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

>Osa01LNT0021700.1

CTACGCCGCACCACGCCACCCCGCACGGCTGCTGGCTCGATACACAATCAGCGTGAGTTGTAACATCTCTTATTGCATAAAGAATGGTATTACAAAGTTACCCATCTTCTCTTTTCTCTCAAGCTCTTCCTTTTCAGCAATCTGTTTCAGCGTAGTCCACCCCTTTCTTGCCCGCTTCCTTGAACTACCAGACATCTGAGCAGAACCACTTGCTACAGATTTATTTTTCACACGGTCCTTTGGAGCTGACTTGGTAGGCATTGTAGGGGCCTTGCCAGTAACTGAACTTGGCATCTCCCCTTTCTTGTTCTGAATGCTTCTTGTCTTGACCAGTTCTGCAGAATCCTTATGGTCCGTCACATCCACCAGTTTGTTCTTTCGAGGAGTAACAAAACTTGATCCGACTGGAAATTCTGCTTTTGAAGGAAAATCGGGTTGGCATATTGCAATTTTGTTAGCAGAAACAGGCTCAGTTTCATGCATACCTTTTTCACTTGTGATTGTTACCACTATTTTCTGTGAGACATTCTCCTGATCAGTAGCTGATGCTGACTGATTCAGTTCCACCGATGAACACGCTACCTCCTTTTCCATAGATTCGTCAAGAAGATTGGGTACTGGACTTTCCTCATACTCATTCTTTTCAAGATTTTGTTGTTTCAACCCAGATGTTGACTCTAGTTGTGAGACCGCTGCCTGAGAATATTCAAAGCCCTCTTTTATAGTTACTAATCTCTTGTTATTACTGTCCCCTTTCAACTTTATGCTGGTTACATCCATGCCAACTGGCTTTCTTGATGATAACAAGCCCTTCATAATATTCTTTCCGCTGCCCCTTATTAGGTTTTGGTCTCCACAGAAATGGCACAGGTAAGAAATGCTGTTCTGGCAAGTGTTTAACTTCTTGCGTCGCTTTGCTTTTCTTTTGTTGTTCTTTATGCGGATTGTGCAGTTGAAGCCTGGCTGTAAGACTGTTTCACACCTTTGCAGACGAGGGGACGCCATTGAAGTTAGTTGTCCTCTGTTGTGGCTGGGTTTTCTTGTTCAGCATCTACTATGACATCCGTGCCCTGTTCTGGGGTAGATGAGCCAGTAACTTGGGTGGCTGGATCGACATTTTCATTGACTGCCTCTGCTACTTCACAATTCTCCAACAGCGCCTGAGCTGACGTGCTGGATGAGAGCACATTGTTGGAATCATTGTGATCCACATACATAGGTTCCACCATTAGTTCAATCTGGCCCATTTAGTTAGGATTTTCCAGATGTCCATCTTGATCAACACTAGTGCTTTGCTGTGGGATTGCAGAGCCTGGAGCAGGAGTGGCTGTATCACACTCATCGATGGCTGGTGTAGCTGAGTGACTGTGTTCCTCCAACTCCAGTGAAGGACATGGGCAGATGACATTGTTGAAACCATTATCCTCCTCATCCATAGGCTCGAGGGTCATTGTTGCATCATCCACCATGTGAAGCTCTTCCTCTTCCTGATGCTGAGCTTCTTGATCGGCATCAACAATGTTCTGTTCAGCTTCTAGCAAAAGTAGAGGCATGTCTTGAGCGGCAGCTGATTCAACATGTGGACTAGTAGCGGAACCACCATTTTCCTTGATCTCGCCAAGGTCATGGAGAACATCCTGAAAGCCATGCAGAAACTCAAAGACCAAGGCTTGTGTGGTTGTATCAGCTGTGGATGTCATGGCCATCTTGGCCTTCTTTACCATACCATGCAGTTTATCAACTGCTTTGCGGATCATAGGAGCCTTGGCTTGATACTGAAGATCAATGGAATCATCAGGCTGTAATGAAGGTCCTGCTTCCACATCATCACTGATTGATGGTACAAGATACCGCCGTGTAACTCCTGAGTACCAATGCAGGTACTCCTCATAAGACGATGGGTCATACTGCTCTGACTCTGGAAATATGCGCTGCCGGCGGGCTTCCCATTCCTGAATGTACTCATGATGTGTCTCTTCCCAGTTCTCATGTTCTCTGCCACGTCGACTAATACGATGCAGCGCCTGTAGGGTAGGTCGAAAAGGTGGTGGAATGGATTGGCGAAGCCCAAATTGCCGCATCACTCGCTCAGGCAAATACATCTCGACTATCGGAAAATTTATTAGTGGAGCTTGTGTAAGCCACAAATCTGCATCTTTTGTACAAAGCAATGGCAAGCTTGAAGACTCAATGTGCAAGTAGGGTTCCCACTTCACCTGATCAGCTCGCTGCAGGTTCAGTTCATCCCTGTACTGCTTAAGACAGCGTGTAGCATTCTCACTTTGTGTGCGCGCACCTACCCAACGAAAGCCAACAGGTGGCACATCCTGTGGAATGTCTGTCTCTGGGCACAGGGGAGACCGGACCAATGGTCTGCCAACATGGGAGCGCTCCCAGCTCCAAAGCTGCAAGAGAAGCAATGAACCACCAATATTCTTGATATTGTGGGAGGAAGCAACAGAACAAAGAGAACGGTATAGGAAGGCCAGCACTGCAGATCCCCAGCTGTATGTCCCAACACGAGAAAGATCAGCAATCAATGGAAGATATATCAGACTCATCCGTCCTGTTCCATCTGGAAATAGCACCCCACATAAAAGGCTCAGGATATATGCTCGAACATGCCTCTCCACAGTCTGATCATCTGCTCCTTCTGGTAATTCATAGAAATGCTTCTTCAGCCATTTGTAGTGCAGAAAAGATTTTCCAGGCATTGATGGTCCTCTTGGATCATGACCTAGACAATCAATGACCATCTGCGCATAATCATGATCAGTGGTAGAACAAACTGGACGGCCATCGATAGGAAGAGCTAACAACATTGCTACATCTTGTAGTGTAACTGCCATCTCCCCAGAAGCCAAGTGGAAACTATGAGTTTCTGGTCTCCAACGCTCAACAAGGGCAGTGATCAATGCCTTGTCCAATTGAGGCATCTTCTGGCAAATTTGTGAGAGCCCAAGAAGGCCAGCATCCCTCAAATAAGGACGGTATCTCTCATGAAATTTTAAAGGTTTGTGATGTCGCAACTTCAACTGCTCCACAGCCTGATCACCGAAGATTGCATCCGATCGGTGGTTGATCTTAGGGTTGAGTAATGTGTTGGATACATGCTCTGCTGCTGGGCTTACAAGACAAGGTTGCTGCGAAGTGAACTCGATATTGTCCTCTTTATCAGAAGTAGTGCTCGGGGAAGAAAGTGCAGAGGTTTCATGAAAGTCCATATCATTTTCTGCCAAAGCACTTCTCCCACGGCCACGGCCACGACCACGGCGGCCACCACCTCCTCTCCTTGAAGACATGGTCTTGTACTGTTCTGAAGTTGTGAGGGTGTGAGGCCAAACTTCGATCGAGGTAATATTGATGCAGTCGACAAGAGGCTTCGATGCGATTATGATCAAACTTCTGCTCGGAGAGTTTTGGAGCTTGCAATGAGGTGCACTAGCCGGTCCTCTATCAAAAGACCAACAATAGCAGAAGTTGTATCGTTCTTGGTCAGTTTGTCCTAGATTTTGGCCTTCACAACCTTGCCATCAAGCCAGAGGGAGTGGTCCTGCCATACCTTCTTGATGTCGTATGTTTCTCCTATTTCCAAGTACTTAGCTTAAATGTGAAAAACCTGGTGGATGGGCGGGTACATGGAGTTGGTGCAGACGGGGCACTCGAGCAGCTCGTGGACACTCGTCGCCGGCGGGACGACAAGGCCCCCAACCACCACCCGGACCCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCCCCCGTGCCCCCTGCCCCCCTCCGCCGTCGACCTAGAGGGGCGGACTTGGACGCCGACGTGGGAGGCGGCGGTGTGGGACGTCGACGGGGGAAGAGGGATAACGCAGGGGCGCTGGAGAGGCCGGCGACAGAGCTCCTAGGCAGCGGCCATGGCGCCGACGTGGGTGGTGGCGGCGGCAGCGGCTGGAGTCTCCGCCTCTCGCCTCTCCTGGGGATTTGCCGATTTGGGGGAATGGCCGAATGGGG

Coding Potentia
Explanation CPC Score
noncoding -1.00444
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0021700.1 1 19111872 A G
Osa01LNT0021700.1 1 19112044 A G
Osa01LNT0021700.1 1 19115245 T C
Osa01LNT0021700.1 1 19115265 A G
Osa01LNT0021700.1 1 19115362 A C
Osa01LNT0021700.1 1 19115381 C T
Osa01LNT0021700.1 1 19115436 T C
Osa01LNT0021700.1 1 19115573 A T
Osa01LNT0021700.1 1 19115653 C T
Osa01LNT0021700.1 1 19116212 T A
Osa01LNT0021700.1 1 19116829 A G
Osa01LNT0021700.1 1 19117126 A G
Osa01LNT0021700.1 1 19117146 G A
Osa01LNT0021700.1 1 19117385 G A
Osa01LNT0021700.1 1 19118039 A C
Osa01LNT0021700.1 1 19118623 A G
Osa01LNT0021700.1 1 19118925 A G
Osa01LNT0021700.1 1 19119160 G A
Osa01LNT0021700.1 1 19119173 G A
Osa01LNT0021700.1 1 19119220 A G
Osa01LNT0021700.1 1 19119290 T C
Osa01LNT0021700.1 1 19119362 C T
Osa01LNT0021700.1 1 19119546 A G
Osa01LNT0021700.1 1 19120167 T C
Osa01LNT0021700.1 1 19120318 C G
