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

>Osa04LNT0273000.1

GATTTGTAAATGCAGAAAGAGATGGCACGGTGGAATTGCAACTGAAGGGTCTTGCTCTGTATTGACTGAGTGGCATGATCCTTTCATATCGGTAGGAATTTTTAGTTCACTTTCCTGCCATGCCAAAGAGATAAGGCACTATACTCATCTATCCAAACATGCCTAGGGTGCACTAGAAATGTGCCTTGAGTAGTGGTGGAAATGTCAAAAAGCACTCGTCGCCTATAGTTATTCCTTTCTCAATATGCTGAAATGGCTCTAGTTGAAGTCAGGCTTCTCAGGGTAAGTGCAGCCTGAGCGTTGGATGATAACGTTTGCAGCATAACAAGCAGCTCTGACACATTCATCAATGCTCTTCTCCTGAACCAATTGAGAGAGAAAACCCCCAACAAAGGCATCGCCTGCACCATTGGTGTCAACAAGCTTTTCCTTGGGCAAAACGATAACAGGGAATGTTTTGACCTTTCCATCATCAGCCACAACTACTGGGTCACAGCCTTGAGTAATGACAGTAATCCTCTTGTGTGCTCCTGAAGCCTTAGGCAATTGCGAGATCTTCAAAGCAATCTCCTCAGTATTCTCAGTCTCCCAACCACGAACTTTAGCAAAGGTCCTTGCTTCAGTTTCATTTCCAAAAATATAGTCAGCATACGGAAGAGCCTTCTCTTGGGCATCACGGAAGAATTCACATATAAAGGGAGCAGAAAGGTTCATCATAAACACCTTGTTAGTTGCAGCAGCATGCTCAGCAACAAGTTGAATGGAATCCGGGGATACCGTGAGGAAAAAGCCAGCAATGTAAATATATTTTGCCTTCTCAACAAGTGTCCAGTTCTCTGGCCTCTTCAGATGTTCAGACCTGTAGCAGTTCGCTGCAGACAAGTTTGCAACAAGTGACCTTTCACCACCAACAATGCAGACAGCACATGTGCCAGTAGGAGCATTATCATCCTCATAATAATGGGCCTGTTTAAAGATGGTAAGGTCAAGGCAGTATGTGCAGTGGTGCAACTGAGTGAAGAGGCATAAAAATGGAAGAAATTTAAAACATAAAGAGGAACTTATAACTTGCATTAACACCAGCGGTTTGTGCGTCTTTCTTCATCTCCTCACCGAACTTGTCCTTCCCAATGCAACCCATGTAACTTGTTGCACCAGGAATCTGGAGCATCCACTGAGCAACCCTAATAGAATTTTGAGTGGATCCTCCAGCGATATATTCAACATTGACCTTGCTAGCCAATTCATTGTACATAGGCAAATGCTTCTCCTCTGCTAGAATTGCATTCCCTGGCTTGATATCATATTTTGCGAGGAAGGCCTCGTCGACGACGGCGGAGATGTCGAGGAGGGGGTTTCCCATGCCCAGGAGGACGCCCTCGTAGCTTCCGCTCTCCATCCTTCCCTAGATCCCCGGCGAACGGTGCGGCGGCGGCGGGGGCGGCGGAGAGAGATTACCGGCGTTGCTTTGCTTCTGCGTGGAACAGTTGGGGAAGGA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.983648
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0273000.1 4 25902003 G T
Osa04LNT0273000.1 4 25898378 A C
Osa04LNT0273000.1 4 25899749 A G
Osa04LNT0273000.1 4 25899280 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa04LNT0273000.1 DTM_#DNAt_MULE_japo_Os0098 Chr4 - 25899172 25899777 605
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0273000.1 osa-miR166l-5p Translation 5.0 15.903 1 21
Osa04LNT0273000.1 osa-miR815a Cleavage 4.0 8.869 1 21
Osa04LNT0273000.1 osa-miR815b Cleavage 4.0 8.869 1 21
Osa04LNT0273000.1 osa-miR815c Cleavage 4.0 8.869 1 21
Osa04LNT0273000.1 osa-miR1870-3p Translation 3.5 15.716 1 24
Osa04LNT0273000.1 osa-miR2101-5p Translation 5.0 12.847 1 22
Osa04LNT0273000.1 osa-miR5517 Translation 4.5 21.254 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0273000.1 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0273000.1 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0273000.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0273000.1 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0273000.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0273000.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0273000.1 4 gpp4 Morphological trait Seed RZ569 RZ565
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