Seed RM130 RG1356
Osa03LNT0243700.4 3 QFll3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0243700.4 3 QSn3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0243700.4 3 Qbp1 Resistance or Tolerance Insect resistance R1925 R2443
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