Osa01LNT0021700.1 1 19120673 T C
Osa01LNT0021700.1 1 19121316 A T
Osa01LNT0021700.1 1 19121319 T A
Osa01LNT0021700.1 1 19113710 C T
Osa01LNT0021700.1 1 19112750 C G
Osa01LNT0021700.1 1 19112869 A G
Osa01LNT0021700.1 1 19113078 T C
Osa01LNT0021700.1 1 19113110 A G
Osa01LNT0021700.1 1 19113142 A G
Osa01LNT0021700.1 1 19113170 A G
Osa01LNT0021700.1 1 19119367 T C
Osa01LNT0021700.1 1 19116424 C T
Osa01LNT0021700.1 1 19120765 A G
Osa01LNT0021700.1 1 19112304 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0021700.1 DTM_#DNAt_MULE_japo_Os0205 Chr1 - 19112436 19113631 1195
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0021700.1 osa-miR812t Translation 5.0 10.194 1 24
Osa01LNT0021700.1 osa-miR812u Translation 5.0 10.194 1 24
Osa01LNT0021700.1 osa-miR5818 Translation 4.0 16.945 1 21
Osa01LNT0021700.1 osa-miR171e-5p Translation 5.0 24.676 1 21
Osa01LNT0021700.1 osa-miR166i-3p Translation 4.5 16.567 1 21
Osa01LNT0021700.1 osa-miR415 Cleavage 2.5 13.666 1 21
Osa01LNT0021700.1 osa-miR395v Cleavage 4.5 20.883 1 21
Osa01LNT0021700.1 osa-miR1428a-5p Translation 4.5 12.736 1 21
Osa01LNT0021700.1 osa-miR1439 Translation 4.0 17.495 1 21
Osa01LNT0021700.1 osa-miR1857-3p Cleavage 3.5 18.317 1 21
Osa01LNT0021700.1 osa-miR2095-3p Translation 5.0 13.95 1 20
Osa01LNT0021700.1 osa-miR2095-3p Translation 5.0 17.795 1 20
Osa01LNT0021700.1 osa-miR2100-5p Cleavage 4.0 22.754 1 22
Osa01LNT0021700.1 osa-miR3979-3p Cleavage 5.0 7.256 1 20
Osa01LNT0021700.1 osa-miR812n-3p Translation 5.0 10.194 1 24
Osa01LNT0021700.1 osa-miR5489 Cleavage 5.0 17.649 1 21
Osa01LNT0021700.1 osa-miR5507 Translation 3.5 16.206 1 21
Osa01LNT0021700.1 osa-miR5510 Translation 4.5 22.724 1 21
Osa01LNT0021700.1 osa-miR5513 Cleavage 3.5 23.961 1 21
Osa01LNT0021700.1 osa-miR5523 Translation 5.0 16.895 1 22
Osa01LNT0021700.1 osa-miR5524 Cleavage 4.0 13.865 1 21
Osa01LNT0021700.1 osa-miR437 Translation 4.0 17.298 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0021700.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0021700.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0021700.1 1 nan Morphological trait Root RM23 RM306
Osa01LNT0021700.1 1 qNVB-1-1 Morphological trait Culm/leaf R2159 C178
Osa01LNT0021700.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0021700.1 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0021700.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0021700.1 1 nan Physiological trait Source activity RG532 RM472
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