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

>Osa01LNT0016700.3

GGCCAGATTCAAGATATGGTTGTTGATTTGAGTTGAAAAACATATGAACATCCAAGACAAAGTATACCCTGCAAAACTATGAATAAACGAATTACAATTGTGTATGATACCGATACGAGGGCACAAACTGCTGCAAAATGGTGCTCAATTAAAAAAGAAAAACTATTCCTTCCTATTTGTTTTACAACAGTCACATCTCAGCCAATGACACTAGAAAGAAATAATGGAGAAGAGCACATATTCACTGCTTCTCCAGAAGCTCATATTTATAGAAATAATTATGCATCATCAGGAGCGTGGCTCGTGTCAATGCTGAACCGAAGGGCATGCCAACTCTCAGTTGTTCAGATCTAATCCTTGCGGACAGTTAACTTTACAGGCTCACAAATGGTTGCTGCAATTTCACGCAACATATACAGGTAAGAGCGATCTACATCACCTTGAACCATTTGCATCAGGTTTGAGATTACTCTATTTGGCCTTCTCTGGAGCAATGTTTTTGGCCTTCTCTGAAGCGGAACACATCGTGGTTCCTTCTTGTTGGCAAGCATTGATGGTTTGGGTTAGGGATAAACCGTTTCTTGATATCACTTTGTCATCTCACTGAATAAGGCTCTGAATCATTCGTATTTGTGGTATTTACTGACTTCTCAGTAGACAAATTGCCCATGGCATTGACACAATCACCACCAGCTTGCCGTGATGCTTCTGTGTTGTCTGCAGAACGTTGATGCTCCTCAGAATGAACACTATGCTCCCCAAAAACGCCATTGGCTTCAGAGCCTGACGAACTTGAGGCAGGTGAACGGGGTTCCTGCTTCTCTAAATCATCCATGCGTTTACTAACCAGGTTAGTCGAAGCTCCAATCTTAACACTAGTAATTCTCGTTTCTATCTTTTGTCTCTTGTGGAACTCCCCATCAGACTGTTTGCCATCCACTTTACTATTCATTAACTTTCGCTTCAATTTGGCTATAGTTAGGGGTTCATCATCCTCTTCAGGCCTGTCAGGCTCCTTAGGTGGAGGATTGAAGTCCTCATCATCATCATCAGCATAATCCACTAGTCCACCAGATTTAGGCCTTGAGGAAACATCATCAGCTTCACTGCCATTAGTTAACTTAGCCCCACCATCTTGTTTCTGAGCATGTTTCGTCCGCCGGACTGAATCTTCTTCGTCGCTGTCCTCATTGAAATAGTCTTCCTCTTCCTTCTCAAGGCCTCTTTCTTCCGCTTTCTTTCTAATATCAGGTACATTGGCACTTAACTTCGTTTCAGCACTCTCCAAGTACTGTTGATACTTAAGTCTAAAGGCCTGAATACTCCCAAAGTGTTCAAACTTCATAAGTTGATCCCAAAAGGACTCATTGGCATATATAATAAGTTGTTTTAGACCTTCCTTCCGTATGTATTCCAAAAGTTCGAGTACTCCTGACTGTAGCATGTTATATCTATCCCCATTTTCAACAAAGGCGTCAATTATTGGTTTGAACAAATTCATCTTGACAACATGACGAATAAGAAAATCATCATTTCTCGATATAGTAGTTCGCATAAATCTAACTGCTGCAACAACCAAAAACTTCTCCCTCCGTCGAGTCAAGGCAAGGATTTTCTCTATTGCATTGTTGATTAGAAAGTGGCACTTAATTTTGTAGGGATGATGAACTATGCAAAAGCATAATAGTTCACAAACATTTAACAAAATTTCAGGCTTAGTGCGATTCACTTCAGTTTCGGTATTTCCAGCAGAGTTAGATGCTCTGGAAATGTTCCTCGGAGGACATGATGATGCTATTACATCAACCAAATAGTCAAGATGCTTTTCATAGAAAATTTCAATAACAGCATCTCTATGTGCTCCAGACATGGTAAAAGAATCCATCAAAATACGAAGAATTTCCAGAAATTGACAGTGCATTGCCTCACCGAAGTCAGTTACCATTCCTTTGACCAGAAGTCCAAGAAGAGAATTCCCTTCTTGTTGGACAATATATGACCTCAGTAGGTTGGGGTCCTGATTAAGAAAAAGTATGAGGACATCTGTCCCAGCTGAAACAATCTTTCTATCTTGACTCTGCAAGACATCCGAAATGATATCAAATACACCTTCACCTGAAAGATCCCTGAAGAAAGTAGGTGTTAACTCATTTAAGTTCAGCTATGAAATTGCACAGCAAAACGCAGAGCTCACATTTATTTAACTAAGGAAAATAAAACAACAGCAGCTTTGGCTTCAGATTAGTTTGGTGGAATAGATAAACCATATGCATTCTATCACAAGGAATGACAATATTACACAGGTAACGTGAGTAAACATATGAAAATGCATAATAAGCCCTATATACCTAATTACAAGATATCCTTGAGCAAATCTGAGGCTAAATGATAGCAAAACAAAGCATAGGGCTGCCAGATAGTGAATACAATGGCACCACCACCTCAGGCACACCAGTATCATAGGCTCTATTTCAAAAGAAGACAGGACAAGGGGGTTAAAACTTAAACACAAGGAGCTAAGTTACAGAAAATAAGTGTGTTGTTTGAGCATTGTCCTCAAGAATTTGACAAACAGTCAACAAAGATCTAGCACCATTGCATGTTGTTGTGTAAAACACTAAAAGGCAAAATTTGTGTACATTAAGTGTTCTGGAACCATGTGCTGAGCAGCCTGAGCTGTTTGTCCACAGGTAGCACCCCCACTTCTATCATCACGAAATGATCAAATAAATAGGTTTGGCCAAATGACATAGTAATAGGGCTCATTGTGCATATTAATGACCCACATACAGTTTTACTGCTGCATAACCAGCTGGTGTAAAACAAAGTATAAAACTGTTTGACTGTTATCTTTTTTGTAAAAAAAAATGCATTAGATCTTTGTGTTCCCACTATACAGATTTACCACTGTGGTTCTAAGTTCTTAACGATAAAACAATACACAAGCAGCAGCCCAATCTCCAGTCACTCTAGTATTACAGTGAGGTGACCAGACGAGCACCAGAAATTTTTGACATTGGTTGCAAACAAAAATCACAGGTTTTATGTTCATTTCTCCTTCAGTAAGTTCGCTAACTACTATCATTCTCACAGCCAAAAGGCATCAAGATGCAACATTCACCATTATAGGTTTTAGTTTTAAAATTCTCTTCAAATTATGGAAGTGCAACATTATGAGAATAGCTTATATAACGAATTTATTAGCATAATTTCCATGTATGAGTCTATTAAAGAAGATTCTTTTTTTTTCTAAGACCAGGTTCTTTTATCACAAGATCCAAAGGTGATACCAATCTGTAATTGAAAGTAGGTTGTGTAGTAACTAGTAACAAATAAACTGGCCATGCTACTTAGTAATCTACATGAGTTGTGGTGCAAAAGGAATAATGCACCTCAGTGCGTAAAGGAATATAGTTTCTAGATGGTTTCAATCTATGAACATCATATCACATAATCCCTCCATCCCAAAATATAAGCACTTCTGAACTTTTCACGGGGATTAAGGAGAGGTGAAATTAAAAGAAGGATGGTTGTGATTGGTTAAGATGAGAAAGTAGGTCGAGAAATTAAATGAGAGATGGCTGTGATTGGTTGAGATGAGGGAATAAGGAGAGAAGATACTATATTCTGGTACAAATTGTGAATGCTGGATGTTGCTATATTTTGGGACAAAGGGAGTAATAACTAATAAATCAGAAATATAACATCAGAAATGAAAACATGGGATATTTAATTATGTTTTCCCAATGACTGAAAATGTCTAGTGCTGGCAGATAAACAACTGCAAGAAATTAACTGTTTTGGCCACTGCTAGACTCTTATGATAAGTAAATGAGATGCTATGGTTTAATCAACACTTCACATTTCAAATACAAGTTCTCCAAAAGGAATGGAAGAGGACAAGGTAGGCATAGTTTTCCCATTGTGCCTGAAGATGAGTTAATAAGTTATTTCCTTCCGTTACAGGTTTCATCTACTTGACTTTGGATGTGTTTAGTTCACGCCAAAATTGGAAGTTTGGTTGAAATTGGAACGATGTGACGGAAAAGTTGGAGGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGGAAAAGTTGGAAGTTTGAAGAAAAATTTTGGAACTAAACTCGGCCTTTCACAAAACAATACGAAACTTGGAAAACCAAGCTTACTGGAAAACTAGTAAAGAAAACCAACACATCATTTGAAAAGAAAAAAAAAGAATCTAGCAAAGAGAAGTCTAAATACCCCCCCTAAACTTTGTCTTGAAGTCCAATGTTCATCTAGCACCCTGAACTTTAAAACCAGACATCAACCCCCCCCCCCCCGGAACTATACAATACCATTCATACGACACACTATGGTGGTTTTGCAGAGTGGTTTTTATCTAGTTTGGATATACGTTGGATGAGTTTATCGGCATCACATATGCATTGAACTTATATGTTAAAATCTCCACCTAAATCTTTCTTTTTTACCCCTTTTTTAGCTCTCACTTACAAACAAACGTTGATATTAATATTAGTACGACGTCACTAGAGTGCATAAATTGATGACTGATTATGGATGATATGTAAATATGTGATATTAGCTATTCAAAACCATTCTTTTAAGCTTCCAATTACACAAAACCAGCATCCAAAACCACCTAAGGGGGTAATATGAACGGTATTGCAAAGTTTGGGGGGTTGGATGTCTGGTTTTAAAGTTCAGGGTGCTAGGCGGACTTCTATCCAAAGTTTAGGGGGGTATATGGACTTTTTCCTTACCAAAGGTTTCAGCTATTCTCTAACTAGCAAATGCATAGCCAAACAAAGATTTGGCTCGATCCACTTGTCAAACAATTGATTTTCTATTACATCTTGGTATAAATTCCTAATGGTGCACCAGATAACCACTTACATCTTGGTATTCAATAAGGAATGAGGGTGCTATTCCAAAAGACAAGCAAAACCGAATGGCTTATTGTTAGTCTAAGTCTGCTAAATACAGCCCATATGCCACTGTTACCACTTTGGAATATTGACGCATCATCATGTGTTATTAAGCCTGTGAAGTCTAATCACAGGGCATAGGACAAAAAGAAAAGGACCAAACAAATACTTACCGGAACAGTCGTAATTGTTGAACAAGCGGCAAACTCTTACTGAGAGTGCAAAATTCATGCAAGAACAGCACCAATTCTCTTTTTGATTCCATAGAAATATTTGATAATCTCATCCTAGCAAACAATTCTTGGATAAAGCAAGAATCATCCTTTAGTAAGGAAATAACAGCGGCATTGTTCGAATGTATCATCGTGTTAAGACTAGCTAGAGTGCCATCATCCAACACTCGAGGTAATATAACATCCTTTAGATAGCCTATTCTATATGTTTGATGTATCTTTGAAACCACAGAAACATTTTTAATAGGTATGGCCTCTTTGAAAACTACATGATCCTTTAGAAAAGCGCGATGCTTTTGTACTTTAGGAACATCTGGGTCATATTCAAGGGCACCTATGATGTCAAGAATAAACTCATCTGAGAAAATCTTGTCAAAGATTGATGAACTGTTCAGCAATATGATTCCCCTGACTAATTTGAAGATCATGTGAAGATCATCTAAGTTCTCTAAATCCTCGCATATTCGAAAAATGTCCAGTAACTTTGGGAAAAACTCGCGATCTTGTGTTATCAACTCTGCCACGCGCATCTGATCTGTAATGCCACCCTCCAATATAGTCTTTAAAATTAAAGGAAGATTGGATAACTCAACAGGTGGAAGCTCCCTCAGCTCACCATTAACGGAGCGGAAGGATTCATCATTTGAATGCAATACTCTAGAGGCTTCTAGAGAAACCGAAGTTGGACGAGGACCGACTTCAAGAGCACCAAGGTTATTAAACTGAATGTTTCTCTGAATGTCACATATGTTGTCCCATATGTATGAGCACCCAGCAGCTTCCTGAAAGCTCAACGCTAATTCTGTTGCTACTTCTGGATCCCTCCATGAGATGATTGTATCTTCTTGCTTTCTGTAGATATCTTCAGAAGTAATGTTGTGCATGAGCAATGTTTCATTGTCTTCTTCATCCAAAACAGTCAAACCAAGTTCTTTAGAATCCTCAAGGAAGTCAATATTTACATGCCCTGTGCCCCGATCATCCCATTTCCCTCCATCAGTCAAACGGTATACTTTCACACGCTGCATACCGCTGGTGTTCGCCGCCGCGGCCTCGCCGCCGCCGCCGCCGCCCTCCGCCTCCCGCCGCTCCTGCTCCCTCTGCCGCCGCCGGGGACGCTTCCTTCAGTCGCTGGACGTCGCGGGGCCGCGAAACCCTAGCTAGCCACCATGAACCGAGACTCCTAGAGAGAGAGAGAGAGAGAGAGAGAAAGAAGCTCCCCGAGACCCCGAGCCGAGCCGA

