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

>Osa04LNT0289100.1

ACAGAACTCCCAACTTATATTCACATTTTTCGTGTAAAAAGTCTACAGGCTACAGAGAAGACTACAGGAAAACAAGGTTTTGAACACAAAGAGGTACCTGCATATGTCCAAGTACAACAAACAAACAATTCAACTAATCCTGAACTTCAGATGATATTGCTAAGCTTGCATAGGCTCTTCAGTAAGGCGTCTATGGTCTGAGGAAGCTGTGGCTGAAGAACTCTTGGAAGGACAACCTTTTCACTGGATTGCTACACAGAAGTCTGGTGCATATATCAATAGAATCAGGACGTAGCTTGGAAATAACGACTTCTGAGAATGGAAGAGACACGGTTCGGTTTATGCATTGAAGCAGCTGGACATTGCTTCTACCACGGAATGGTGGATAGCCATTCAAGAGCTCGAAGAGAATCGCGGCGATACTCCACAAATCTACCCCACCATCATACTTCTGAAACAGCATAACTTCTGGGGCCATGTACAAACAAGTGCCACAATTTGTATCTGTGTATTCCCCGGGACGAAGAACTCTTGACAGGCCAAAATCAGATATCTTGAGGATCGCATTGCTGTCAGGAGAAGAGAGCAGGATATTCTCGGGTTTTAAGTCCCTATGGACGATATGGTGTCTGCGGAGCACTTGCAAGCCAGCTCCTACCACAAGGTGTTGGGCAAGCATAATTTCTTACACATGATTATCTTCTTGTTGTAATTGTAACACAACTCTACTGTAAACTGTGACATTTCTCTTAATGGAAATGGAGGACTAAGGCCCTTTGATCCAAAAAAAAAAATTTGTAACACAACTAACTAAGGTTGCGGGTAATGTGATAGATTGGGGGGCAACAAGAGAAAAGAGATGCTACTAGGGCTAGAAATGAAATTGATATGGCAAATATTACTAGGTGAATTACCGATCTGTCTCATGAAATTGCTGGCGACGCGCTCCTCTACCCTCCCGTTGCGCTGGATGTAGGCCGCCAGGTCTCCTCCCTCGCACAGCTCCAGGACAAGGTACAGGTTGCTCTGGGTCTGGATGAGGTCGAGGAGGCGGATGATGTTGGGGTGGGTGACGGCGGCGAGGAAGCGGACCTCGCAGTCGAGGCTGTCGCGGAGGGTGCTGGGGAGGCCAGTCAGCCGCACCTGCTTCACCACCACGGGGGATCCGCTCGACCGCTCCACGGCGCGCCACACCACCGTGGACGGCGGCCGGCCGCCCAGCCGCTCCCGCAGCTCGTAGCCTCCCACCGTCGTCTCCGGCTCCGGCGTGCTCGCCATCGCGAAACCACTGGAAAGGAAAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.779792
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0289100.1 4 35089862 G T
Osa04LNT0289100.1 4 35090252 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
Osa04LNT0289100.1 osa-miR396a-5p Cleavage 5.0 19.493 1 21
Osa04LNT0289100.1 osa-miR396b-5p Cleavage 5.0 19.493 1 21
Osa04LNT0289100.1 osa-miR396c-5p Cleavage 5.0 19.493 1 21
Osa04LNT0289100.1 osa-miR1846d-3p Translation 4.5 23.037 1 20
Osa04LNT0289100.1 osa-miR1861n Cleavage 4.0 21.999 1 22
Osa04LNT0289100.1 osa-miR2118o Cleavage 4.5 20.831 1 22
Osa04LNT0289100.1 osa-miR3982-3p Cleavage 5.0 23.6 1 21
Osa04LNT0289100.1 osa-miR2275d Cleavage 5.0 21.764 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0289100.1 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0289100.1 4 Sh3 Morphological trait Panicle/flower nan nan
Osa04LNT0289100.1 4 iSh3(t) Morphological trait Panicle/flower nan nan
Osa04LNT0289100.1 4 Sh3-gla Morphological trait Panicle/flower nan nan
Osa04LNT0289100.1 4 gpps4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0289100.1 4 Sh(t) Morphological trait Panicle/flower nan nan
Osa04LNT0289100.1 4 nan Morphological trait Panicle/flower RG620 RG214
Osa04LNT0289100.1 4 nan Resistance or Tolerance Drought tolerance RG143 RG620
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