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

>Osa02LNT0175800.4

GCTGAATAGTTGAATCAATTAGACGATTGAAACAACCTCTTCCACACTTCAAAACCTGTCTTATCTCCACAGGGGTTAAAAACAAAAAAGAAAAAAAAAAGCGAACAAAGAATCAAGAAATAATAGATGTAGCAGGTACAGTAGGCAAGCACCAACACCTCCCCTCCAACCTCACACTATGGAAACTACTAATTTTTTACAGAATACAACTCACACTTCAAGATCAGCTTCAGGGCAACAGAGGCAAGGGAAGTTTGATATTCTCCCTACCACAGATTTTCGTCGGTTTGTTTGTTTACGCGTTCTCAGCTGCTGCATGCGATCGCTTTGGTCGCCACTCTGTGTGTGCCTTCACAATGTCAGCCTTCACAAGATGGTCGCACTGGATGGCAGAAGCCTGCTTGTCGGCGCCAATGCTGGTGCATTCCCCTGACACGGTGGTAAGTGATTGCAGCACGCTGTCTCGGCCACACTCCTTCCTGTAATCCAGGGTCATGCTTGCAAGCTCATGCTTCTCCAGTACTGAAATTGGAGCACTCTCAAGGATCCACCCAATATATTTAACATTGTTCACATGCTGATTGACATCGAGGTCACCCCATCTAGGAGTGAGCCCCTTTCTTATGAATTGCTCTGTAGCATCATCACCAACTTTATTTCCTGTCTAGGCTAACTTTTCACTCTGCTCCTCTGTTATAGCTGAACGGTCATTGAAATATGGGCCTATTTCAGCTCTAACTTCATCTGGCATTTTTGAAAGTCTTCTAGTTTTCTTGTGCATCATCACCCAAACACTTGTAGCTCTCAAGATTGTTCGGCCAGAGTTGTAGTCACGAACATGCCAGTCTCGACGCATGCCATTTTTGCCAGCAGCAGCGACCCATGTGTCAACTTGAACCATATCTCCCCATGCGGGGTATTGCTCAACAAGAAGCTGGATTTTGCTGACAACCCATATCAAGTTCCGTTTGCTCATCTCCGGTGTAGCCCCAAAACCATCTCCAAGAAGACCAGCAGTCCTTACATGGTTAAGAGCCGTTTCCTGTAAATGATTCATCAATGTCTCTATAGAAGCTGTACGATCAGCGCCAATCTCGTAGGACCGAATCATGAAGTTCTGCCTAAACACCATACCGTCCTGGATGATCCTACCAAAGCCAAATGTGTCAACAAGCATGTCAGGTTTCTTCGGCTTCCAATCAAGCAGTGTCCACTGCTTCTCTGCGGCGAGGAAGATGGTTGTAATAGCCGCAAGAAGCATGCTCCAATCCGGCAGTTGGTTATAGAACGTCTTTGGAGCACTGTGAGGCACCGTTTCCTCCATGTCAGGCTTCACCGTCTTGAGGTTAACCTTCGTACCATTAACCTTGGGAAGGGTTTGAGCCTGTGCCTTTACTTGCATGGCTGCAGGAGGTGGGTTAGGCTTTGCGACAATGCCACAGACACTCAAATTCTCCGGCAATTCGCCGGTAACAGCAGCATTCTTGGAGCTTCTAGCTGATGCTGCAGGAGATGAGCCTGGACCTGGGAAGAATGCTGAGGCGGCAAGAGACCCTGCCATGATTGAACTTCCCCTCACGGCCCAAAATTCGTTTAGAAATCAATCACACGCCAAAAGCGCTAACCAGGATCCCCTCCCCTGCTCTGCTCTCCTTGGCGATGGAGATCGGCGCCCCTCCCCTCCGGTGTTGAGCCGCGGCTCGTCTTTCTTGGCGCAAGGAAGGAGACGACGGGAGATTTTCTCTTTTCTTTCATTTACGCCAAAAAAAAGGAAGGGGAAGATACTCTCCGCCTTTTATCTCTAACATTTTTTTTCTTTATTATTGGCTGGTGGCCCACGTATCAGCAATACTAAGAGAAAAAAATAAATATTTCGATTAGAGATTGTGTCAGACTACCAGAAACCACTTTTATTTTAGCCAAAAAAAAAGAGAAGGAGAAGATACCCCCACCTTTTATCTCAACATTTTTTTTCTTTACGATTGATTGGTGGCCCACGCATCAGCAATACTAATAAGAGGAAATAAATTATTATTATTATCAAACTTGATTAGGGATTGTGTCAGACCACCAGCAACCACTAACTTTAGTGTTGTTACACGCACGGCCGCCACCGACGCTTTTTTTTTTCGAGTCAAAAAGGGAAGGAAGGGGAAGATACTCCACCTTTTATCTCAACATTTTTCTTTATGATTGGCTGGTGGCCCACGGATCAGCAATACACTGCCACCGACGCTCTTTCTTTTTGAGCCACCATCGTTCCTTCTCTCCGCCTTTGTATGCGCAGCCGCGCCCTTTGGTTATCGACGTGTCTTTTCTCCTTATGAAATCATGAAGTTGATTTATAGTAGCTGACATATATAAGGTCTGAAAAGGGGTAAAATCACATATTATTCATTGCGCTATGCTGCAAACTGGATCGAATTCTCACCTGTGGAATTTTTTTCTGCATGATAGAAAATTATTTGATAAGCAGAAAAGGAGTGCAGCCTTGAAATTTTCCGTATCACTCTCATGGAGAGGAAAACTAAGTTATCGTCAGCAATCGTTTCTTGGAAACGTAAAATTCTCTTCAGGAATCAGAACAGAATTGAATACAAAGGTAGAAATGTCTAATCAAAATTTACCTCGTCAATTAGGGTCAGATCGATCATGTAAGTGACATTACAAAAGATAAAACATAGCGATATTATCAAGTTATATGTCCAAAAATGGGGCAATCAGAAGAACACATGCATGCTATTTTACAAAAAGGCAGAAAAAAATGAGTACAATCATCAACTCACCTAATAGCTATGTTCCAATTTGGGGATCGAGAAAATAAACTCAGCATTGGAGAACGGAAGAAAACATGCACCTGATCAAAAACTTGAAAACTGATGGGATTAAGAACGGTAAACACAAAGAAGACACCATGCAATCGGCTAATGTTGAAGCTACCATCAAATCATGTAGCCGAAGGACAAATTAACCATGAACCCTGTAATATGCCCAATATAGTTTCCAGCCAATGGGGCAGACTGAAGAATACCTAAAGCTTCGCTATTTGATGTAAGGGGAGAAAAAAAAAGAGAGTACAGTATAGACATCAGCTTAACCAAAAGCTGATAAATTTGGGATCGAGCCAATGAACTCAACGTAGGAGAATAAGGGGAGAGAAAATGTACCTCATCCAAATACTGATGGGAGTAGGAAAGATAAACACCAGGAAGACACCAATCGCCTGATGTCAGGAGCTGCAAATGAAATCATGTTGACGGAGGACAAATTAGTTGTTTACCCTGCATATATGCCCTATATAGATCTCATTCCCAGCCAAGATCGACCAATGTTTTCTGAATCGAAAGATCAAATCAATGCCCGGATAATCCATATGAGCCACCAGATGAATTGGACGGGAAATTGATGAAAGCCCTGATAATCCGCATGAGTACTGGATAATGATAAGATATCGTGGTGAGCGCCGCGCCGGGATTGAAAGCCTGCATACTTGATACTCGCAGAGCATCGGGAGAAAGCATCGATATTTAGCATGAAGAGGAGGAATGGAATCAGGAGAAAGCTAAATATTTATCATCGATATTTAGCAAACGGAGCAGCGCCAGGGGAGGGGGGAGGGGAAGGGGGAGGAGAAGCGCCGGAGGGGGGGTGTGGAGGAGAAGCGCCGGGAGGGAGAGGGTTGGAGGAGAAGCGGCGCGAGGATGCGAGAGCTGCCGGCGGTGGGCCCGCACCTGGCGCGCGCGATTGGGGAAGGAAGCGAGCGGTCGGCGTCGGGCCCGCACATGGAGCGCGCGATGTGGAGGAAGCGAGCGCAGGATGGGGAAGGGAGGAGTCGCGCGCGGCGGCGGGGCGGAGAAATC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.975571
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0175800.4 2 25949097 A T
Osa02LNT0175800.4 2 25951243 A G
Osa02LNT0175800.4 2 25953946 G A
Osa02LNT0175800.4 2 25954361 A C
Osa02LNT0175800.4 2 25954395 A G
Osa02LNT0175800.4 2 25954666 C T
Osa02LNT0175800.4 2 25955178 T G
Osa02LNT0175800.4 2 25955229 A G
Osa02LNT0175800.4 2 25952902 G A
Osa02LNT0175800.4 2 25954948 T G
Osa02LNT0175800.4 2 25950134 A G
Osa02LNT0175800.4 2 25949892 T C
Osa02LNT0175800.4 2 25949840 A G
Osa02LNT0175800.4 2 25946755 T A
Osa02LNT0175800.4 2 25947209 C T
Osa02LNT0175800.4 2 25947311 C A
Osa02LNT0175800.4 2 25947477 T G
Osa02LNT0175800.4 2 25947669 T A
Osa02LNT0175800.4 2 25948816 T C
Osa02LNT0175800.4 2 25950052 T C
Osa02LNT0175800.4 2 25950174 A G
Osa02LNT0175800.4 2 25950470 G A
Osa02LNT0175800.4 2 25950937 A G
Osa02LNT0175800.4 2 25951068 T C
Osa02LNT0175800.4 2 25947289 G A
Osa02LNT0175800.4 2 25951350 G T
Osa02LNT0175800.4 2 25951520 A G
