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

>Osa04LNT0271100.2

TCAGGACAAACCATCTGACAGTCAAGAGTGATGTATTCTCTTATGGAGTTTTGCTCCTGGAAATTCTTTCTGGTCGTCGTCCTATTGAGGTCAGGAGAGCTTTGTTCTGGTTATTTTCTTGCCCCCCTGACCCCTCTTGCCCCTGCATACGCTCTTGCTTTTCTTTCTCGAGCAGTTATCTGTGGACCTATTCGCCGAAAGTTGATGGCACTGTCTTACATTGCTGACTATCCCTGACAATAAAAGGCTGTTCTCAGTTCTGGATTTAACAAATTCCCCTGTTTAGTTGACACAAAACTTCCCCCAAACTCCTAACTTTCCATCACATCACATCACATCCGAAACTTTCCTACTTATATAAACTCCCAACTTTTTTTCCAAACTACCAACTTTCCCCAAACTTCTCCCCAATTTCAGAAACTAAACACAGCCGCATTGGACGCCAGATTCTTCCTTCATCCAACAAGCTCTTCCATCCATTCATTCCTCTGAATATTTTAGTTTGCTCCTGAAGGAACCATCTGGCTTAAACGTTCAATTGCATAAAGCTTCGCAAGACATCCTAGTGTACAGACAAAGCTCTCAAGTCTAAAATTTCTCCGAGGGATTCACCCTCATATATATAAACCCTGCTAGCGGTTCATGCTCTAGGGAATTTGTACACCGGAATTTGCCTCCTCTCTAATTCTGTATCCTAAACTACCAAATAAACCTTTGTGTCCCAGGCTCATGTTGCCACTGGAAAGGTCTGAACAGAAACATTGCCAGAGTGAAGAAGTCAACAGCGGCATAAAGAAACCCCAAAGCAAGCAATTTAACATTGCTGATCACTGGAGAATGAAGAACCAGTATGACCAATGGAATTGTATAGTATCTAAATTCAACCAATGGGGCAGGGATGAGAGCAAGGGCAACTGATAGAACAAAGGACAGCACCCAAAGTCTTGTCTGTGACTTCCCTAAGATATTAACAATTGAAAACCATGAGTACACATAAACTGGAGTCAAAATGTATTTCATCATCCAGTGAACTTGGATAACCTTCCTCCAAATATAAAAGGTGTAGTGTCTATTGTCAGCAAGAAGATATGGATGAGCAATGCTGAATAAATGTACAGCAACAAGGCTTAAACCAAGAGCCACCAAAATTGCAAAAGAACTATATGTTTTGTTCTTTCTGCACCAGTGGAATAGGTCTGATGCTCGGGTAGGAGTAAAATGCCATGGCAGGAGGGCAGCAGCTGACACTAGACCAAAGTACAAAAACTGTGCAAAGTGTGGTGAAACAACATGAGCTTCCTTAGCACCTAGCACTATGCCACCATTCCAGACTATGAATGCCACAAACACCAAAAGAACCATTGCAAATGGTATAAAAGCAATTAAAACTTCACACTTTGAATTCCATAACTTGAAGATGGCATCCCATATTTCCTCTGTAAAACTGGAATACATAATGTTTGATTCAGAAACAACTTCTCTCTTGTTTATGGGATTATTGTTTCGCCGCCTTCTCAAACCTGGAGCAGTGGTTTTATTATCCATGTGAGATGCCTCTTTGTTTGACTTATCTGTTAGTTCACTGTTCTCGTAACAAACATTGTCCTTGACATAAAGATATTGTGCATGAGCGATGGCTCCATTGGCAGCAAAAAATATCATCCATATTACATTAGTCTGCCGGAGAAGTATAGAAAAAGCACCAAACGCTGCACTGACCCAAAATTGTTTCTTCAAGCAGAAAAGGTACATCGCAAGAACTGCCGCTAATGATGCAACATCAGTATAATAAAGGAAAGTAAAGAACCAATGAATAGGGTACAAAGCTACTAAAATAGCAAATGCAGTTGCCTTCCTCTTGCCAATTTTTGGCCTGATGCACAAAAGCAGGTCATGGACTAGAACACCACAGATCATCGCCATGATAACATTAGTGGATCTCAGAAGTGCTGTAGTGCAAAGGGCATCAAATGCCTCTGCTATTCTAGTCACCCATGCACCAGGAAACAAGGAAGCAACATATGCTAGTGAAATGTAGTACAGGCCAGGAGGGGTGGTGATCATGGGATCCCATATTAAGAAATCTCCACGGCAATAGCGCTGCACCTGGGGAACATGGAAGATCTCATCCATGTAAGGGTCGGGCACGATGGAGGCGACCAGAGCAGCGAGCGGGATCGCCCATGCGGCCACTGCCGCGGCGACGGTCAGCCTCCCCATCCCCCACCCGTACTGGCTCCTCCCCGCTGCGCTGCGAAACCCCGCTCCAGATCCAGCCCCGCGCGCCCCGGGAGCACAGAGCTTACCACCAAACGAACCCTGAGCTCGTCACGACCTCACCGGAGGCGCTCCGGTAGGCCTTGGCGCTGGGGCTCGGGAGCAGTTTCCCGGAGTCGACTGACGAGGTGCGGTGCAGCGGCGGCGCAGTACAACTCCCTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.24246
