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

>Osa02LNT0176300.1

AGAGAAAATGGAAGGAGTAGAGCAATAAGTTATAGCTCGATATTGTTACACAAATGTGCATACATACACCAAATAAATGACGATTCAAGCCTAATCTCTGGTGGAATCTCCAGGCAACCGCTCATAGAGCCGATATATCAGCCGCGATTTTGTCATCTGAGGTTCCCTCTCGAGGACACATATTACATCCTTCATAGAAATAGTTCTTTGTGGTCCTTTTGGATGAGACGCTGCAAATGGACCCCTGCCTTGCCTGTTCATGCCTCCAGTTCCAAACGCTGCAGAATGGGTCCTCTTCGAAGCTTCGTGGTGATCTGTGGGACCTTTCCCAGCCATATGCGACCTGGAAGCTGTCCCGCGCTGTGAAGAAGCAGCCAGATCAAGGCCTTCGCGTTTCTGTCTAGCTTGTTCAGCCATCAGTTGCCATTTGGACAGCATATCACTTCCTCCAACAGCCTGTCGGGCGGCAACATTTGCAGCTGTTGTTCTCATCTTGTCATCTTCTTCTTTGTTGGGCTTTGCATTCTTTGAACGAGTTTCCTCCTTTTCCTTGTCTAATTCCACAGTGCCACCGCCGTCAACCTCATTTTGTTTCTTGTTCTTGTCTGTTTCCTCTGCTTGTTTTTTATCCCATTCTTCCTTAGCTTTCTGGTTCATCCGCAAAATTTGCCGGCCAACATCTGATGTTATAACTAGTTGATGGCCAGACTTTTCTGTGTCAATTCTCTGCTTTGAAACTCTTATGAGAGTACTGATAAATCTTCGCAATCGCTCCTCCACGCACATTGATAAACAATGCTCAACATCACCACCAATGCTCTTCAAATTGCATTTAGGAACGATTGCTGCTAGTTTCTTCAGAAGTGGGCCTTTCTGCAGAAAAAGCTTGCCATCTTCTTCCTGTGCAATTTTCCTTGCTTCTTCTGAGGCCCAGCTCTCTTCCTTTGGGGCAGAGAGTAGCTGTTCTTCTTCTTCCCTAAGATTAACACCACTAACAGCCGTGACATCATTTAGTTGATCGAAGCTTTGTTCTTGGAAGGTTCCAGAAGTCTTCTGCTTTTTGCTAGGAGGGGGTGGTGTAGAGCCTGATGTTTCCAATGACTTCTTCTGCCCAGCAGTTTTCTTGTTACTCTTTGCAGCGGGAGGTGTGGAAAAGTTAGGGGGGCCCTGACAGTCCAGTCAGATAATTATACGTACAGCTACATGTGAGAAGGCATATAATAGTTTCATGGTTGCTGTGAACCTATTGAAGTATGCATGCATAGCCATACAACTGGAAATCAACCAAATACACTTTCAGCCATTTTCTGACTAAATCACATGTTACTCCTCAGAAATAAGGCCTTCACAAAATTATTTTCATAGGATAATAAGGCCTTCACAAAAAAAAAAGCACTCAAGCCATCACCTGGTTGACCAGGATGCAGCAGAAAGTAGAGGAAACTGGAGTGAAATAGATTGAGAAAAGAGAAATGGCAGAAAAACAAAGATCCCAAAAGTTGTGACTAATGTTTAGCCCTCTCCATGAACCAATCCCCCATCCCCTATTTTTTGTGTCAGGTGTTAAGGCCCTGTCCAGACACAGGGACCCAGGTGAGGTGTCAGATGGTGGGGCAAGTGGCCACTACTTAGTAAACACCTTGATAACAATGAAATAACCCTGCATGTAACAGCGGGATGTACTACAGATGGCCACATTCTCAAAATGATAAGAGTGGTCGTATGAGCAAATAAAAAGGGCAATTACTGAGTGAATTTGTATGCAACTTAGTGTAACAGCAAAAATTAAAACTTCAAAACAGTGGAGGTTCTCTGTTCTGGTACTACATATTTCCATTCCTCCAAGATATTGATACAATCAAGTGCAGGCTATCCTAGGTAAGTTTGATCAATCTTCTACCTGAAGAATTATGGCATCAGATCTCACTAACATTGATCATTTCCGTTTATTATGGCGTTCATCAAAATTAATTGTGTTGAGTCCAACAAAAACTAATTGTGATGGAATGCAAATAAACTTGTAGGAATTTTTTTATGCATGTAACTATCCCTTTGTAACATGGGGAATTGCATAAATGAAAATTATTGGTAATTCAGACTATTTAGATGGATCGAGGAATTGGGTTGCATATGAATCTGGAAATTTGATTTGAATATATCATAAGACAGATAGGTGAGATGATGCAGGAATTGAATTACCTGCTTCCCTTGCGATTTCGTTGAAGAACCTCCAGTGCCAACTGCACGACCCTTACCTGTCCCCGAATCTTGCTTTGCATTACTCCTTGGATTAGAAGCATTAGTCTTCACATCCTTGTTCTGTTGCATTTGCTGCGCAGCTGCATTTTGTTGTGTCATTGGATGAGAAGGAAGAATCTCCATTTTTGCAGGATGAGAGGAAGGCCTTATTTCTGATTCTGAACTCAGTGAGCTAAGAGGTGTTGAACCACCGATTGGCCTAGTGTATGGCTGGTCAGGGCGATTAGTTGTTCCATATATTTGCTGTGAGGCTTGCTGGACTTGTGTGGGTTGCTGCTGTTTGTTCATTGTTTGTGCAGAAATTGCTGAGTTCATAACAGGAGGTCGGTTCGGCGTAACATGCATTCCCTTTGCATCTGGCCGTTGGATGGAATTATCATGAGCAGTCATACTGCTCTGCACCTGAGTGCCAGATTGCACAAAGGTTTGGGATGAAGACAATGCTTGGTTTTTTTGGCCCTGATTAGGTGTGGTGGACACGTGAACTTGCTGATCATGTAATTGAGCTGAACCGCTGGAAGATACTTGGGATTGTAAAGAATACTGATTTGCATTAGCCTGCTGATTTGCATTTGCCTGGCCACTTCTCTGTGCCTGGGCTTGCATCTGTGCAAAAACTTTATGGGCTGCTTGCTTTAGCATTTGATCTCCAACGATGTTCCTGATAACTCTCAAGAAATCATCTTTATGAACTTCATTACGCCTAAGTTTTGCCCACACAGTTTGAAGCTGCATATCCTTGTCTCTGTCAAGATGAGCCTGTAGGATTGGAATCAACATATTAAATGGTATAGACGGTTGGTATCCCCGCTTCCTTGCGTCCTGTGCACCAGGTGGTGCTTGCTGACCGACCATCTGTTTTACATGCTGCTGCTCTCCTGAAGTCTGACCCACATCCACCTTGGGGCCTGTGAAATTCTGTAGACCAGCATAGCCTGTTTCCTTTTCAGCGAACTGGAAGCTGTTTGGCTCTGCCTGTTTCAGATGGTTTTCAGAATGTGGTGGTTCTTGTTCTGGCTGGTGATCGTGTTCCGTTAATTGGGTAGACATTATTTTCCAAACCTTCAGTTAACGATTTTGGCTGAGACAACTGGCCTGCTAAAATCATATGTTGCTGCACTGCTTGTTGGTTTGCCTGGCCATTTCCTTCCTGCTCTTCTGCTTGCACCTGACCAACTATAGATTTTGACACATCACTGCTATTCTGGGGTAAAGTACCAGGAAGCGGCGGAAGAAGCAGGACGAACGACGGCGCCCCTGCTCGCTCGCTCGCTCGCTCGCGGGACGGTTGGGGGATCGGCGCAGGCGGCGGTGGCGGAGGATGCGGCGGAAGCAGCAGGACGAGCGACGGCGCCGCCTCTGCTTGCTCGCGGGACGGATGGGGATCGGCGCTGGCCCTGGGACGACCTACTGATTGCCACTCTGAACCCGACCTGTGTTCCAACC

