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

>Osa02LNT0174400.1

AATCCGTGCAATGTGCAAATACTTTATATCTCTGAAATGTAGCAAGAGTTCATTAGCCTGAAAGTGGGTGGAAAGTACAGATTTATATAGTATTCCTGAATGAAAAATGGCTGTTGGAAAATGGAAACCCAAAATGAAATTCATAATTGATACCTATTTTGACTATCTGGCTGGACTATTGACCCTCGCCTGTATCCACTCAAATTTTAGAAAGAGAGTAATGGTAGAGCTATCTGTAAAACAATCTAACAAAAATGATCGCATGTAAAATCTGCTTGAAATTAACAATACAAGCAAGGGTGCAGAGCACTTCTTCCACACCCCATGTGTTGCCTACTCTGTATCTCTTACCCGAGCAGAAGTGCTATTGTTGAATCTTTAGGACTGGAAAGGCAATAACATCCCTTATACTCGCCGAGTTGGTCAAAAGCATTACTAGTCGGTCGATTCCAAGGCCCATTCCGGAAGCAGGTGGCATTCCGTACTCTAGGGAAGTCAGGAAGTCTTCATCTAAGGTAACTTCATACGAAAAATCATCTTCCTCGTGTTTACCCTCAGTAGATTTGACCTCCTTGGTCATTGCAGCACGCTTAGCATTGTGCTGCTTAATTTGATTTTCAAAACGACCCCTCTGATCAATTGGGTCTGTGAGCTCAGAAAATGCATTACCAATCTCACGACCACATATGAAAAGTTCAAATCGCTCGGTAAGACCAGCATACCTCCTATGTGGTTTGGCCAATGGTGATATCTCAACTGGGTAGTCAAGAACAAATGTTGGCTGTACCAGACTTGATTCAACAACAGTCTCAAAGACCTCATTGAGAACATGTCCAACAGATGAACAAGCTTGCAATGAGATATTCTCATTGCTCTCTGTTTTGATCCCTCTTGCAGCATTTTTGGCGGATTCAAGATCTTCTCCAAAGCTATTAAAGTCAATTCCAGTTGCTTCTTTGACAAGAGAATGCATGGTTTCCCTCCTCCATGGTCTTTCAAGGGAGATTTCAGTTCCCTGATAATCAACCCTAAGTTTGCCATGAGTAGCCATTGCACATCTAGTAACAATTTCTTCAGCCAAATTCATCATGCTTTCATAGTCTGAATAGGCTTCATACATCTCAATTGTGGTAAATTCAGGATTATGGCGAGTGGAAATGCCTTCATTCCGAAATATTCTCCCAATCTCATAAACTTTCTCAAGCCCTCCAACCAGCATCCTTTTCAAATGCAGCTCTGTTGCAATCCTCAAGTAAAGATCTCTTTGCAGTGAGTTATGGTGGGTTATAAATGGTCTTGCTTCAGCACCACCTGCTGCTCCCTGTAGAACTGGCGTTTCAACTTCTATGAAGCCAAATGATTCCATTGTCTTGCGGATTTCAGATACAGCCTTTGCTCTTGTTCGGAATACATCAGCAACCTCAGGATTTGCAATCATGTCAACATACCTTTGGCGATACCGCTTGTCCACATCAGTTAAGCCATGGTACTTATCAGGTAGTGGGAGTAAGGATTTTGTAAGGATTTCAAAGTTTTTCACGTAAACAGATAGTTCCCCTTTTTCTGTCTTCTTTATGGAACCATTTGCACCTATTATATCACCAATATCAATAATTGTCTTCAGTTGTTCAAACTGTTCCTCAGTAAGGCTGTCTTTCTCACAGTAAAGCTGAATAGTCCCGGAATCGTCTCTTACGGTCATAAAAACAAGCTTTCCAAACGCTCTTCGGGCGACAATCCTCCCAGCAATGGACACCGCCACGTCCGCGCAGACCTCGCCATTCTCGAGATGGGTGTACCCATCCTGAAGCTCCTTGGTAGTGTGAGTCCTGTCCCACTTGTACGCGTACGGCTCGTAGCCCTTCCCTCTCAGCTCCTCAACCTTTTTGAGGCGAATGGCGCGGATGGATTCGCGGTCGGAGGTGGAGGACGAGGACGAGGAGGCGCTTCGGCGGCGGCGGTCCTGAGGTGGGGGCGGGGGCGGCTTCGTGGTGGAGGCGGCGGCCGGGGAGCAGCAGCGGACGTGGGGGCGGAGGGGCCTCGCCGCTGGGGCGGCCTTGGCGGCGCGAGAGGCCGCGAAGCCGAGGAGATTGGAGGAAGCCCTCCACGCCCGCAGCGCCTCCATTCTTCCGC

