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

>Osa02LNT0163900.2

AGGACAATAGGAAACCTTAGCATCAATAAAGAATTACAAATGAAGATGAAACTGGCTTGTCTGACAGAGATCAAAGACTGTACTTAACAGCGCCATCTTAAGCAAAGATGAATCGCTAATATTAACCTATTCTATACACTGCCAAATGTGGCACTATGCTATGGACTACCTATATATACATGGTGCACTAACCTCTTTTCTGTGGTCTACACTAGAGCCTTGTTCCAGGCATTCCTCAGTCATACAGGTGCATATATGGGCTAACTATACGCTATTATTGTAAGTTATAAATAGGTGAAAAGAAAACGATGAAGTAGTCATGGCTTCCGGAGAGCTGACGCAGCTCCCATTATTACAGCCATTACAACCCCGAGTCCGGCACCAAGTGATGCACCTACGGCAGCAGCTGTAACAGAGCCATCTCTCTTCTGGGGCTTCCGCTTCCCTTGCAGAGATGCTGCTTTCTCTCTCTCCAGCTCCAGCGACAATCTCTCACGAGAAAGCTCCTCAAATGCTGGCTCTTCATTGCTGTGAATTACTTGATGTACAAGTTGACGAAGGGCAGTGACACCCTCAACATGCATAACAATGTCCTTCCTCTGAAATGGTGAGAGTGAAAAGTTTACTGGATAAAAAGCAGCTCTGCCTGAAGGATTCTCGTTCCTCAGACTGCCACTAGCTGAACTGATGGGGCGCAAACTATTTGTGGCACTTGGCATTAGAAATGGGGAAGAGTTAACAACTTTAGTCATGTCAGGAGAGGCTTGATAAGCTTCCATTGCTGAAGTGATCAATGCGTTCTGTTCATGTGCACTGACGGAGAATTTATTAGTTATTGCAAGGATCCATGGAATGCCAAGAGCCTTGGCTTCATCCAAGAGAAGTGAAAGCGCTGGCTGTGGTTGAGAAGTGTTGGACTGGTGATACTGAGGAATTCGATGAGCAAGGTTATGCACAACAATAACTAAGTCAGTCTTCCTGCTGAGATCATGTATCCCTAACTGCAATTCTTCTTTGAACTGCCTAACTTCTAAAGGTAGTTCCTGCAAGTTCACTGTTGCCGAATCTACGTAGCACAAACCATTTGAAACTCCTTTTCCATGCAAATCTACATGTATGCACTCAAGAACTGCTTTGCTTCTTTCTTTAAATTGTCCTAACAATGCTTTTAGCAAGGAAGTTTTACCTGCTCCCTCTAGTCCAAGCAATCGCACCCTCCTGGTCCTCACATAGACCTCTTTACATATAGTTACAAAATCACTTGTACCGTATATAAGAAATTCATTCAAACCCTTGCAACAACCTTTATCTTCAAACAATGAGTCAAATCCATAATCTGGATTTGACCCTGTACCCGTGGCCACAGAAACCATAAAATCTTCACTGATATAATTTGGAGGCTGCTTTAGTGGCTGACCAACTAGAATGCGCATTTTTTGCAATGTAGGCTGCACTTCCTGATCTGATGAATATGACACCATTGGTAGAGTTTCAATGACTGTTGAATACCAGTTTCCATTTATCTGAGCCTGGAAAAGAGTGCACATATGCAGGTCATGTCCAATTATATCAACTTTCAGGGGTTCAGCACTTTTATCACCAGGGTAGCCATTCCATCCAAGAGGAAGAATAGAAGTGGCAGTTCGAATAGTAGGAGGCTCCACAATATGGCCAAGTTCAACAGAATCAGCAGCTGTTAGACCGAGTAGTTCTTGTAGATGTGAAAATTGTGGCAATTGTTCAATGCCTGTAAAAAGCTGGGCATTTGCAGACATGCAGATGTCATATATTTTCTGGAAGCGAGCCCTATAAGATTTCATTGAGTGTGATTGCAAACGCTCTCTTAATTCCGTTATAACTGACTGCACCGATGTCATCTTGGAGTACTCTGAATCTGAAAGTGTATTGACTGATGAATCTCCCAACAGGTATAGCTCACCAAATGGAACATATGAAGGCAAAGAAGGTACTCTGTTCCACCGTTTTGAACCCCCAACTTCAGAAACATTAGTTTTATCAGTCTTGTTATTTTCTTCAGTGAGCCCTCCATCTTTATCAGATAAAGGGGTAAGAGCAATTCCTTCTGAACCTTCTTGAATCTCAAGAGATTGCAGCCCCTCTTCTGATTCATCAACCTTTGATTGCAAGAAATTATCCAACTGTGATGGTGCCTTTCCAAAACTATTTGTTTGTTTCTGAAGCACACTTAAACTTTTTCGCACTCCTTCCAAAGGAACAAGCTTTGAAAGTCTCCAGAGTGACTTTTGAACAGGACCAACACCTAGAACAAGTTGCTCCCCATTGTTCTCTTTTGAACATACAGATTTTGTGTCCTTTTCTTCATCAGATTTTGCGTTAGTGTTATCAGGTGTTTGGGCATTATAGTGGTGAAAGTATGCCGGCGATAAAATACGTGGCACCAAGTCCTCTGGAATACAGTAGGATTTGAAATAATCTTGCCATCCTCTTCGATGAACGTAGTCTCTCAGTGCAGCATTCCCAACTGGTGGCTGAGAAAACGTGATACACTTCACCTGAAGCCTGTCAGGCTCTTTAGATGGAGATGAGGATGCAAGTACTCTTAATATTGCAAGGGTAGCCAAAGCAGCTACCGCTCCACCAAGCGAATGTCCGCACAGAACAAGTTTCCTGTTCTTTTTCTGAGCAAGTTTGTATAGCTCCAGAGCAGGAATTCCATTGGCACGTGCTAAGAAACCCCGGTGTGCAGCAGGTTTTGATTTTCTCAACTGTTTTGATTTCTCTCGATAAGATGTCCCGAGGTTTTCTTCACCCTTCTGGTCATCATTTTGCACACACTCAACAGCATCAGCCAAATCCTGTGCGGTATCCTCATGAAATACGGTTCCTTGGAGTATATTCACATCAGCAATAATATTTGTATTGTTTTGTACCGATAAATGTAGCAAATAATGTATCACCAGCCTCTGCTAACACATACCTATGTCCTACATGATCCAAGGATGGCTGAACACGCTCAAGAGACACAATGTGTCCACCAAAATCAGATTTGAACTTATTAATATATCTCATCATCTCAGAAACAGGCCTCTGGCACAAAAAAAAAAAGGAGACTAAGTAAAAATAAAATAAACAGGCCTCTTGCAGAGAGAATAAGTAAAAATATTCTAGATAGTAATTTTCTGATTTATAGGGGAAGAGGTGAAGGTAGTCAAAACACATTAAAAAGCATGGAAGAGTAGGTTAACTGAATCTAAACGGTTACATGAAAATTGGAACAACGAAAATGCACTTATTATGAAAAATCACAGTAGTTTCTCTTAGGTTGGTCATTCCTTTTCATGGTTCCAACGTAATGTCATATGAATAGAATAACACAAATAGAGATA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.91939
