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

>Osa03LNT0222900.2

GGCTATAAAATGGAAGTAATGTTACATTAAGGATTTCATTGGTTTACATTCCAGTACATCTGACGAGTGCAAAAAGGAAAGGGAACACATCAAAAACTCTTGGCTGTGATACATCAAAATTGCTATTGCAGGAGTATAACACAGTAGAGCAATCCATTTCCCGATACAAGAGAAATAAAAAAACCATTGCCATGTTGGTGCTTTGTTGGGGAGATTGCAAAAACATTCTTCCAAGTAGCTTTCATGCAAGTGACGCTCCGTCTCCATATTGCTAACAAGGGAGTTCTGACCATCTACTTTTGTATTTCGGTGTGTCCACAAGCTAGAAGTTACAACAGGCAGTTAAAATGGAGCATGCAAAGGCCATTCGCTGTGTCTAAATCTCCAGTACCCAAGAAAGATGGTGAACTGAACAGCATGGGGAATATAATCAATATATTTACACACACTAAATATGGAGAAAATGTTACCGCCTCCTTTTTCTGCCCTTCCCTAGCTGTCCAGATTTAAAAGCATGTTCCTGCTCCTGAAGGAAAGCCATGGCTTTTCCATACTTTTCAGCTCTCTCTTGCTCTTGTTTTATCCTCTCCTTCTCTTTCACAGCAGACAGGAAATAATTATCTTTACGCAGTTCGCGCATTGCACCCTTCTTCTCACTCTTAAGGCGTTTCTTCATTTTCTTCATTTGTGCCCTTTCCCGATCAGGGTCATAATCAAGGCCTTTAATGTAATTCTCTTCAAATTTCGGATTCAACTGCCTGATTGGTTCAGGCTTCTGCTTTCGCATTTGGAGTGGCTGCCTTGATGCATGGACTTCATCACTTCTGTTTTTAATCAACTCAATGACTTCATGTAAAATGTATTGTAACAATCCAGGCAAGTCTGATTTATCCATAATTTCTTGCATCAAAGAAGAGATTGGCAGGAAAATTTCGGGGAACGAACATAGTTCTTCGTGTATAATAACAAATCCCCTTAAACATTCAGCCACAGATAGAAGTACACTAGCCTTGAAATTATCAGAGGAGAAATAAGGAGCATCAGAATCCATGCATATGACTTCCAGGATATTCGCTGGATTCACCTCGTGCACTTTTTCATGGATATGAAGCCATGGTTCCATTGTCTTGAGCTCCAAAAATTGATCATTGATCTTTTTTCGTAGGTCAGATCCCAGGTTTCCTCCCAGAGATGTTACCAAAAGAGATTGCAGAAAAACGACAGCTTCAGGGCAGAATTTCTTAGACTCTTTAGTAGCCTGCAATCAGAGTTATTATTATGCAGAACTGGAAGAAGAGAAAAAAGGAAATTCATGTCGAGTAAGAAATTCAGCTAATAGTTCTTCATCATTCATATAAGAACTTAATGGAACAAGATTTAGAGTTACAGAACATACCACAAGCACCATGGAACACAAGAAAGAACCAACGGCTACATCTCGACCAGATTGTATGGGGCATCGCATCAAATATTCACACATAAGCAAAAGCATTGGAGTTGCTACCACATGGCGGAAGTCAGAGCAGGGAAATATAAGAGACCATAACCGCAGAAGAAGTAATGTTTTCAAACTTGGCCAGCAGCTCTTTCCTGAAACCTTTATATCTTCACATAGACGAGTACGTGTGTGGATAAGTCGCTGCCTCGCACAGATGGCAGCAAAATATGGAGTCTCCCCACTCATCTCAATTAAAGGCTTAACAAGGGTGTCAATTAGTTTGAATCTCACTGGACTCTGAGTAGCTAATACTGCAAAGTACTGCAGGAGAACACCATAGAAAACTTGCATCTTCTTTCTATTTTCAGCTGCAAGCCTTATTGAATTGCATGTACGAATTCGACTAATAATCTCAATTATTTCAGTTTCTGACCAACCATCTAGCAAGGAGCATAGATCTTTCAAGTTACTTGGTGCTTCTATCACAAAAGGAAGATTGTCATCCTTGACTTGCGATTCTGCATTAGACTCTTTCTTTGAATTTTGTAGATCTTTTTTCACCACTTTGCCACTGATCTTCTGTTCCTTTTGTTTGAGACCTTCCATTTCATCTTCTTCCACGGTAACCTCATCATCGTCACTTTGCTCCCAGTCTCTAGCAGACATATTACCAAAGTCATTATCACTTAAATCCTCTTCTTCATCTTCATCCTCAGCATCATCATCACCATCCTCAGCATCATCATCATCGTCATCACCATCATCATCAGATTCTTCATTGTCTGACCCTTCAGCATCTTCACCAATCTTTTTACCCTCTCTTTCATAAATTTCATCGACCCAGCCCTTTTCCTTTCTTGCTGGCTCATCAGTAGAAAAGGAATCACCAAGATCATCACCAGATATAGGTTTTGAGCTGTCTAGCTTCGTGCTGCGGTCACCCTCCTCGTCATCATCATCATCTTCATCAGAGGACTCAGCAGTTCCAAGCATTCGTTTCTGACGCTCTTTCTCCAACTTCTCAAGACGTTCTTTTTCCTCCTGAGCTATTTCTTCTGGTGTTTTTGTCCTGTCTGATGGACGAGCACGTTGATCCATAACCATTTCTTTCACTAATTTATCATATGCATCTGGTTTTTCCTTATTAAAAATCTCCTTGGCAGTCAAACCAAATGAATCTTTCTGGACTGTACTTGAATTATATTTATTTGCATCCATTCTAGCTGATCGAGTCAAGGACAACATCGCCTGTGTCTGGGCTAACATTGCAAAGTCACTATCCAACTTGTCTACAAGATGTTCATCCTCTTCCCTCTCCTTGGCCTTTTGGGCCTTGTAAAATTTGCTCTTTAAAATGATCTCTGACATAACTTCCTTCTTGCTCTTGTGAACATTAGTTCCTTCAGGAAGACCAATTTCTGAAGGAACATCACCACTTTGGAGAGGTATGCGGTTCTTCGAGAGGATCATGTGACCTTCTTCATCACTATAATCATCAAGAGGCACTTCTTCATCAAAATCATCTTTTCCCGAGAGAGAGTGAGGCAGGTGAACATCAACCTCATCTTCCTCATCATCAGATAGATTGTATTTGCTTTCTCGTTTCAGCTTTGCCATGTGCTCACGCTGCTGGCGGAGGATAACTTTGTCGAACTCGGGCAGCGTCTCGTCCCTCTCCCCGATCCGCCGGTCCTGGAACACGGACGACTTGGCGCTCTGCTCGAACTCCTTGAGCAGAGTGTTCTCCCTCTTGTGGATGGCCTCAGAGCGGGCGCGGCCGATGCGGCGCTCCTCCCCCTTGCGCTTCTTGCCCAGCACGTCGAACTTGCGGCGGGACCAGATGGCCTCGAAGGGGTTGTTGCTCCCCGACGCCGCCGCCGCCGCCGTGGGCTTCGTCTTCGCCATTGCCGGGGGACGGGGGGAGGAGAGGAGCAGCGGGGAGGCTAGGGTTTTAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.78871
