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

>Osa03LNT0220800.2

ACTCGTAGTAATCTCCAATTTACCAAGCTTGTGGGACTCAAGTGCAAAAGCACCAAACATGTTAGACTTTACAAAACTTCTATTGATTGGGAAATTAGTAAATATAGCTTTAGATTATCCCACCGAACCAGCTTTGTTGAGGTGGCAGCAAGCCCTTATCCAACCGGCATGCGAGCTGGTGAGTCACTTAGCTTTCATTAAAAATTCACACATATATTAGCCTCGGTTTGGTCGTGCAGATCAACACAGGCAGCAAGCAGTTGCAGTAGTAGTAGCAACAGCAAGAGCACAGCCATGGCGCAGAAGCCTCAGCCGCAACAGCAGTAGCAGCAAGCAGTTCGTCCGGAAAACCACCTCAAAAGAGAGAAATGGCAGAGCAGTAGCTAGTAGTCCGGCACCACAGTCACACCATATCTCAATAGTAGCAGCCATAGAAAAACAACCAGGCTTACCATATAAACCATAGCAGCAAGAAGATGCTGAAGTGAGACGGCAGAGAGACCAACCTGAAGAAGGAGCAAGTGGTGTTCCAGCAGTCCAGCTCAAGAAGAAGAAGAAAATGCCCAATTACTATAGTTTCTGGAGGAGCAGCTGGTGCCTGAGCAAGGAGGAGAAATATTCAAGTGTTCCAGTTCCAATAAAGGAGTGAAGTTACAGTCCCAGCAGGAGAAGCGGTAGAACCAGAGAGGGAGAAACCACACAATCTTCACAGCCACACTAGAGTCATTGACAAGGTAATCCTGAAATAAGAATGAGAGGGAAATCACATCATGGCATGATTCTTGGTTGATGCATATATTAGTATGTTTAGGAGTTATGTGCATGCACATAGTTATATCCATTAAACCTGAAAAATGAACCTCAGTAGATGGCAGCCATGTTGATATGTGCATATACTAGTACTATGTGTTGGGGTTATATTACTGAATATGCATCCTTAGTTCAATAAGCAAGACATAATTTTTATGAGTAATTGGACAAGATAGTATCGTCTAAAATTTAATGGACTCTTAGTAGGATAATTGAAGTATAGATCAGCCATCTCAGTGCATAGTTGACAGCAAGAATTATCTTGGATGATCTATAAGCGCATTTGAGTTAAGGATTTATATCTGTATACAGTGATATAAATCAAGGTTCAGTAAAGCCGTCATAGGATGAATTTTTAATGCATGCGTAGGAGCAGAGCATAATTAGAGAAAAGAATGGCATCTATTAGTGTGCGCAAATATATCTTCAGTTTAAGTATATGAAATCGCAGTTTATAAAATTGTCAGGAAACAGGAGAGTATAGTATCTGAATAAAAACCATAGCATACAGTTAGGTCATCAAATAGTCTAATTTCTCCTTGCATGAATATTTCAAATCAAGTAAATTACATAGAGGCAAGAGGTAGTACATATAGTCAGTAGCAGTAAATTATTTAAGGAAATTAGTCAACATTTACATAATTCCATTATCTATAGCATACATCTTGCCATGATCATCAAGTGTAGAACCATGCAAGTTACATCACCATTCAATAAGATTTATTATTGAATCTAATCCGCTTGATGTGTTACTAATTTCAGAAATTCGGTTATTTCAACATGCAAAGCATATACATAAGGATCTGATCATGTTAGTGTTTTAACAATTTCAGTATTTCAGTTAATTCTACATGTAAGCATATATATATAAGGACAAAATCATGTTAGTGTGTTTTTAGTTTCAGTACTGCATTTTCATATGATATATTATGCAAGCATTCATTCATCCATCCATAGCATATGGTTATCATCTAATTATAGCAAATCAATTAATCTAGAACCTACAGATAGCAGGATAATTCTGAGTATAGCATCATCAAGTTGGTCATTAGGACTAGTTCACAAGCATAGAAATTCACAGTAGGTAACTATATAATAGAACACCAATCAGATCACATCACAGAAGTAGGGAATGAAGGGATCAGAGAGAAGGAGCTCGGGGAGACACGGCTGGTCTGAGTCATGCTTGGATCAGGGGCGCCGGGGCTGGGAAAATTCCAATCCCAGTCGTTGAGAGCAGTAGCCAGCAGCAGCATCGATTGGAGAGGGGTTGATGGCTAGGGTTAGTTTGGGGATAGACTCATGAGGAGCCACGAAACCGATTCAGGCCGGCAGCGGCTGCGGGGCGGCTGCCGGAGGCAGGGAGCATCGGCCGGCGTGGGGTGGAGCGGCGGCGAGACCTGAGGATGCGGCGGCGCAGGGGAGAGCGAGAGAAAAAGAAAGAGAACGAGAGAAAGAGAGGAGAGAAAGAAGGTGGGTTTGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.972873
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0220800.2 3 19866559 C G
Osa03LNT0220800.2 3 19864818 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
Osa03LNT0220800.2 osa-miR156f-3p Cleavage 4.0 3.207 1 22
Osa03LNT0220800.2 osa-miR156h-3p Cleavage 4.0 3.207 1 22
Osa03LNT0220800.2 osa-miR398a Cleavage 4.0 20.92 1 21
Osa03LNT0220800.2 osa-miR398b Cleavage 4.0 20.92 1 21
Osa03LNT0220800.2 osa-miR156l-3p Cleavage 4.0 3.207 1 22
Osa03LNT0220800.2 osa-miR167h-3p Cleavage 5.0 23.391 1 21
Osa03LNT0220800.2 osa-miR1442 Cleavage 4.5 14.666 1 20
Osa03LNT0220800.2 osa-miR2101-3p Cleavage 5.0 21.925 1 22
Osa03LNT0220800.2 osa-miR2863b Cleavage 5.0 14.04 1 21
Osa03LNT0220800.2 osa-miR2863b Translation 4.5 14.763 1 21
Osa03LNT0220800.2 osa-miR5073 Cleavage 4.0 12.896 1 23
Osa03LNT0220800.2 osa-miR5498 Cleavage 3.5 15.388 1 21
Osa03LNT0220800.2 osa-miR5519 Cleavage 4.5 12.736 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0220800.2 3 ccf3b Physiological trait Source activity RM16 RM282
Osa03LNT0220800.2 3 ccfs3 Physiological trait Source activity RM16 RM282
Osa03LNT0220800.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0220800.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0220800.2 3 qDLR3 Resistance or Tolerance Other soil stress tolerance RM338 RM2453
Osa03LNT0220800.2 3 sho2 Morphological trait Dwarf nan nan
Osa03LNT0220800.2 3 nan Morphological trait Panicle/flower RZ403 RZ452
Osa03LNT0220800.2 3 An5(t) Morphological trait Panicle/flower C1677 R19
Osa03LNT0220800.2 3 nan Morphological trait Shoot/Seedling RZ284 RZ403
Osa03LNT0220800.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0220800.2 3 gw3.1 Morphological trait Seed RZ672 RZ474
Osa03LNT0220800.2 3 qGW-3 Morphological trait Seed G332 C80
Osa03LNT0220800.2 3 qGL-3 Morphological trait Seed R19 C1677
Osa03LNT0220800.2 3 qLWR-3 Morphological trait Seed R19 C1677
Osa03LNT0220800.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0220800.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
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