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

>Osa03LNT0196600.2

AGAACCCTAGCCGCCTTTGCCTTGCGTGCGTCTCACGTCCAACTCGGCCGCCAGGCGCTCTTCTCGCCTGCGCTGCCTCGCCCTCCTCTCCTCACGCGCATCGCCGCTTCGCCCTCCTCCCGCCGCCGCCATACCGTCGCCGCTTCTCTCCCCAGTAAGGCCGCCGCACCTGCTCCGGCGTTCGGTCTCCCGCCGGTGGATCCGGCCACTTGGAGCCTTGGAAGTGAGGGAGCAAGCCGTCGCTACCACCCTCTGCTGCTCTTCTTCTCCGCACCTCCATCGCCCCTCTCCCCCTCTCAGCTCCGCTCAGTGCCAGATCCGGCTCAGGGGCCGCCGGATTTGGTAGGAGGAGGAGGTAGCAGCAGTGCAGCTATTGAGGAGAAGGAAGGAGGAGGGTCGCGACATGGCCATTACTGTGATGAGAACGGTTAGGGCTCGGTTAGGTCGATGGCTAGGAACGACGACGGCTAGCGGCTTGGTCAGGTCGACGGTAAGGAACAACAATGGCTCAGTCTTTCCTACGTTTTTTCTGCTTTTCATTTTATTTTTCTCCGGGAGAGGCAACCTGATATTGTTGGGCTATTTGCGCTGAAATAATATGACATCTTGCCTGGATCACCTACTGATACGCATTGGAGTCACATCGAGGAGCCCAGAGTAACCTTCCGTTCTGTCTTTAAGCAATATACAATCCCAATTGTGAATTTGTGATGTCTAATTTTATATCTCTAAAATCCCAATTGGCATGTCCAAGATACACGGACGAAGCAATATCTGTTCATGAATGTGATTTGAGCAACATATATAACAAGTAGGTTGTGTTCAGTTTTTTTTCCTCGGCTCATATGGGAAAGACTAGGGATGATTTTGATTTATTTATTTTCTTATTGGTACTTAAAAAAGGATCATTTTTACCTGTTTACACATGAGTGCTTGCAGTACTAATACGAATCATTGCCATGGGTTAACATTGAGGCGATTACGCCACCCAATTTGGTGAGAAGATAGCAGGTGGAGGTTAGCAGGGCTGGGCATCCCTTGCTTCAGGTCTTGCTGTCCATTCATGCTGCTAGGACATTTACCACGTTGGTGCTTCATATGCAACAGCATGGACCAATTTACTATGCCATGTCCTAAGAAGGTTTGTGCATGACAAGAAGGTATCTAAGATAACACTCTTTCGTTAATGCCAACTGTTAAACATAGAAATCAAAGTAATTTATTTTGCTACCATTTCCTTTAGGTGGCACTCACATATTGTTCAATTGTACTGGGGACATTAGGCTTTATTACTGTTATTGGGATCAATCAGATATGCGTTTTCTGCTGGTTTTGCTCATGGCTATGTACACAAGAAATTTTAGATTATAAAATAAATATGATGGACCAATGTTTCCAGCTACTACTTCCGGTGTACATCCTTTTTTATTATGTGTCACTTCAGATTTGGTCTTTGTTCAAACCTGCCTATAATATCAACAAGAACTAAAACTGAAAGATTTCAACAAGAATCATGTACTTGCAAAACCATTGTTCAAAATCCAAGATTTCATCCCTGAAGTGTTCGTTTAAAAGTTAAGGCAATTTTCTGTTCCGGATTAGCCTTTCGGCCTGCATCAATGGTTTTAAACAATCTGGTTGGATTCAGTTGCCCTATGAGTTACTTTTGTAGTACTGATGAATCTGAAAATTTACCCTGAGTTCTATTGGGTTCTAAGTTAATCCATGGTGTATTCATTCAAAGTTGGCATCCCATACCACATACCGCTGAGATAATATATTGCTAGTTTGGTGGAACTATTTCACTGATTATCATATGTTATCACATATTGGTTGCATATTTGTGCAAATGGCTGAAACAATTCTATTTTTATTTAATCGCTTTGCCTTTCAAGCTATATTATTGTTTCAGACTTTGTGATGAACTTTCTTGCAAGATATCTAAAGCTTATCTCAAAGTTGATAAGTTATGTACTAATTTCAGTATTATGTTTGCTTTTGTCAGGGCTAGAGAATATATGCATTAGTGTACTTGAAACAAAACAGGGTAGAGTGGCCCAATGGCACTATTTGTCTTTCCAAATCGCCACTATGTCAGTACAGATAAACGAATAGAGGTATGATCATTTGTATATGGTTTAGATTTTTCAACAATATTGTATCAAAGTATTGTTTTCCTCATATCTTGGACTGTAGTATGTCCTTGCAGGATGTAAATGTTAACTCAAGTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.915397
