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

>Osa01LNT0012000.1

GGCTATAAATTATAATCTAATTTGAGTTTAATTCCAAAAGAATATTACGAGCCCTTAGCCCGGTCAAAATATCGGGCGTGGAAAGCCGCCATTCTATATCAGCTTCATGCTAGAGCACCTCTGCTGTTGATTCAGTAATTCACTTCTAAATTTCTAGGACAAAATTTCTATGTTTCCTTTCCTAAATAATATGTGGAGCTCCAGAGTCCAGATTCCGGCCATTGGATCAAGCCATCCGAGCACCGTATCGCGTCATTAGCCCTGCACAATTTCAGAACTTCCAGCAGGAAGAACACGGGAAGACTATCGAAGTGTGTACTCAGAAAGCTTATTTGCAACTGTCAACTTGGGAGAATTGCCCTTCAAAGCTATTCGTCAGCTTCTCGGCAGCTGCTTCTACCCTCTGATTGTCCTTCCCAATAAAACTCACAACCAAAGGCCCAGATCTTGAGATCCGATAACAACCTATGTATACATCAGAAAAATCTATGCATAGTTTTGCAACCACTGGGGCAATTTTAACATCTAATAGCGACGTGCAGAGATGCTTTGACACAAAAGATTTAGCCATCACTAAACCGCTCTCTTGTGTGTCTAGAAGACAACCCCACTCCGTTTCAAGCTCATCCACATTAGTTGCAGCGAGAATGACCACATTTTTGCATTTGATCAATGGCAACGGTAGCATTTTGTGATGCAATAATTCCGTAATACCTTCTGGCAACAAAGCCATCTCATTTCGATCACCAGTGTAATTGTCTCCTATCAGTTGACTAAGGTATTCTTCAAACTCTTCATCAGGAGCCAGACGAACTCCAAATGCTTTTGCAACGCCAGCCAGCGAAATGTCTGAATGTAAAGGCCCAAGTCCTCCAACAAGAAACACCATGTCATCTGTAGATTTGCAACGTTCAACTTCTTCAGCAACAGAATCAATTTCATTGGAAACAACTGCTACATGAGAAACTCGCCAGCCAATTGCATGAAGCTTCTTGCACAAGCCTGCACCTAGCTTATCCTCAACTGTGCCGAACAATATTTCATCACCAACTACAATGATCGACGCTGAGCGTGAGATCGTCTGTTCCACCTCAGTACTGTTTGTACCATTGCTTGAAACAGAACTAATATTCTTCTTTGTTCTGCCAGCTCTTTCAAGCCTTCCGTCTGATAACATGTATGCTGGCCTAAAACTTTTCCCAGTTGTTGAATCACAAAGAAGCGCATTGGGAACAGTATCATATATGCTTCCAATGGAAGTATACCCTTGATCATAGAGGCTGCAGTATTTCACCTTACAGGTCAACAGGAAAGACCAAACATCCCTGTATGACCAGTCCAATATAGGATTGACCCTCATGAAAGGAGGCCAGCCAGGTGAACTAGGCGAGAACTGCTCTTGACCAACTGCATTTGGATCGCCAATTCTAGTACCAATAAAAATTGCTTTAGTAGGCCTCTCTTTCAATAGGCCTTCTAGGCCAGACTTAAAATCCGAGCGGATAGTTTCCAGTGGCAAACCATAAGTTGAGACAGTTTCATAAGTGAATGAGTTGATTTCAGGGAAAGCACAAGGGCTCTCAAAATAGATGGTGCGCACAGGACAGTTTTGGATAGTATTCATTTCGACTTCACCATCAGAGCTTGATTTGTGGAGGTAGTAGCCAGCCCGAAGTAAATGCAACAGAACTGTTGAATCCTTCCCACCATTAAAGCTGAAGGCAACTTCCTCAAACGGGTAGAGCGCGAAGGCTCGCTGCACGACGTAGACGGCGTTGTCGTACTTGGTCCGCAGGCGGCGGTCGCTGCTCCCCCGCACCGCCCGGTCGATCTCCATCCCCACACCTTACTCCTCCCTCCTCCTCCTCCTCCTCCTCCGGAGAGATGCCGAGCCGGCGCGGAGAAACGACCAGGGGGGGCCTCTCCACCGCAGAGGAACACGGCCGCCGCCGCGGCGGAGGGGAGGGTGGAGAGCTCCGCCGCCTTCTACCGCCGCCGCCGCGGCGCTGCGTAGGAGGAGCGGGGAGGGGAGGGGAGGCTTGGCCTGGCCTCCACAAAGGGAAGGGAAGGGGAGGAGGGGAGTGGATAGACGGGGGCACGTTTGCGGATGCTGTTTCTGCGTCGGG

Coding Potentia
Explanation CPC Score
noncoding -1.21061
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0012000.1 1 8702156 G T
Osa01LNT0012000.1 1 8705913 A T
Osa01LNT0012000.1 1 8706040 G A
Osa01LNT0012000.1 1 8708531 T C
Osa01LNT0012000.1 1 8705335 T 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
Osa01LNT0012000.1 osa-miR166a-5p Translation 5.0 11.1 1 21
Osa01LNT0012000.1 osa-miR166b-5p Translation 4.0 11.1 1 21
Osa01LNT0012000.1 osa-miR166e-5p Translation 5.0 11.1 1 21
Osa01LNT0012000.1 osa-miR395t Cleavage 5.0 18.492 1 21
Osa01LNT0012000.1 osa-miR395u Cleavage 4.5 18.492 1 21
Osa01LNT0012000.1 osa-miR395o Cleavage 4.5 18.492 1 21
Osa01LNT0012000.1 osa-miR395w Cleavage 4.5 18.492 1 22
Osa01LNT0012000.1 osa-miR2100-5p Cleavage 4.5 16.313 1 22
Osa01LNT0012000.1 osa-miR2101-3p Cleavage 5.0 8.192 1 22
Osa01LNT0012000.1 osa-miR2871a-3p Cleavage 4.0 21.528 1 21
Osa01LNT0012000.1 osa-miR2871b Cleavage 4.0 21.528 1 21
Osa01LNT0012000.1 osa-miR5506 Translation 4.5 16.084 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0012000.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0012000.1 1 An9 Morphological trait Panicle/flower nan nan
Osa01LNT0012000.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0012000.1 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0012000.1 1 nan Resistance or Tolerance Insect resistance RM576 RM3412
Osa01LNT0012000.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0012000.1 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0012000.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
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