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0163900.2 2 16605458 C G
Osa02LNT0163900.2 2 16604121 A G
Osa02LNT0163900.2 2 16608722 T C
Osa02LNT0163900.2 2 16608923 T C
Osa02LNT0163900.2 2 16606446 C T
Osa02LNT0163900.2 2 16606914 G C
Osa02LNT0163900.2 2 16607998 T C
Osa02LNT0163900.2 2 16609109 T A
Osa02LNT0163900.2 2 16609313 C T
Osa02LNT0163900.2 2 16609317 A C
Osa02LNT0163900.2 2 16609453 T C
Osa02LNT0163900.2 2 16609846 G A
Osa02LNT0163900.2 2 16610540 G C
Osa02LNT0163900.2 2 16610792 A G
Osa02LNT0163900.2 2 16605279 T A
Osa02LNT0163900.2 2 16604361 T C
Osa02LNT0163900.2 2 16604947 G T
Osa02LNT0163900.2 2 16603436 T C
Osa02LNT0163900.2 2 16603931 A T
Osa02LNT0163900.2 2 16603958 A G
Osa02LNT0163900.2 2 16603815 G A
Osa02LNT0163900.2 2 16603963 A G
Osa02LNT0163900.2 2 16604048 G A
Osa02LNT0163900.2 2 16604743 T C
Osa02LNT0163900.2 2 16604827 A G
Osa02LNT0163900.2 2 16605948 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa02LNT0163900.2 DTM_#DNAt_MULE_japo_Os0089 Chr2 - 16603426 16604140 714
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0163900.2 osa-miR5544 Cleavage 4.5 16.158 1 22
Osa02LNT0163900.2 osa-miR5825 Cleavage 4.0 14.161 1 24
Osa02LNT0163900.2 osa-miR6248 Cleavage 4.0 14.228 1 21
Osa02LNT0163900.2 osa-miR159a.1 Translation 4.5 13.756 1 21
Osa02LNT0163900.2 osa-miR159b Translation 4.5 13.756 1 21
Osa02LNT0163900.2 osa-miR159f Translation 4.0 13.756 1 21
Osa02LNT0163900.2 osa-miR415 Cleavage 5.0 12.177 1 21
Osa02LNT0163900.2 osa-miR1430 Cleavage 4.0 13.123 1 21
Osa02LNT0163900.2 osa-miR2863b Cleavage 4.5 15.381 1 21
Osa02LNT0163900.2 osa-miR2871a-5p Cleavage 5.0 16.296 1 24
Osa02LNT0163900.2 osa-miR2871a-3p Translation 5.0 21.53 1 21
Osa02LNT0163900.2 osa-miR2871b Translation 5.0 21.53 1 21
Osa02LNT0163900.2 osa-miR2931 Cleavage 5.0 11.637 1 20
Osa02LNT0163900.2 osa-miR2931 Cleavage 5.0 19.001 1 20
Osa02LNT0163900.2 osa-miR2931 Translation 5.0 15.885 1 20
Osa02LNT0163900.2 osa-miR1862f Translation 4.0 12.675 1 20
Osa02LNT0163900.2 osa-miR1862g Translation 4.0 12.675 1 20
Osa02LNT0163900.2 osa-miR5152-5p Translation 5.0 13.857 1 21
Osa02LNT0163900.2 osa-miR5832 Cleavage 3.0 19.705 1 21
Osa02LNT0163900.2 osa-miR6248 Translation 5.0 14.136 1 21
Osa02LNT0163900.2 osa-miR6251 Translation 4.5 14.715 1 21
Osa02LNT0163900.2 osa-miR396c-3p Cleavage 4.0 16.248 1 21
Osa02LNT0163900.2 osa-miR1429-3p Cleavage 3.5 9.599 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0163900.2 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0163900.2 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0163900.2 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0163900.2 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
Osa02LNT0163900.2 2 d50 Morphological trait Dwarf nan nan
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