Osa02LNT0175800.4 2 25951582 A G
Osa02LNT0175800.4 2 25951672 A G
Osa02LNT0175800.4 2 25951850 C T
Osa02LNT0175800.4 2 25952171 C T
Osa02LNT0175800.4 2 25953095 A G
Osa02LNT0175800.4 2 25953449 T C
Osa02LNT0175800.4 2 25949363 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
Osa02LNT0175800.4 osa-miR812t Cleavage 4.0 17.178 1 24
Osa02LNT0175800.4 osa-miR812u Cleavage 4.0 17.178 1 24
Osa02LNT0175800.4 osa-miR5821 Cleavage 4.5 9.687 1 21
Osa02LNT0175800.4 osa-miR5836 Cleavage 5.0 12.536 1 21
Osa02LNT0175800.4 osa-miR1437b-5p Translation 3.5 23.15 1 21
Osa02LNT0175800.4 osa-miR393a Cleavage 5.0 18.376 1 21
Osa02LNT0175800.4 osa-miR395u Cleavage 4.5 16.362 1 21
Osa02LNT0175800.4 osa-miR156k Cleavage 5.0 20.917 1 21
Osa02LNT0175800.4 osa-miR166h-5p Translation 4.5 11.632 1 21
Osa02LNT0175800.4 osa-miR393b-5p Cleavage 5.0 18.376 1 22
Osa02LNT0175800.4 osa-miR419 Cleavage 5.0 13.487 1 21
Osa02LNT0175800.4 osa-miR528-3p Cleavage 2.5 20.416 1 21
Osa02LNT0175800.4 osa-miR535-3p Cleavage 4.0 14.803 1 21
Osa02LNT0175800.4 osa-miR535-3p Translation 5.0 13.584 1 21
Osa02LNT0175800.4 osa-miR1432-5p Cleavage 5.0 15.965 1 21
Osa02LNT0175800.4 osa-miR810b.2 Cleavage 4.5 11.47 1 20
Osa02LNT0175800.4 osa-miR1848 Translation 3.5 19.948 1 21
Osa02LNT0175800.4 osa-miR2874 Cleavage 2.5 7.176 1 24
Osa02LNT0175800.4 osa-miR812n-3p Cleavage 4.0 17.178 1 24
Osa02LNT0175800.4 osa-miR5076 Cleavage 4.5 22.013 1 22
Osa02LNT0175800.4 osa-miR5081 Translation 5.0 9.022 1 22
Osa02LNT0175800.4 osa-miR5145 Translation 5.0 13.817 1 24
Osa02LNT0175800.4 osa-miR5486 Translation 5.0 10.625 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0175800.4 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0175800.4 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0175800.4 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0175800.4 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0175800.4 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0175800.4 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0175800.4 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0175800.4 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0175800.4 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0175800.4 2 Hbd2 Physiological trait Lethality nan nan
Osa02LNT0175800.4 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0175800.4 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0175800.4 2 nan Others Others 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