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

>Osa04LNT0267000.1

ATTTACGAACTAATTTCATTTATGGCACTTAACTCATAAAGCTTATATACTATTTTGATGTTCAATGAGAAAAAGGGAGTGTGCGCAACTATTTTCAACCTTTTGTTTCCATCTCTGTTTCATTTCCGGAGGAACTTCTTGAACCAACGGGCTGAGTTCTTGGGGTATCTCTTCATTCCGTTATCGTAATCCACAAAGTTTATCCCAAACCGAACTGTGTAGCCCTCTGACCACTCAAAGTTGTCAAGCAGAGACCATGCGAAGTACCCCTTCACATTTGCTCCATCCCTCATAGCACTTAGCAGGGCGAGAAGGTGCTTGTGATAGTATTCAATCCTGATATCATCCTTCAGGGCCTCCTTGAGTCGCATGGTCTTATTATTGATTTCATCAACACCATTTTCAGTGATGTAGATGGTAGGATTGCCATAGTTTTCCTTAATATGAAGCAACAATTCACGCAACCCTTCAGGGTAGATGTAAAACCAAAACGAAGCAGCCTGAGGCCCTATGGGAATCCCGTTTCGACTACCAGTAATCTTAGCATGGGAATCAGTATTATAGCTGTTGTTATGGCCATATGATGGAGGATCATTATCAGCATAGCTTGAAGCGTAGTAGTTGAGTCCAATAAAATCGAATGCACCCTTGACCATTTCAGATTGCTCTTTGCTGAACTCTGGCAAGCGATTTCCAACCAATTCTCTCATGCTTAGTGGGTAGTCTCCTCTAATGAGAGGATCCATAAACCATCCAAGCATGAAGTCTAGAACACGTCTTGCAGCATCATTGCTGGATTTGGATTGGGAGAAAGGAACAAACCACTCTGAGTTCAAAATTATTCCAATCCTCCCCTTTTGTAAAGCCTTTGCAGATCTTCGATTTAAATTATTATCACGGATGAACGGCGACTGCCTGATAGCTTCTTCAGTGAACTGATATTTCTCTTTATAAAGCCGAACAGTTTCTGCATGAGCAAGTAGTTGGTGATGGCATGCAGTGTAAGGCTCCCTTCCTGAATCTCCAACTCTGCATTTTCCCTTCTCCCAGGATGAACACCGGCCTGGTGCCATGGTGCCAGATGCATAGCCCATAGAGCAGAAGTTCCAAGGCTCATTGAAGGTGATCCAATGTTTCACCCGGTCACCAAACTCTTTGAAGCATATTTCAGCATAGTCCTTATAGTCATTTATGATATTAGGGCTAAGAAATCCTTTATATTTATCTTCCAGTGCCTGAGGTGTATCAAAATGGAATAGGGTAGCAAATGGTTGGACCTCTTTTGATAATAGTTCATTGATCAAATTGTTGTAGTAGTTGATGCCTTCTCTGTTGACTCCACCGCTGAGACTTCCATCTGCCATGACAGGGAGATTTTAACCCTGGTGGGATCACTTGGAAGAATTCTTGACCACGAGATGGAAAACCTGTATGCATCCATTCCCATCTCCTTCATAATGCGCACATCTTCCTTGTAGAGATGGTAGCTATTGCAAGCACCATCCCCGTTGCTCTTGTCGGTGATTTTGTCTGGATACTGATGTGTGAAGGTGTCCCAGATGCTTGGTCCTCTGCCACCCTTCGCCGCGGCACCCTCAAACTGATATGACGACGAGGACGTCCCAAAGATGAACCCCTTGGGGAAGCTTCTCCGGCTGATCGGCGGCAGCTCGCCGGCGTCATTGTAGGCGGCGCAGGTGAAAGCCAAGAGGAGAAGGAGCACGCCACCTGACATCACCATTGCACCTGCAACCGCCATGACCTACATAGACAGAAAAGAGTGATGGGCTGATGAACACAAACGGTGCCCAACAT

Coding Potentia
Explanation CPC Score
noncoding -1.15678
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0267000.1 4 23728637 G A
Osa04LNT0267000.1 4 23728736 T A
Osa04LNT0267000.1 4 23730433 C G
Osa04LNT0267000.1 4 23730975 T C
Osa04LNT0267000.1 4 23731111 T C
Osa04LNT0267000.1 4 23731222 C T
Osa04LNT0267000.1 4 23732093 T G
Osa04LNT0267000.1 4 23728218 C 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
Osa04LNT0267000.1 osa-miR5806 Translation 5.0 23.563 1 21
Osa04LNT0267000.1 osa-miR6246 Translation 4.0 17.587 1 23
Osa04LNT0267000.1 osa-miR6246 Cleavage 5.0 17.641 1 23
Osa04LNT0267000.1 osa-miR416 Translation 4.5 14.197 1 21
Osa04LNT0267000.1 osa-miR5083 Translation 5.0 13.655 1 20
Osa04LNT0267000.1 osa-miR5500 Cleavage 5.0 18.922 1 22
Osa04LNT0267000.1 osa-miR5534b Cleavage 3.0 18.181 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0267000.1 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0267000.1 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0267000.1 4 d11 Morphological trait Dwarf nan nan
Osa04LNT0267000.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0267000.1 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0267000.1 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0267000.1 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0267000.1 4 nan Morphological trait Culm/leaf RM3337 RM3785
Osa04LNT0267000.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0267000.1 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0267000.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
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