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

>Osa03LNT0205800.2

CTAAAATTTAGTTGCTTCTGTACAACTGGAAGATATGATGAACCCATGAAAGACGTTGAAGGCAGCAGGTAATTGTTGCGATAGCGCTTTTTGGTTTAACTATTCTCTACATACATCCAATGGCGCAAACCAGGTAAGTCAATGTTTCGTGGTGAAAAACACGATTACCTGAGAAACTTACAGATCATGTTTACCTAGAGCTATGGATGTTTGTAGAATCAACGATTTATGTAAACACCACCACCAACCTCTTTTTCTCACATGATGATGCGTCTCAGACTGAGCAACATCTGGTAATGTTACAACTTAAAATATACATCATCCCCAATCCCCATCTTCCAAAGCAGGAGTGAAATAGCTTATGTAACGTCCATCATATGTGCATTGCTCACATTTGAGACCAAACAGTGCAAAGTTCCGTAGCCTGATAATGATGCCATGTTAAAATTCTCACTTCTCATGTGGAGTTTCTCTTCGGAGCTGGAGCTGGAGGCCCTGGCGGGCGAGCCAAATCTAAGTTCTGCATCTCACTTGCAAGAATCGCCCTTCTTTCTTTCAAGAAATTGAGTCGATTTGTCAGCTTGGCTAATGCAGATGGTGCCCCGGAATCCTCTGTTCTAGATCCAAGCCTGCCTAATAGTGGATTATTTGAGTATTGTTTCTGTGCAAGGTTCCACTTTGATGCCAATGGATCTTGGCCATCCTTGACAATCTCACCCTTAGAAATCAACATTCTTTGAGCCATGTGTGTAGCCGATACCATGTCAGATATAGAATTGGGCCCAACATTTGATGATGTGGTACTCTGTTCACCTTCGGTTAGCTTGTCTGTATTTAGCAGTCGTTTGTTGCATGAGTCACATAATGAGGCGGAGCTCATCTGGACCTGGTTGTTGAGTTGTCCACGGAGATCAGAACCCTTTTGTTTCAAGTTCAAAATATCAGCTTCAGCAGTAGCAACTTCCTCAAGATCAGCCTTAGTCTTGTTGTCAATTGTTGATGGGAAGGACGCCTGCCCTCTTCGCAAATTCATCAGCCCTGACTCCAATGAGACCCTCAAATTTCTCTCCTTCTGTAGCTGATCTCGCAAATTTTCCACTTCTTTTTCGAGTGCTAATCGGCGTTTATGCAATTCTACTTTCCTTCTTTCGAGACTTGCTTGTAGGATTGAATTTTCTTTCGCCTCCTTAGTAATTTTAGATTGGAGATCTGTCTTGCTGTTCTCAAGCTTCTCAATAAGAGTCTCGTCATCACTGCAATAGTCAATCTCCTCTGCTGACAGGTCTTTTCTTGCTGAAGTACGGCCCCATAAGGTCTTTTTGCTCTTATTTCTTGAGCTGCTTGATTTCTCCATAAATTTTGCTCTTGCTGATGATGAGCGAACATTTAACTTTTCTATTTGGTCTGTGGATCCATTTGATTCGTATAATTCTTGTTTTCGATTGGATGGATCATTGCTTTCAATTTGGCAGGTGTCTTCCCTTACCGCACCATGTCCTGTTCTTGCTGCTTTCTTAGGAGGTTGTAAACCCTGATCGTTGCCATTAGATGCTGTGCCAGAGTTATTGCTTTTAACCTTGTCATCAGAGACACTGGTCTTAATGTTGTTGTCACATTCACTGCCACCAGATGAGTGCTCAGTATCATCATCCATGTCTTCTTCAATGTTATCTTCACCAGAATCATAAGAGTCATCCTCTTCAGGGCCATCGTTGTCTGTGGAATATTCCTTGTCAAAATCACCGTCTTCGGACTCAGTATATGCATCTGAAGAGTAGGAACCGTCTTCCAAGTCATCAAATATCTGATCGTATTCTTCGAGCATAATGATGACGATTGCTTGAGCATGGTTGGCAGCAGCTGCAGCTTGAAGCAGCTGGAATGAACCATCCCCAGCCATACTAAAGTCGCTATCAATTTCACATTCACCGAGAAGAAGAGGTCGGAGAAGGAGTGGTGCCATGCAAGCCGCCAAAGCAGATTGAGACATCCTATTCACAGCTTTGTGTGATTCAACAATCTGCATCATCTTAAGAGTCCTCTGCAAAAGTTGTCGGTTTGGTTCTGGGAAAACTTCATAAATTACTCTATTCATAGCATCAAGCCTTCTTGTCTTGTCAGTTCGGTAAGCTCCAACCAGTGCAGTGCAACATGGTGCAGGAACTGGAGATGAAGGCATCTCTCGAAGAACATACTTGATGCAGTCACCAATAACATGTGCATCCTCTTCTGGGGAGAACTCATTTTTCCCCTTTTCATAGTCCCGAACTCTTCGTTTGACTTCTTCAACATCAGCAGACTGACGTAGGATTCCTTCCACCTTGACACCATAATCTTCAATGAACTTTAAGGCCTTCTCCAGGAAAGCTGGACTACCATCAGCATCTACAAGGGCAAACTCTGCAGGTCTGCCAATGATAGATTTATTGTCCGACTGTTCAGCTGGAGCTTCAGCAGGCTCTGCTATGTCAGTGCTGAAAATTGGATTTTGGCCAACAGTATTTGCTACAACAGGTGCCTGTGCCAGAGCATTCTCTAGTGCACTTCTCCATTCATTGAGTTCTTCTGTAGTTTCTGCCTTGAGAGTGAAAGTTCGCCCATCGCGGCCATCAGGAAATAACACTGTTAAAAGTTTCTTGTCTTCTTTGACCACAACACTTCCGGAGTTATTCAAGTCAATTCCACCTAGTGTAACAATCGGTTCATTTCCTCTGGGAGGTGCATTAGGATCACTTCTGAAGAACACCAATGATGCCCTTGTAAGAATAAACCAGCGCTTTTTCCATGTTGTCCAACCAATTCCTTTAGATGAGAGCAGTAAATGTCCACTCTTAAGAACCTGGCAATTAGGACAACTAGTTGGTGATTTATCACCAGTTTCAGATGTGTTTGTATTTGGGTCTCCTTCCCCACATCGGCAGATCTTGAACTGGCCTGCATTCTCAGTAGTCTGTGAAGATGATACTTGCTGGTAAGGAATCCTGAACTCCGAAGCTGACATTGTCTTCTCTAAATGGCTGAGTTATGAACACACCAGAATGTTTCTTTTCCACCAATGAGTTGATATTTCTCTAGAGACTGATACAGCATACAAGGTTACCACAAGAAAGTGAAGCATGTAGACTTATTTATTAGCCCCTCATGCAGTGGCTTCAAATCTGTTGAGTTGGCTTCCACATCCACCCTAAATATCAGCCTTCGGACTGCACCCCCAGCGATCCGCATGCAGAATCAGATTCACTTCACCATATCAAGCAGACATGCGAGAAGTCAATCCCCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.507205
