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

>Osa05LNT0309000.1

GGCATATCTAAGAAAATAGACCATTTCAATAGTGAACTTAGGTTATTTTGGCTTCAATCCAAACACAACTTTGCCTTACCAAAATTAGTCATGCCAAAACTTATCAAAATTTGGCACTGACAAAATTTGGTAAGGCCTATTTAGATTGAAACTATGCCAGTGGAGCAAAAAATTGAAGTGAAGGAAAAAAAAACAAGATCCTATTCGTGTTTTTTCTCCCGATTTGCAATTGCCTGTTTCTGACGCTTCTCCCATGCTGGCATCTTGCCTGGGAACGCCCATCGCAAAATCCGCTCCCATCCATAGCAGCCACAAAACATAAGGATAGCCCAAAGCATCAGTTTGCCCCTCATTCCTTCAGGCAGGGGTTCAAGCTTCATGTAGTCATTTAGATCCCTGAACATATCTGATGTGATCACTGTGAAGAAAGCAACTGCTGCATATAGAGCATACTTGAAGGGCTTGTTCTCTGTTATACTCTGGTTAAATGGGTGCCCCATGTAGTTTACTGCAAAGGTTGCAACCTGGATCATCATGTTCACCATGTATGAAACTGTGTTCACAAGGTTTGGGTGGAACTCTGAATCAGGCTCAATGCACTCCTCTGGCATATACTTGGTTGCTTCATTGACGGCTGAGATCAGGAAGAACAAGTGCATGGCAAACTGACCAAGAATGGAAAGGAAGACGTATGCACAGAATATGTTTGGATGAGGCCGCTCTGCAGACAGTGTTTGAAGGGGACGAGCATGGGAAATGAAGAGGAAGAAAGCTGCAGTGAAGACCCCGCTGATAGTAGCCTGAACATCACCCAGCTTGACACCATCCAAGTACATGACACTCAGAACGTATGCAGTGGCAAGGCAGTTGAGCCCAAGAATCTTGAACATTTGAAGGGTAGTGACTAGGGTGCTTCTCCCCTGGCGGATGATGTCAAGTGTAGGGGCAACAGAGGCATGCTTTGCTGTGAAAGGTGAAGCCATGGAAGCATCCCCAAGCTTCACAATAGGAGCTGAACGGCCATCACTTTCCTCATTCATTTCATCCATCATCTTCTGCAGTCTTTCTCTCTGCCTCTCAGCTGCAGTTAAAGGGCGGCTACTGGATGCTCTAGCGGAGCTGTTAGCTGGTTGGGTCAATTGTGATGATGATCCTTCCTGAGAAGGTTTCGGTTTTTTCAACTTCCCTTGTTTATTTTCAGATTTTGATGCCTGGGATTTTGTATCTGATTTCTGGACAGGTTCAGCATTCAAAAGAGCTATGCCAACATGAGCCTGTTTTAGTGCACCAACATCATTGGTTCCATCCCCACACATCAGTGTAACCCTCCCAACAGTTTTGAATGTAGTCAGAACAAGTTCTTTCTGTTCTGGAGCAACACGTGCAAAAACCTTCACATATGGAATGACTTGGATAACAGCATCAGTTCTTTGTAGCATTTCAAAGCAGTCTCCACTGATGCAGAGATCATGCGATCCAGACACCGCGGCAACCTCCTCAGCGCTGTATGGAGCTCTGTCGGTTTCATCAGGGGAAACCCACTCAAAACCACCAGTCTTTGTACGTGTCAAAATTAAAACAGGTTTGGAACAAATATGCACTTGGCCAGCAACATGGCAAGCAGTCAAAGCTTGGTCCCCAGTGATCATAACCAAGTCATGGGAAGATTGCTCCAGTTCTTGTAAGACAGCACCGGAGTCACTCCTTATAGGACAGTTGAAAACCGCAAAACCTGCAAAAGTTAGGTCACTCTCTACTTGATCCCTTTCCAAACTTCTAGCTTCATTTACAGGCATATCCGGAAGCAATTTGTATGCAAGGGCCAGGACTCGGGACCCCTGTCGAGTGTATTTTTTGTATGTCTCCACATATCCAGCGGGTAAATCAACTAACCTCTCCTGAATGGTCTCTGGTGCACCCTTTATGAAAGCATAATATTTCTCATGTATACTGACAACAACAGACATTCTCTTCAAGTGTGAAGCAAAATGGTATCTGTGTACAATCTTTACAGGTTGACCACCAGACTTTTTAGATATGGCCTTCTCATCAGATGTGTAGATCCAGTCTATGCCCTTTATAGCAGCTTTTTCAAGGGGGTCACCAACCAGTTTGTTATCTACGAATACTAATGCATGGCAACTGGACAATACTTCTTGTGTGCGGAGTGGCAATTTATTTGCATCTGTTATTAATTCTTCATCATCTTCCAAACTAACAACACCTTGGAATTCCATGTCATCCGATGTCAATGTCCCAGTTTTATCAAAACAGCATATGTCAACCTTCCCAGCAAATGGTATCCTGAATGGCTCTGTGCAGAAAATACCACGGCGGGCTAATGCAATTAAAGATGTATTGACTGCTATGGAGAGCTCCATTGGCAATTCAGGGGGTATCACAGAAGTAAGAATCAATGAACAACTTAAGAAAAGCTTATATCTACTCCTTGTTGGGTCCTCCAGTCCCTTGACAAGCACATAACCGGATGCAATTACTGCGAAGAATAGCAAAAATAGGATAAACAGGCCACTCTCCTTGCTGTTTGCAGTAACCCTCTCAGTTGAAAATAAGATAGTTCTCATCAACTTTCCCTGGCTAGTCTCAAATCCAGTCCTCAATACAAAAGCTATGCAACCACCATCAGGTGCTCGGAGATTTATAGACTTATCTGGAGTATGTTGCAATATCTTAGTGCCACCAAATAGGATATGATTCTTATCTCGCTTTACAGATAGTGTTTCCTCAGGACCACGACCAGCAACTTCCACTGTGGAGTAGATTCTCCTGTGAGAATAGCTTCATTTACTATTGCAGATCCAGCCAGCAATAACATATCTGCTGGCACAGACCTGTCTTCTCCACTTACTGAGCGGCCTATTGACACAATGTCTCCAGGTAGTAGTTCTGTCCCAGGTATTCTAACCCATTTTCCACAGCGATAAGTTGCAACAATCTGATTATCAACTTTCACACGCCTTAGCTCAGTCAATGTCTTCAGTCTATTCTTTGCCATAGTAGAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.930017
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0309000.1 5 19615897 A T
Osa05LNT0309000.1 5 19616247 A G
Osa05LNT0309000.1 5 19616158 G A
Osa05LNT0309000.1 5 19609700 G A
Osa05LNT0309000.1 5 19609794 A G
Osa05LNT0309000.1 5 19610772 T A
Osa05LNT0309000.1 5 19610973 T C
Osa05LNT0309000.1 5 19612827 G A
Osa05LNT0309000.1 5 19613456 C G
Osa05LNT0309000.1 5 19613898 A T
Osa05LNT0309000.1 5 19613936 T C
Osa05LNT0309000.1 5 19618973 C T
Osa05LNT0309000.1 5 19621444 A G
Osa05LNT0309000.1 5 19617185 G A
Osa05LNT0309000.1 5 19617256 G A
Osa05LNT0309000.1 5 19617446 A G
Osa05LNT0309000.1 5 19617486 A G
Osa05LNT0309000.1 5 19618019 G C
Osa05LNT0309000.1 5 19618031 A G
Osa05LNT0309000.1 5 19618052 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa05LNT0309000.1 DTM_#DNAt_MULE_japo_Os0208 Chr5 - 19616701 19618338 1637
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa05LNT0309000.1 osa-miR2873c Translation 5.0 11.151 1 21
Osa05LNT0309000.1 osa-miR5337b Translation 4.5 16.842 1 21
Osa05LNT0309000.1 osa-miR171f-5p Translation 5.0 23.839 1 21
Osa05LNT0309000.1 osa-miR528-3p Cleavage 4.5 13.487 1 21
Osa05LNT0309000.1 osa-miR528-3p Translation 4.5 22.246 1 21
Osa05LNT0309000.1 osa-miR1432-5p Cleavage 5.0 11.842 1 21
Osa05LNT0309000.1 osa-miR1428b Cleavage 4.5 13.985 1 21
Osa05LNT0309000.1 osa-miR1428c Cleavage 4.5 13.985 1 21
Osa05LNT0309000.1 osa-miR1428d Cleavage 4.5 13.985 1 21
Osa05LNT0309000.1 osa-miR2872 Translation 5.0 12.596 1 21
Osa05LNT0309000.1 osa-miR3982-3p Cleavage 5.0 18.035 1 21
Osa05LNT0309000.1 osa-miR5494 Cleavage 4.0 12.189 1 21
Osa05LNT0309000.1 osa-miR5497 Cleavage 4.0 11.021 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0309000.1 5 nan Morphological trait Seed RG13 RG573
Osa05LNT0309000.1 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0309000.1 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0309000.1 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0309000.1 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0309000.1 5 nan Physiological trait Eating quality RM163 RM31
Osa05LNT0309000.1 5 dcs5 Physiological trait Source activity RM440 RM430
Osa05LNT0309000.1 5 dcfs5 Physiological trait Source activity RM440 RM430
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