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

>Osa07LNT0381400.1

AAAGATGAGTGTAGGTAAAAGTGACCTTTTGTTAATGTCGCTGAATGGACTAGTTCTTTTTTCTCATTGGCTTCGGTTAAACAGTAGTATTAGCTTTGTTAGTGTTTTGATGATTCTGTTGGTGGTAAGCAGCCTGTTTGAAAACCTCTTGCCACTCTATCCAATGGGAGTTAAAGTGCCCTTACCACCGAAGTACAAAATGGTATGCAGAACAGCTGAAGGCCCTTAAACCATGTATTGCATAGCGACCTGCATCATCCGGGAGGGCGGTATGCTCAGCGCCGCGATTCCTCTCCTGCAGTTCCTCCTCAAGAAGGCGTAGAAATAGTTGATCACCAGCTTCTTGACAAAGAAGGACTCCTTCCGAGCTCTGATGTCGCCGTGGCCCAGGAGGTACACCACGCCGGACTCCTTGGCCTTGTGGATGAACGAGAGCTCGTCGTCGAGGCTTCCCCTCCCATCGATCGCCTCATCCAGCGATCCGTCGAACGACATGCTCGATCCAATGGTTGGGTGCTCGGTAGTACCAGCCGCCTCGGCAGGTGGAACACCGAGAGAATTGATACTGCCATTGGGACCGACGAGAGCTCTTGACGAGGCTGATGCAACCTCCTCTTCTGAGTCTGTACCGTCGTATTGGTCACTCTCTAGGGAGCGCTCTTGGGCTTCCCGCCGCATGAACTTCTCGAGACTCTCTATCAGAAGCTGCTGAAATGATATGTAGTCCTCCTTGCGTATGTCCTTGTACCCATACCTAGCAATGCAGCGAAACATATGATAGCTCTTTGGACAGACCCGACGAAAGAGAAATCTTTCATTCTGAGGTACAACAGGAACTGGAACCCACTTGATGCAGACAAAAATAATCATTGAATGAATGGCTGGCATTGTGGCGAGGAATTGACCAAAGATTCCAGGAACTCCCCTCGCAAGTTCGTTATAAAGTAATCCAATTCCAGGGACTCTGACTGTACCCAGATTACAACCTAGCTCCATCAACAAATCCATTGAAAGTTTTTGCTTAACCTCAGTTTCGTACTTCAACTTGGTTCCGTAGTTCCATATGTACATTATCAAATACAGTACAGCAGCAAATACCAAAAGAACCCAACTCCCATCTGCTACACTGCCCAATACTGAAGAAAAGAAAATTAACTCCAGCCCCAGGGAGAGGGTGAGAAAACACAGAACTACAATGATGTTGATCTGCCATATCAAAAGCATTATGATGGTCACCAAGACTGTAGTCATCATCATGACCCCAAGTTCAGCTATGCCATATGCATTTCCAATCTCATTGATGCTCCCAAACATTGTAACAAATGCAAGGCAAGAAACCAGCAAAAACCAGTTCATCATTGGGATATATATTTGACCCATGAAGCTTCTAGAAGTGTGAATAATCTTGAGGCGGGGAAAACAGCCGAGAGCTGTGGCCTGCTTTATTGTTGAGAATATAGCAGTTGTCATTGTGCGACTAGCAATTATGGCTGCTAGAATTGCTATGAATACCACTGGCCAAAATGCCTGATTCGGGATAGATAAAAAGAAGACCTGCTGATTTTCTGTTAGATTTTCCATAAGAAATGCAGCTTGCCCTAGGTAACCCAGTAGCAGGCATGGAAGAACAAGAAACACAAAGGTAAGCTGAACAGATTTGACAGAGAAATAGCATAAATCAGCAAACATTGCCTCAGATCCAGTAGCACATAGAAGACAGCCTCCAAGGGACATCCAAGCTTGGGTTGGGTTCCTTTCAAAATAATAGTATATATACATAGGATTAAATGCCTGTAATACAGCTGAACCATATGTCTTCATGTTATAAATTCCTATTCCAGCAAGGCAGCAAAACCATATGAACAAGGCAGGTCCAACAGCAAGCGCCACTTTGCTTGACCCAAATCGTTGTAGAGTGAACAGGACAATAAGAACTGCCACAGTTATCATGACAACTTCACCTTCATTAACACTAGATATTCCAACCTTTAAGCCATTGACAGCAGACATCACTGACATTGCTGGTGTGACAACACCATCCGCTATCACCATAGAAGTACCAAAAAGAACAAGCATCAAAAGCAGCTTCTTTAGCATAGATGAAGTCTCAAGACGCTCCTTGATCTTCAAAGACCTCTCCAGTTCTACTGAAGGCACCTGGAGTTGGAAGCTTGATATACGAGTATCAGAGCGTAGTTGGTTAGGAAGCAGACTAACCCTTGCATTCCTGCATATTAGCGAGTATAAAGCAAATGTCCCTCCTTCTCCATCATCGTTTCCCCATAAAGCAATGAGAGTATACTTCAGCAATGGTATTAGAATCAGAGTGTATATTACAAGTGAGAGTGCCCCAAGTACATCCTCCTTCGAAGTAATAGGGTACTTGTTGAACATTACATCGAAAGCATACAATGGACTGGTACCAACGTCACCGAAGACGACACCTAGTGTCTGAACAGCCAGCACAATACTCCTGCCTACGGTAATTTCCTGGTGGCGGTTCATGCCTGCGACGTCCTGCGCCTCGACGTCCAGCGAGTCGGCGCGCGGGCCGGTGCGCACGAGCCGCTGGCGGAGCATCTCCGCCTCCTCGTAGTTGTCGTCGGAGTCCGAGCAGCCGCCGCGGGAGCCCGAGGCGGCCGCCGGGGTGCCGCCCCCGCCGTCGGAGCTCTCGATCTCGTCCTCCTCGTAGGCGCCGCCAGACACCACCCACCGCATCTCCGCCGACTCCGTCTTCCGCAGCCTCATCCTGCCGCCGCCGCCGCCGCCGCTGGCGCTGCCGCTGCCGCCGCTTCGGGTCTCCATTTGGGTCGGCGCGGGAGGCGCCGGTGGCCGGCGCGTGGGTGTGGGGCACTGGCTCCGTGAAGCGGAGGAGAACGGCAGAAGGGGAGGATCGGAGCGGGGGAGAAGAAGACGCTGGAGAGTGATGAAACGGAAACTGCAGTAGCAGGAGATAGCTGCCGTCTTCGTCTTTTC