Coding Potentia
Explanation CPC Score
noncoding -1.03833
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0016700.3 1 13247194 A G
Osa01LNT0016700.3 1 13249376 C T
Osa01LNT0016700.3 1 13246574 T C
Osa01LNT0016700.3 1 13246788 G T
Osa01LNT0016700.3 1 13246859 C T
Osa01LNT0016700.3 1 13248458 A T
Osa01LNT0016700.3 1 13249108 G A
Osa01LNT0016700.3 1 13249263 A G
Osa01LNT0016700.3 1 13249532 A G
Osa01LNT0016700.3 1 13249541 T C
Osa01LNT0016700.3 1 13249572 T G
Osa01LNT0016700.3 1 13249675 T A
Osa01LNT0016700.3 1 13249682 A G
Osa01LNT0016700.3 1 13249698 C A
Osa01LNT0016700.3 1 13251467 T C
Osa01LNT0016700.3 1 13252016 G A
Osa01LNT0016700.3 1 13252782 T C
Osa01LNT0016700.3 1 13253247 C T
Osa01LNT0016700.3 1 13253255 T G
Osa01LNT0016700.3 1 13253279 G A
Osa01LNT0016700.3 1 13253366 C G
Osa01LNT0016700.3 1 13253551 C T
Osa01LNT0016700.3 1 13253774 A G
Osa01LNT0016700.3 1 13253806 A G
Osa01LNT0016700.3 1 13253839 A G
Osa01LNT0016700.3 1 13253914 G T
Osa01LNT0016700.3 1 13254706 C T
Osa01LNT0016700.3 1 13256297 G A
Osa01LNT0016700.3 1 13256598 C T
Osa01LNT0016700.3 1 13256720 C T
Osa01LNT0016700.3 1 13256984 C T
Osa01LNT0016700.3 1 13257061 T C
Osa01LNT0016700.3 1 13257645 C T
Osa01LNT0016700.3 1 13258310 C T
Osa01LNT0016700.3 1 13258431 A G
Osa01LNT0016700.3 1 13259946 A T
Osa01LNT0016700.3 1 13260078 T C
Osa01LNT0016700.3 1 13260201 T G
Osa01LNT0016700.3 1 13260647 T G
Osa01LNT0016700.3 1 13259758 T G
Osa01LNT0016700.3 1 13249838 A G
Osa01LNT0016700.3 1 13250292 T C
Osa01LNT0016700.3 1 13252920 G T
Osa01LNT0016700.3 1 13260709 A G
Osa01LNT0016700.3 1 13258093 T C
Osa01LNT0016700.3 1 13259034 G A
Osa01LNT0016700.3 1 13254397 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0016700.3 DTM_#DNAt_MULE_japo_Os0182 Chr1 - 13253944 13254474 530
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0016700.3 osa-miR5530 Translation 5.0 14.208 1 21