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0271100.2 4 25144174 T A
Osa04LNT0271100.2 4 25145706 T C
Osa04LNT0271100.2 4 25145675 T C
Osa04LNT0271100.2 4 25145741 C T
Osa04LNT0271100.2 4 25146317 C G
Osa04LNT0271100.2 4 25148758 A G
Osa04LNT0271100.2 4 25148124 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
Osa04LNT0271100.2 osa-miR5543 Cleavage 4.5 16.512 1 21
Osa04LNT0271100.2 osa-miR5079b Cleavage 5.0 17.579 1 22
Osa04LNT0271100.2 osa-miR395c Cleavage 4.5 16.753 1 21
Osa04LNT0271100.2 osa-miR395f Cleavage 4.5 15.522 1 21
Osa04LNT0271100.2 osa-miR444a-5p Translation 4.5 20.116 1 21
Osa04LNT0271100.2 osa-miR395o Cleavage 4.5 16.753 1 21
Osa04LNT0271100.2 osa-miR1428a-3p Translation 4.5 15.329 1 21
Osa04LNT0271100.2 osa-miR1850.1 Cleavage 3.0 0.909 1 21
Osa04LNT0271100.2 osa-miR1850.1 Cleavage 4.5 1.806 1 21
Osa04LNT0271100.2 osa-miR1850.2 Translation 4.0 7.311 1 21
Osa04LNT0271100.2 osa-miR1850.2 Cleavage 5.0 10.62 1 21
Osa04LNT0271100.2 osa-miR1428b Cleavage 3.0 15.329 1 21
Osa04LNT0271100.2 osa-miR1428c Cleavage 3.0 15.329 1 21
Osa04LNT0271100.2 osa-miR1428d Cleavage 3.0 15.329 1 21
Osa04LNT0271100.2 osa-miR1428e-3p Cleavage 3.0 15.329 1 21
Osa04LNT0271100.2 osa-miR2873b Cleavage 5.0 21.195 1 21
Osa04LNT0271100.2 osa-miR5503 Cleavage 2.5 19.679 1 22
Osa04LNT0271100.2 osa-miR1850.1 Cleavage 1.5 3.801 1 21
Osa04LNT0271100.2 osa-miR5079a Cleavage 5.0 17.579 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0271100.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0271100.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0271100.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0271100.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0271100.2 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0271100.2 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0271100.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0271100.2 4 nan Morphological trait Culm/leaf RM3785 RM1388
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