Coding Potentia
Explanation CPC Score
noncoding -1.02242
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0381400.1 7 19380361 T C
Osa07LNT0381400.1 7 19380377 T C
Osa07LNT0381400.1 7 19380729 T C
Osa07LNT0381400.1 7 19382168 A T
Osa07LNT0381400.1 7 19382893 A G
Osa07LNT0381400.1 7 19384109 A G
Osa07LNT0381400.1 7 19385145 A T
Osa07LNT0381400.1 7 19385250 C G
Osa07LNT0381400.1 7 19381881 A G
Osa07LNT0381400.1 7 19382723 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa07LNT0381400.1 DTM_#DNAt_MULE_japo_Os0229 Chr7 - 19382292 19382763 471
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa07LNT0381400.1 osa-miR5534b Translation 3.5 22.568 1 21
Osa07LNT0381400.1 osa-miR5793 Cleavage 4.0 19.54 1 21
Osa07LNT0381400.1 osa-miR159c Cleavage 5.0 13.744 1 21
Osa07LNT0381400.1 osa-miR1424 Cleavage 4.5 12.428 1 21
Osa07LNT0381400.1 osa-miR1856 Cleavage 5.0 15.149 1 21
Osa07LNT0381400.1 osa-miR1846e Cleavage 4.0 17.414 1 20
Osa07LNT0381400.1 osa-miR2090 Cleavage 4.5 14.639 1 22
Osa07LNT0381400.1 osa-miR2096-3p Cleavage 5.0 13.058 1 21
Osa07LNT0381400.1 osa-miR2100-3p Cleavage 5.0 19.085 1 22
Osa07LNT0381400.1 osa-miR3981-5p Cleavage 5.0 16.2 1 21
Osa07LNT0381400.1 osa-miR5155 Cleavage 5.0 14.753 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0381400.1 7 qHd-7 Physiological trait Flowering RM125 RM432
Osa07LNT0381400.1 7 QRl7 Morphological trait Culm/leaf CDO497 CDO385
Osa07LNT0381400.1 7 Ph7a Morphological trait Dwarf RG650 C285
Osa07LNT0381400.1 7 Ra7a Others Others RG650 C285
Osa07LNT0381400.1 7 qLTG-7 Resistance or Tolerance Cold tolerance R1440 R1357
Osa07LNT0381400.1 7 qLTG-7 Physiological trait Germination/dormancy R1440 R1357
Osa07LNT0381400.1 7 dth7.1 Physiological trait Flowering RM125 RM336
Osa07LNT0381400.1 7 qSDS-7-2 Physiological trait Germination/dormancy RM320 RM234
Osa07LNT0381400.1 7 sp2(t) Morphological trait Panicle/flower nan nan
Osa07LNT0381400.1 7 nan Resistance or Tolerance Insect resistance RG773 CDO59
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