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

>Osa02LNT0175300.1

AACGAAAGAAAATACAGCATTAATTTGTTTTCGATCATATATTTGTACAGTGTACACTCATAGCAATGGCACTATGCATTGAATTGATTACTAGTTTGGCTAGCTTTGATCAGTAAGAATATCTCTGTAACAATGAGGCAAGAGGGTTTGAGATATGTACAGGTTAGCTGGTCAGGTGAAAAATAGGAATGGGAAACAGGGAAAATTGTGAGCTCTTTGCAACAGCACGGAGCACATTGTCATCTCTTTTTCTTGCTTTCGTTGGGTTTGATCATCTGCACAGGAGCGGCTGGAATGCGGGCCCACCACTCTCTAATCCGCCGGCGGAACTTTTCAGTGTTCTGTTTCCTTAGCGGCATCTCTCTTGTGTACACCTCCAGGACTGCAATCAGGAGCAGATGTCTCCAAGGTACAAAGATAAGAAATGCAGATGCAGCAAGAAATGCCACTGCGACCATTTCAGTTGTCTTTGGAACAGCTGCAAACAAGACAGCTCTGAACTTTAGAAGAACAATATTTACAGACTGTAGAGTTTCTTCCAACTTGGATATAGCATCCTGCAAGGTCAAGATTTGCTCAACAGGATTTTTACTTGGAGGAGTTCTTACTTCAAGCACTCCCAATAATTGCTCCCTTCCATTGTACTTATGCCAGAGCATAACAACAGCAAATGCCAAAAAAAATGAGGGCAACATGTAAGCAATAAATCCCCTTTGAATAACATACAGGGTAAAAGCTAAGAACAGAAATGATTTCAGAGGATCTTCCCACTTGGTCAATGAGTAAGTGAGTTTGACTACTTGAGTGAATGGGAAAAGTAACTCCTGGAATATAAGCGCGATCCATCAGAACTCAAGTCACAACAAAGGTGCATGATATTGTAGTAGACATCTGGGTGACACTAAAGTTCATGAAATTGCACCAAATAACTAGTGAAACGTGCTATCTTTTCTTGCTGCACTCTAGAAACCATTCAATCCCAAACCAATAAGAACAATTTAAGTTGATTTATCACCAAAGTACCTGCATGAGGGCAAGATTTGCATCCACACCTTCCACCTTTACTTGATCTATAGTTGCACGTGCTGCATCTATTCTCTCAGAGTAACAAATTGACTCTTCCAAAGCAGCCTCTAGAGATTTTGTTACACCAAAGCAAACAGCACAAAAGCTTATCTCACTTTGAGCTTCATCTTTTCTCTTCAGTAATATAAATCCCATTCTAGAGAGAGCATATAATGAAAATGGTAATGAATGGTTCTGCAGCCTATTGTCAACGGGTGACTCAGTCACCAAATGACTCAACGAAGTGTCCAACAGTTGAAAGTAGTTAGCATACAAGGCTTTTAAGACCATGTCTCCTTTTGGAAGTTTTTCTGCTAAGCTAAAAGTGAGTGTTGTCTTAAAGTGAGAAGGAGAAATATGAAAAGCTTCTTTCACAGCAGAGTATCTCAAGATGCCCAGGATAGCTTTTGAGAGTGCTTCCGCTCTCTGAACGTTTTCAAGATTGAACTTCCTGATGAATTTATTCACCTGCAATACTTCACGAGCGATTGCTAACCAATAGTCTCTTCGTGAGGGACCTCCTAATTCAGGGAAGTCAAAATAAATTGGCTCTGTTAAAGTGCTTGATTTGTACATCACAGCCTTATCAAACAGGCGAACACCCAATGGCCCAGTAAAATCACGCTTGATAACCTGATCAGAATCTGTTGCTAAATCATATTTAACAATCTTGTCACCATAACCCACTTTGATACTCTGAAAGTAAAGAGCATGAGTTGTAAGAATCAATCTTCCTGGCCATGCTGATATTCCAATGTGTTGAAAAACAGGATGAATAGGCCTGTCTCCATCCATAGCTAAGATACATTCCCCAGCATCAAGATGAAAACTTGAAGCAAGCGGTGACTGCAATATACCTTTGACAGATCTGAATACCTTGTCTAAACTTTTGATATACTTGTCAAACACGAAAAAGTGCAAGCGGCCACCAGATGAACATGTGAGTGCATCGAACAGATTGTGGACAGTAACCAAGTCAGCTATTATAGGGCATGAAGGTGCTATTCGTGCAAAAGCACCTAAGCCAACTGTCTTCTTGTCATTGACCTGAAAATGGACCGCAATTGATCATGTGTGTGCACAGTGAAGAATTATTTCCAGGTTAGAAAAAGCAATGTAGTTTGTAAACAGAACTAACTTGAACCGCCAATCTTGTGGAATTTGCATAAAAAATTGATCCCTCGTCATCATCTTCAATATCCACAGTTGTACGCAAAGCAGAATGATTTTCTGATAATTCATCCTCAACAACAGCACCTGGGTGTTCCCACGCAAGCATCATATCAAACATTAAACGGCGAAGATTCTTATCAGCCAAATGATCTGGACGTGTAGTTACTTCATGGAGAGCTTTGTGGCAGCAGTACTCTAAAAATTCCTTTGCATATGTATTAGACTCCTTACAACTATCGGGATAGTCAACTTCAAAGTTTTGCTGCAAGGTTTCGGTTGCAAGAGCAAGAACCCTGAAAATGTTAATTTGAGAAGAAACTTGTTAGAAGTTTGTCAGGCATAACAAGAAATTACAACTTAAATCATATAAGAGTGGTCAAACAAAGCAGAAACATGATCATGTCAGTGTATTTAAAAATTAAAGATAACTACAATAGACAATAGTAAGCTATGGAAGTTGATCCAATTGTGGCTAGCATATGATTCTCAGTACTCCCCTTAACAAGTTAGCATGAGTGCTTGATCAGTGATTATTGCATTAATTAACCATCCTGCAACGCTACAGGTTGTTGCCTTTATTTGTTTGTGTTCTGTTGACCTCCTTCAGACCTGGAGCAGCGGGAGACGACGGAGTTGGCGATGGAGGAGAGCTGCGGGATGCTCCGGTCGCCGGGCTCGCCGTCGGCGGACGCCGCGGCGGCGGAGGAGGAAGCGAGCAGGGCCGCGGCCCCCGCCGCCGCCCGGCGGGTGGAGAGCTGGGCGAGGAAGGTGCGGATGGGCTTCTCCCGCATCCACGTCTCCACGATCCCCATGCCCGACGGCGCCCTCGCGCTCTTGCTTTGCTTCAACCGGAAGCCTCTGCTTCGGGGGCTTTTTCAGCCGGGCAGCGGCAAGGAAGCCAGCCAGCCTCCAGCCTCGAGTTGTTTTATTTCCGCCGCCTCGTTCAGTCCGTGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.941023
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0175300.1 2 25570386 T C
Osa02LNT0175300.1 2 25570502 A G
Osa02LNT0175300.1 2 25570671 T A
Osa02LNT0175300.1 2 25571297 T G
Osa02LNT0175300.1 2 25572045 T G
Osa02LNT0175300.1 2 25572153 A G
Osa02LNT0175300.1 2 25572841 A C
Osa02LNT0175300.1 2 25574649 A G
Osa02LNT0175300.1 2 25569941 T G
Osa02LNT0175300.1 2 25573735 G A
Osa02LNT0175300.1 2 25573875 T C
Osa02LNT0175300.1 2 25573923 G A
Osa02LNT0175300.1 2 25571949 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa02LNT0175300.1 DTM_#DNAt_MULE_japo_Os2081 Chr2 - 25573637 25574028 391
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0175300.1 osa-miR5543 Translation 4.5 9.576 1 21
Osa02LNT0175300.1 osa-miR5804 Cleavage 5.0 23.175 1 21
Osa02LNT0175300.1 osa-miR5826 Cleavage 4.0 12.061 1 24
Osa02LNT0175300.1 osa-miR319a-5p Cleavage 4.0 17.328 1 21
Osa02LNT0175300.1 osa-miR415 Translation 4.0 22.257 1 21
Osa02LNT0175300.1 osa-miR2098-3p Translation 5.0 16.791 1 20
Osa02LNT0175300.1 osa-miR2100-5p Cleavage 3.5 19.235 1 22
Osa02LNT0175300.1 osa-miR2868 Cleavage 4.0 17.314 1 20
Osa02LNT0175300.1 osa-miR3979-5p Translation 4.5 19.743 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0175300.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0175300.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0175300.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0175300.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0175300.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0175300.1 2 Hbd2 Physiological trait Lethality nan nan
Osa02LNT0175300.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0175300.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0175300.1 2 nan Others Others C424 G45
Osa02LNT0175300.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0175300.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0175300.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0175300.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
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