Coding Potentia
Explanation CPC Score
noncoding -1.16259
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0176300.1 2 26396907 C G
Osa02LNT0176300.1 2 26396910 T G
Osa02LNT0176300.1 2 26397040 A T
Osa02LNT0176300.1 2 26397475 T C
Osa02LNT0176300.1 2 26397660 C T
Osa02LNT0176300.1 2 26398700 C A
Osa02LNT0176300.1 2 26398969 A T
Osa02LNT0176300.1 2 26398977 C A
Osa02LNT0176300.1 2 26399156 A G
Osa02LNT0176300.1 2 26399543 A G
Osa02LNT0176300.1 2 26399810 T A
Osa02LNT0176300.1 2 26400086 A G
Osa02LNT0176300.1 2 26400462 A G
Osa02LNT0176300.1 2 26400956 A G
Osa02LNT0176300.1 2 26401099 C T
Osa02LNT0176300.1 2 26401152 T C
Osa02LNT0176300.1 2 26401316 A G
Osa02LNT0176300.1 2 26401536 A G
Osa02LNT0176300.1 2 26402990 A T
Osa02LNT0176300.1 2 26403041 T A
Osa02LNT0176300.1 2 26403103 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0176300.1 osa-miR5528 Translation 5.0 18.704 1 21
Osa02LNT0176300.1 osa-miR5529 Translation 5.0 18.593 1 21
Osa02LNT0176300.1 osa-miR5529 Translation 5.0 20.618 1 21
Osa02LNT0176300.1 osa-miR5807 Cleavage 4.5 14.775 1 24
Osa02LNT0176300.1 osa-miR5827 Translation 5.0 19.554 1 21
Osa02LNT0176300.1 osa-miR5837.2 Translation 4.5 15.776 1 21
Osa02LNT0176300.1 osa-miR393a Cleavage 3.5 15.579 1 21
Osa02LNT0176300.1 osa-miR393b-5p Cleavage 3.5 15.579 1 22
Osa02LNT0176300.1 osa-miR5071 Cleavage 5.0 22.751 1 21
Osa02LNT0176300.1 osa-miR5157a-3p Cleavage 4.5 15.412 1 24
Osa02LNT0176300.1 osa-miR5157b-3p Cleavage 4.5 15.412 1 24
Osa02LNT0176300.1 osa-miR5158 Translation 5.0 7.952 1 24
Osa02LNT0176300.1 osa-miR5485 Cleavage 4.5 19.226 1 21
Osa02LNT0176300.1 osa-miR5492 Cleavage 4.5 18.72 1 21
Osa02LNT0176300.1 osa-miR5504 Cleavage 4.5 21.394 1 21
Osa02LNT0176300.1 osa-miR5517 Cleavage 5.0 15.886 1 21
Osa02LNT0176300.1 osa-miR2275d Cleavage 4.0 10.615 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0176300.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0176300.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0176300.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0176300.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0176300.1 2 Hbd2 Physiological trait Lethality nan nan
Osa02LNT0176300.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0176300.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0176300.1 2 T2-2tiller Morphological trait Culm/leaf C424 C747
Osa02LNT0176300.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
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