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0222900.2 3 22286970 T C
Osa03LNT0222900.2 3 22286270 A G
Osa03LNT0222900.2 3 22286344 A G
Osa03LNT0222900.2 3 22286497 A G
Osa03LNT0222900.2 3 22286670 G T
Osa03LNT0222900.2 3 22286873 A T
Osa03LNT0222900.2 3 22286940 C A
Osa03LNT0222900.2 3 22287344 A G
Osa03LNT0222900.2 3 22288158 C T
Osa03LNT0222900.2 3 22288576 A G
Osa03LNT0222900.2 3 22288738 A T
Osa03LNT0222900.2 3 22288816 C G
Osa03LNT0222900.2 3 22288888 C T
Osa03LNT0222900.2 3 22289137 G A
Osa03LNT0222900.2 3 22289488 T C
Osa03LNT0222900.2 3 22290253 A G
Osa03LNT0222900.2 3 22290362 A T
Osa03LNT0222900.2 3 22290451 T C
Osa03LNT0222900.2 3 22291169 G A
Osa03LNT0222900.2 3 22291338 G A
Osa03LNT0222900.2 3 22291877 A T
Osa03LNT0222900.2 3 22292589 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
Osa03LNT0222900.2 osa-miR5532 Cleavage 4.0 1.714 1 22
Osa03LNT0222900.2 osa-miR5820 Translation 4.5 13.409 1 21
Osa03LNT0222900.2 osa-miR164e Translation 4.5 15.129 1 21
Osa03LNT0222900.2 osa-miR171g Translation 3.5 16.277 1 21
Osa03LNT0222900.2 osa-miR419 Cleavage 5.0 2.272 1 21
Osa03LNT0222900.2 osa-miR419 Translation 5.0 15.024 1 21
Osa03LNT0222900.2 osa-miR390-5p Cleavage 5.0 13.267 1 21
Osa03LNT0222900.2 osa-miR440 Translation 4.5 12.539 1 24
Osa03LNT0222900.2 osa-miR1426 Cleavage 5.0 8.415 1 21
Osa03LNT0222900.2 osa-miR1850.3 Cleavage 4.5 16.915 1 22
Osa03LNT0222900.2 osa-miR2868 Cleavage 5.0 14.551 1 20
Osa03LNT0222900.2 osa-miR5146 Cleavage 4.5 18.988 1 24
Osa03LNT0222900.2 osa-miR5160 Cleavage 4.5 15.663 1 22
Osa03LNT0222900.2 osa-miR5522 Cleavage 4.5 5.325 1 21
Osa03LNT0222900.2 osa-miR2275d Cleavage 3.5 14.901 1 22
Osa03LNT0222900.2 osa-miR5791 Translation 4.5 20.109 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0222900.2 3 nan Morphological trait Shoot/Seedling RZ284 RZ403
Osa03LNT0222900.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0222900.2 3 nan Morphological trait Panicle/flower RZ403 RZ452
Osa03LNT0222900.2 3 An5(t) Morphological trait Panicle/flower C1677 R19
Osa03LNT0222900.2 3 gw3.1 Morphological trait Seed RZ672 RZ474
Osa03LNT0222900.2 3 qGW-3 Morphological trait Seed G332 C80
Osa03LNT0222900.2 3 qGL-3 Morphological trait Seed R19 C1677
Osa03LNT0222900.2 3 qLWR-3 Morphological trait Seed R19 C1677
Osa03LNT0222900.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0222900.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0222900.2 3 ccf3b Physiological trait Source activity RM16 RM282
Osa03LNT0222900.2 3 ccfs3 Physiological trait Source activity RM16 RM282
Osa03LNT0222900.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0222900.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
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