Coding Potentia
Explanation CPC Score
noncoding -1.03609
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0174400.1 2 24850460 G A
Osa02LNT0174400.1 2 24850368 T A
Osa02LNT0174400.1 2 24850476 G C
Osa02LNT0174400.1 2 24848456 A G
Osa02LNT0174400.1 2 24848704 C A
Osa02LNT0174400.1 2 24849276 G A
Osa02LNT0174400.1 2 24849326 C T
Osa02LNT0174400.1 2 24849378 A G
Osa02LNT0174400.1 2 24849538 A C
Osa02LNT0174400.1 2 24850664 A G
Osa02LNT0174400.1 2 24850688 A G
Osa02LNT0174400.1 2 24850716 A T
Osa02LNT0174400.1 2 24850727 T C
Osa02LNT0174400.1 2 24850795 T C
Osa02LNT0174400.1 2 24851302 C T
Osa02LNT0174400.1 2 24851387 C T
Osa02LNT0174400.1 2 24851533 A C
Osa02LNT0174400.1 2 24851804 G C
Osa02LNT0174400.1 2 24851956 C T
Osa02LNT0174400.1 2 24852672 G A
Osa02LNT0174400.1 2 24852876 T G
Osa02LNT0174400.1 2 24852926 G C
Osa02LNT0174400.1 2 24853179 A T
Osa02LNT0174400.1 2 24853221 G A
Osa02LNT0174400.1 2 24853241 T C
Osa02LNT0174400.1 2 24853249 T G
Osa02LNT0174400.1 2 24853316 C T
Osa02LNT0174400.1 2 24853614 A G
Osa02LNT0174400.1 2 24854018 G A
Osa02LNT0174400.1 2 24854033 T A
Osa02LNT0174400.1 2 24854719 G T
Osa02LNT0174400.1 2 24854814 T C
Osa02LNT0174400.1 2 24855421 T C
Osa02LNT0174400.1 2 24855561 T C
Osa02LNT0174400.1 2 24855879 T C
Osa02LNT0174400.1 2 24855901 A G
Osa02LNT0174400.1 2 24856366 G A
Osa02LNT0174400.1 2 24856454 C T
Osa02LNT0174400.1 2 24856465 T G
Osa02LNT0174400.1 2 24856480 T A
Osa02LNT0174400.1 2 24856487 C T
Osa02LNT0174400.1 2 24856535 C T
Osa02LNT0174400.1 2 24857003 C T
Osa02LNT0174400.1 2 24857112 A G
Osa02LNT0174400.1 2 24857211 A C
Osa02LNT0174400.1 2 24857408 T C
Osa02LNT0174400.1 2 24857487 T C
Osa02LNT0174400.1 2 24858548 C G
Osa02LNT0174400.1 2 24858870 T G
Osa02LNT0174400.1 2 24859059 T C
Osa02LNT0174400.1 2 24859269 C T
Osa02LNT0174400.1 2 24851709 G A
Osa02LNT0174400.1 2 24849819 C T
Osa02LNT0174400.1 2 24855422 A G
Osa02LNT0174400.1 2 24849303 C 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
Osa02LNT0174400.1 osa-miR5528 Translation 3.5 8.444 1 21
Osa02LNT0174400.1 osa-miR5542 Cleavage 4.0 12.182 1 21
Osa02LNT0174400.1 osa-miR5834 Translation 5.0 6.946 1 21
Osa02LNT0174400.1 osa-miR396c-3p Translation 4.5 20.908 1 21
Osa02LNT0174400.1 osa-miR399d Translation 5.0 15.082 1 21
Osa02LNT0174400.1 osa-miR171c-5p Cleavage 4.5 14.295 1 21
Osa02LNT0174400.1 osa-miR1866-3p Translation 3.0 18.137 1 22
Osa02LNT0174400.1 osa-miR2090 Cleavage 4.0 15.194 1 22
Osa02LNT0174400.1 osa-miR2095-3p Translation 4.5 14.73 1 20
Osa02LNT0174400.1 osa-miR5491 Translation 4.5 14.346 1 21
Osa02LNT0174400.1 osa-miR5509 Cleavage 4.0 18.486 1 21
Osa02LNT0174400.1 osa-miR5155 Translation 5.0 13.201 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0174400.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0174400.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0174400.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0174400.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0174400.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0174400.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0174400.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0174400.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0174400.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0174400.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0174400.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0174400.1 2 nan Others Others C424 G45
Osa02LNT0174400.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0174400.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0174400.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0174400.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
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