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

>Osa03LNT0235100.1

AGGCAGTGAAATACAACAATTAAATAGCGTCTGGTATCGGAACGATGTCACATATGAAAAAGGTGGCAATGTTTACATACATCATTTCAGGCACTATACTGTCAAGGCCCTTTTAGTGGCTCTGCAACACGTTACACGTTACACTTCGAACGAGGGCAAACCATCCTCTTAAAATGGAGAGTAATGGTATGGTAAACTCATGCTACACATTCCAATCGGGGCGATAATTTTACAATTTGGCTGAAATGCCTTATTGTGCTTCTTCAGACACCTCACACAAATTTCAACTACAGCCAATTTAATTCAAGTATAGCCTCCATTTTAGCTGTCTCAGTAGTCATGCTGCAAATCAGAAACCACGCGCTGATTGAGGAACTCAAAAACATGGCTAAACAGTCGGGGCCTCCTCATTGGTACCCAACTTTTTCGTCACCATATCATAAACGTTATCTACTTTGGCAGGGTCAACCTTAAATAATACATGGGCATCTTCCTTCTTGGCGACACTACCCTTGAATATTTCCTGCATCAAAACCTCCTGCATTTTCAGGTAATGGTTGGGTAGCAATCTGTTCTGACAGCATAGATTTTTTTCACTGGTGCTTAATAGCTCTGCCCCAGGAAAACCAACAATATCCCAGTCATCCCAATGTTTAGTGCCTGCATGCCCTGTGGTTTTTGGAGAATCCCTGCCAGTAGAATCCAAGCTGGCACCACCTTTCTTCTGATCCAAATTACCATCTGACTCGATTTTCATAGGTCGATTCGTCTTATGCACCACTTTAGTGTTGGATAAGAGCTGACCACTTTCCTTAGCTTTTTGGGCATTCACCTCATGTTCCTTTTTCCTCTTTTGCTCTATGTGAATCTTTGCTTCAGCCAATGTACGGCATCCAGCAGAACGACATTCCTGAAGCTCTTGAATCCTCCTTCGAATTTTCCGTTCCTCAAGAACACTCCTAACAAGTGCTTCATGTTCCTCCTTAGAAAGGAAACGCATGAACACCTTATAGCGATGGTAAACTTCCTTGTCTTCATTTGTGAGATCCTTCTCCAAAGGATTAGGAAATAGTAAGTTTCTTTCCAGTATGAACTCTTTTCTCCTTTTTCTTTCATCAAGCCTTGACAAGTAAATACGCAATACCCTTAGCTTCAGTTCACGATCAGTTTCCGAATCAGTTTCTTTAAACTCCATCTCAGCGAGTGCCTGTTCAGCATCGTTATCATACTCTGGGTCAAATTCATGTCTCTTTGAATTGTATCCACTCAGTTCAGTCAAAGAAGGCCCTTCATCTGCAGAATATCGGGGTTTTTTCACACCTATACTTCTATCCACATGACCATCTTCAACTTTTGCTACATTAGCACCATCTTTGAATTGTCCAACATTTGATGCTTTCTTATTTGCACCCCCAGCTATGTGTGAAGGTGATCGACCAGCTAAACCTTCTCCAAGTGCATCTTCCACCTTGACCCTTGGGGGAGAAAATGGAGACTCGTCCTTAGGGGTCAAATCCCCTGGTAACACTGAAGTTCCTTTTTTACTCTCGCCTTGTACTTTAGCCATAGCAAGCAATTCCTTCCTGTTCTTACCGTTAACATGAGACATATCCGGAAGGGGATAACAAGGTGAGTTCATGTATGCAGTTGTATAATGATCAATGCATTGTGCCTTGGTCTTGGTGCCAACATGCTCCGCAACTTCAGCCCAATTTCCCAGACCATACATTTCAATTCCCTCTAGAAGAAGGATTTCCTCGTCTGCATTCCAATCTGGACAAATAAGAGGGAAAGACAGGTTGTCCATGACCCTGTAAGGATGGTTGCTGCGGTGCGGGGTGACCTCGGCGCCGACCGAGAAGCACTCGACGCAGAGGTCGAAGTCGGGGCACTTGGAGCACTTGATCCGGATCTTCCCGGAAATATCCTTATTGCAGTAGTTGCAGTGGTACAGCGCCTTCTTCCCACCACCCTCTCCGGCTCCCCCGCAGGCCGCCGAGAGCGAGTCCGGCGCATCGCCGCTCGACGCGACCCTCCTCCGCTTCGACCTGTGGTTCGTTTCATCGTCGCCGGAATTGGGCACCCCGCGAGACCGGCCCATCGCGGGCGCGCCCCCAAACCCTAGCGCAAACCCTAGAAACCCTAAGCTCGCGCGCACGCCGCCACGGCCTCCGCCGCCGCCGCCGCCGCCTCCACTCGCATCGGGCGGGATCGAATCGAATCGAGGGGATCGATCGGGGCGAGGCGAGGGCGGATTTGGATTGGGGAATTT

Coding Potentia
Explanation CPC Score
noncoding -1.19365
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0235100.1 3 30937025 A T
Osa03LNT0235100.1 3 30937502 G A
Osa03LNT0235100.1 3 30939104 T C
Osa03LNT0235100.1 3 30939166 A G
Osa03LNT0235100.1 3 30939472 G A
Osa03LNT0235100.1 3 30941297 G A
Osa03LNT0235100.1 3 30941458 T C
Osa03LNT0235100.1 3 30942105 T G
Osa03LNT0235100.1 3 30938655 T C
Osa03LNT0235100.1 3 30935669 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa03LNT0235100.1 DTM_#DNAt_MULE_japo_Os1617 Chr3 - 30939668 30940941 1273
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0235100.1 osa-miR5793 Translation 5.0 19.736 1 21
Osa03LNT0235100.1 osa-miR5816 Cleavage 4.0 13.016 1 24
Osa03LNT0235100.1 osa-miR6253 Cleavage 4.0 17.421 1 22
Osa03LNT0235100.1 osa-miR166a-5p Translation 5.0 10.245 1 21
Osa03LNT0235100.1 osa-miR166e-5p Translation 5.0 10.245 1 21
Osa03LNT0235100.1 osa-miR395t Cleavage 4.0 14.236 1 21
Osa03LNT0235100.1 osa-miR395c Cleavage 4.0 14.236 1 21
Osa03LNT0235100.1 osa-miR159a.2 Translation 5.0 12.357 1 21
Osa03LNT0235100.1 osa-miR435 Cleavage 4.0 19.247 1 20
Osa03LNT0235100.1 osa-miR1866-5p Translation 5.0 20.418 1 24
Osa03LNT0235100.1 osa-miR1846e Cleavage 4.5 17.134 1 20
Osa03LNT0235100.1 osa-miR395x Cleavage 3.5 14.236 1 21
Osa03LNT0235100.1 osa-miR812o-3p Cleavage 5.0 9.537 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0235100.1 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0235100.1 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0235100.1 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
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