Osa01LNT0016700.3 osa-miR5788 Cleavage 4.0 9.327 1 21
Osa01LNT0016700.3 osa-miR812s Cleavage 5.0 15.23 1 24
Osa01LNT0016700.3 osa-miR812v Cleavage 4.0 14.827 1 24
Osa01LNT0016700.3 osa-miR5811 Cleavage 5.0 18.304 1 24
Osa01LNT0016700.3 osa-miR5813 Cleavage 4.5 17.821 1 22
Osa01LNT0016700.3 osa-miR5824 Translation 5.0 20.57 1 24
Osa01LNT0016700.3 osa-miR5824 Cleavage 4.5 22.042 1 24
Osa01LNT0016700.3 osa-miR5824 Translation 5.0 12.325 1 24
Osa01LNT0016700.3 osa-miR5837.2 Cleavage 4.0 16.016 1 21
Osa01LNT0016700.3 osa-miR1440b Cleavage 4.0 7.309 1 21
Osa01LNT0016700.3 osa-miR1440b Translation 5.0 11.671 1 21
Osa01LNT0016700.3 osa-miR6247 Translation 4.5 10.949 1 21
Osa01LNT0016700.3 osa-miR164c Translation 5.0 15.396 1 21
Osa01LNT0016700.3 osa-miR444a-5p Cleavage 4.5 15.539 1 21
Osa01LNT0016700.3 osa-miR1425-3p Translation 5.0 11.006 1 21
Osa01LNT0016700.3 osa-miR444b.1 Cleavage 5.0 17.943 1 21
Osa01LNT0016700.3 osa-miR444c.1 Cleavage 5.0 17.943 1 21
Osa01LNT0016700.3 osa-miR1436 Cleavage 4.0 21.77 1 21
Osa01LNT0016700.3 osa-miR1440a Translation 4.5 14.997 1 20
Osa01LNT0016700.3 osa-miR1850.2 Cleavage 4.5 16.578 1 21
Osa01LNT0016700.3 osa-miR2101-3p Cleavage 4.5 12.125 1 22
Osa01LNT0016700.3 osa-miR2875 Translation 4.5 14.685 1 24
Osa01LNT0016700.3 osa-miR2878-5p Cleavage 4.5 11.385 1 24
Osa01LNT0016700.3 osa-miR2931 Cleavage 4.0 15.696 1 20
Osa01LNT0016700.3 osa-miR3980a-3p Cleavage 5.0 17.73 1 21
Osa01LNT0016700.3 osa-miR3980b-3p Cleavage 5.0 17.73 1 21
Osa01LNT0016700.3 osa-miR5518 Cleavage 5.0 14.834 1 21
Osa01LNT0016700.3 osa-miR5524 Cleavage 5.0 14.566 1 21
Osa01LNT0016700.3 osa-miR1862d Translation 4.0 10.855 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0016700.3 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0016700.3 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0016700.3 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0016700.3 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0016700.3 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0016700.3 1 nan Morphological trait Root RM23 RM306
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