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0205800.2 3 8294267 C T
Osa03LNT0205800.2 3 8294868 G T
Osa03LNT0205800.2 3 8295271 G A
Osa03LNT0205800.2 3 8295419 T C
Osa03LNT0205800.2 3 8298064 A G
Osa03LNT0205800.2 3 8298190 T G
Osa03LNT0205800.2 3 8298464 C T
Osa03LNT0205800.2 3 8298608 T C
Osa03LNT0205800.2 3 8298750 T C
Osa03LNT0205800.2 3 8298838 C A
Osa03LNT0205800.2 3 8298848 C T
Osa03LNT0205800.2 3 8300227 T C
Osa03LNT0205800.2 3 8300992 G A
Osa03LNT0205800.2 3 8301292 C G
Osa03LNT0205800.2 3 8301362 T A
Osa03LNT0205800.2 3 8301383 A C
Osa03LNT0205800.2 3 8303680 A T
Osa03LNT0205800.2 3 8303772 T A
Osa03LNT0205800.2 3 8304361 C T
Osa03LNT0205800.2 3 8305082 G T
Osa03LNT0205800.2 3 8305972 T C
Osa03LNT0205800.2 3 8305988 G C
Osa03LNT0205800.2 3 8303677 T A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0205800.2 osa-miR5537 Cleavage 4.5 11.63 1 22
Osa03LNT0205800.2 osa-miR5813 Cleavage 5.0 15.134 1 22
Osa03LNT0205800.2 osa-miR5817 Cleavage 5.0 12.049 1 24
Osa03LNT0205800.2 osa-miR5826 Translation 4.5 15.642 1 24
Osa03LNT0205800.2 osa-miR5836 Cleavage 4.0 20.019 1 21
Osa03LNT0205800.2 osa-miR1861o Cleavage 5.0 12.716 1 22
Osa03LNT0205800.2 osa-miR166a-5p Translation 4.0 23.209 1 21
Osa03LNT0205800.2 osa-miR166e-5p Translation 4.0 23.209 1 21
Osa03LNT0205800.2 osa-miR160f-3p Cleavage 3.5 10.915 1 21
Osa03LNT0205800.2 osa-miR160f-3p Translation 5.0 14.941 1 21
Osa03LNT0205800.2 osa-miR166g-5p Cleavage 4.5 20.456 1 21
Osa03LNT0205800.2 osa-miR166h-5p Cleavage 4.5 23.209 1 21
Osa03LNT0205800.2 osa-miR166i-5p Cleavage 4.5 20.456 1 21
Osa03LNT0205800.2 osa-miR440 Cleavage 4.0 15.124 1 24
Osa03LNT0205800.2 osa-miR1425-3p Translation 4.5 16.969 1 21
Osa03LNT0205800.2 osa-miR1432-3p Cleavage 4.0 23.253 1 21
Osa03LNT0205800.2 osa-miR1861a Cleavage 5.0 12.716 1 22
Osa03LNT0205800.2 osa-miR1861b Cleavage 3.5 12.716 1 22
Osa03LNT0205800.2 osa-miR1861f Cleavage 3.5 12.716 1 22
Osa03LNT0205800.2 osa-miR1861h Cleavage 3.5 12.716 1 22
Osa03LNT0205800.2 osa-miR1861i Cleavage 3.5 12.716 1 22
Osa03LNT0205800.2 osa-miR1861j Cleavage 3.5 12.716 1 22
Osa03LNT0205800.2 osa-miR1861l Cleavage 3.5 12.716 1 22
Osa03LNT0205800.2 osa-miR1846e Translation 4.5 12.476 1 20
Osa03LNT0205800.2 osa-miR5076 Cleavage 4.5 20.007 1 22
Osa03LNT0205800.2 osa-miR5513 Cleavage 5.0 18.439 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0205800.2 3 Gy3a Others Others RG266 C63
Osa03LNT0205800.2 3 S34(t) Physiological trait Sterility nan nan
Osa03LNT0205800.2 3 qTAA3-1 Morphological trait Shoot/Seedling C316 C63
Osa03LNT0205800.2 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0205800.2 3 qGW3 Morphological trait Seed C706 C12534S
Osa03LNT0205800.2 3 qOE3-1 Physiological trait Eating quality nan nan
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