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0196600.2 3 2459903 A G
Osa03LNT0196600.2 3 2460207 A G
Osa03LNT0196600.2 3 2460157 A T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0196600.2 osa-miR5538 Cleavage 4.5 12.303 1 22
Osa03LNT0196600.2 osa-miR5793 Translation 4.5 18.771 1 21
Osa03LNT0196600.2 osa-miR5823 Cleavage 5.0 11.37 1 24
Osa03LNT0196600.2 osa-miR7694-5p Cleavage 4.5 14.865 1 24
Osa03LNT0196600.2 osa-miR1851 Cleavage 5.0 11.854 1 21
Osa03LNT0196600.2 osa-miR2863b Cleavage 4.0 12.497 1 21
Osa03LNT0196600.2 osa-miR2871a-3p Cleavage 4.5 14.188 1 21
Osa03LNT0196600.2 osa-miR2871b Cleavage 4.5 14.188 1 21
Osa03LNT0196600.2 osa-miR2878-3p Translation 5.0 12.3 1 24
Osa03LNT0196600.2 osa-miR2921 Cleavage 4.0 12.429 1 24
Osa03LNT0196600.2 osa-miR2921 Cleavage 4.5 16.471 1 24
Osa03LNT0196600.2 osa-miR3979-3p Cleavage 5.0 13.371 1 20
Osa03LNT0196600.2 osa-miR5076 Cleavage 4.0 14.111 1 22
Osa03LNT0196600.2 osa-miR5500 Cleavage 5.0 12.612 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0196600.2 3 QSs3 Physiological trait Sterility RG348 RG944
Osa03LNT0196600.2 3 dth3.1 Resistance or Tolerance Drought tolerance RG104 RZ329
Osa03LNT0196600.2 3 nan Resistance or Tolerance Drought tolerance RG348 RZ329
Osa03LNT0196600.2 3 nan Resistance or Tolerance Drought tolerance RM231 RZ329
Osa03LNT0196600.2 3 nan Resistance or Tolerance Drought tolerance RM231 RZ329
Osa03LNT0196600.2 3 nan Resistance or Tolerance Drought tolerance RM231 RZ329
Osa03LNT0196600.2 3 qFDN-3 Physiological trait Flowering RZ329 RG348
Osa03LNT0196600.2 3 nan Morphological trait Root CDO20 RG409
Osa03LNT0196600.2 3 qHEJ-3 Morphological trait Shoot/Seedling RM175 RM22
Osa03LNT0196600.2 3 S34(t) Physiological trait Sterility nan nan
Osa03LNT0196600.2 3 qOE3-1 Physiological trait Eating quality nan nan
Osa03LNT0196600.2 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0196600.2 3 rn3 Resistance or Tolerance Drought tolerance RM231 RM175
Osa03LNT0196600.2 3 qDEF-3 Physiological trait Flowering R518 C721
Osa03LNT0196600.2 3 QSbr3a Resistance or Tolerance Sheath blight resistance RG348 RG944
Osa03LNT0196600.2 3 qtl3.1 Resistance or Tolerance Drought tolerance RM7332 RM545
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