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

>Osa06LNT0332800.2

GCTCAAGGCACGACTCCACACTTGCAATAATAGTTCATCCTCCTGTCATCTAAATAGTACAAAACCTATCGATTCCTTAACTATGGAACCCAAAAGTACGTCAAAAGCTGGGTGTACAACATGTACATATATAGGACTAAAGATATTTCTGCATTACACTCCAAAAGTATCCATCTGCATCAAACAGATCAAACGACTGCTTGTTGTGGTGTTCAAGGGGCAGGACCCCAGGATGCACACCGATGAGATTTGGTATGGCCAAAGGCAAAAATATCTGGAACGAAACAAGGTGACAGAATGCCTCCTATTGCTATGTAAGAACTCAGAACACATTCAAGCCTCTTTTCTAGTTATCCTGAAGCAATAGATTCCAAGAGCATCCTTGATTTCATGCACAACAGAAACGGCAAGATGCAGGTAAAGGCCCACTGTGTATGCGCAATACAGGAAAAGAACCAGCAGCTCATCAACTAAAGGAATCCCAGCATTGATCTTTGCTGTGAGAGCATTTGCAATAGCGAAAGGAAGAAACACCAGAGACATGCACATTCCAGTTTTGAGACCTTTGGGTTCATCACATAAATGAGCAAGTATCATCCTTCCCTGTCCATGCATGGCAACTCAAAATATGAGCACTAATTCCAGGAAGGAAAAACAAGGATGATGGTAGATTAGTATTATGCACTATGTTTGCAAATCTCACTCTACAGAAAAATGCTCCATCACTATTCAGTAAAGAACAAAGCGCAGTGGCACATTAGGTGAACCAAGTGGCATTAGGTGCTTCTTCAGCAACAGTATATCAGTACCAATATGTTGTGCATGTTAGCCATAAATGCTTTTCATAAAAATCCAGGCGGATAATGGGACTATCAAGTTTTTAATTGTCGCAATATAACTTGGATGGTTAGATATAACCTAATTAGTGATTTGTGATGGTTAGATAAAAATTCCTAGACTTATAACTGCTGTGCAGATAGATCAAAGTAGATCATAAGAAAGTTTTGCAAAGATGAAAACTATAATGAAAACTATAAGAAAGTAATTAAGGAACTGCAAGTTGATGAAATGCTGATCCACATTTAATGAACACAAGAATATCCAATATGATATATCGTCCACAAAACAAGCTAAACAGTATTCAGTTTACCACCCTTTCCAGATCAAAAGGCAAGGTCAGCTGATGGCAGGCATGTTCAGTTGCGTAACTAATTGCTGCCACAAGACAACAGTGATACAAATGCCCAAATACCATTGGCCTGATTTATCTGCATATGGACCCTTTGCAATTCTGCTGCACAGTTCTGTATAATTTGGTCATTATTTCATATAGTTTATAGTATTTTTATAGGTTAGATGGGTTGATCAAAACCTGATTGAAGCAGCCTATTGTTTTTCTAGTAACCTACTAACAAAGATCCATTTCCAAAATGTAGGAAGTTTTTACTTGCTCTTAGCAGACCACATTTTGACTCTAAACTCTTAGCAGGCCGCATTTTGACTCTAAACTCTAAAACTGGATACTTGACACCCCTCAGGTATTGAAACAAGGCTGGTTTCAAAAACGATTTTTGTCCTTGGTGCCCTCTCAGGCTCTCACTAACTGAAGCATGAAGAATGCTGAAATAGTGAAGAGAACTGGAGCATGGAGTGCCCCTGGTTGCTTTGAAATTTGAACTCATAGCAGGTGGCTGTTTTTAAGGATAGGCAAGGCCTAGCAGGAACCATGTGGTTAGAACTGATAAGCATGACAACAATGGGTATGACAGTGGCTGCTCCAGTGAATTGGTGATTGCGCACACCAAATATCCAAAAGCAAAACCAGTTCCGATCACAAGCAGATGTGGCTGATTCCTCATAATATCTGAAGGAGAGAGGTAAGACCAGACAGCAACTCCAGTTAACAATGCAATGAAAGGAAGGAGCATTGCCAATGCCAATACCATGCTTCCTTTTCTTGCTTCAACTACTTTTTGGACATTGCTGACATTGGATCCAATGGTAGGGATTACGGCAAACAGGATCATAAGAATCATCACAATAATGTATAAGGGGATATCTGGAATAAATGGAAGGGGTACCCAACTTAAAAGGGGTATCGACTTCCGAAAATCTTGTGCCCACCATTCAGCGCCAGTAAGAAAGGTAAAAGAGTGGGATAGATATATCAGCATCAGGCCCTCCGTAGGTCCATTTATTAAAGGAAGAATAAGTGTATTTGTAAAGAAGTGTTCCCATGTTGCAAGATAGAACGGGACAGCAGCAATCACCCAGAAACAGAAAGTAAACCTTCCACACATCAAGGTGCTTCCAAGGGCTAATGCTTCAAAAGCACAGGCAAGAGCATCACATCCATGATCAAAAAGTTCTCCTAGAGGACTTGATGAGCTAGTGCGCCTTGCTTGTTTACCATCAACAGCATCAAAAGTCTGGTATAAGAAGAGAAGTAATCCATGGGCAAGATGGACCCACCTAGGGGGAGCTGTGTCGAGGTGGGGCGAATAGATATAGCCAAGAAGTGCTGATACAACTAGAAACATGAATCCAGTGAGTGTGATCTGAAATTTCAGAAAACATCATAACTGTTGACCATAGACAAGGAAGAACTGAGAATATGTAGATCATATTCTTACCATATTAGGTGGCATCCAGAGCGGGAAGAGGGTGACGCATCTGCTCCAGAAGGGCTGGAGCACGTACTTGGCCACCACCGAGTGGTCCTGCCCGCTGTACCTGTACCGCTTCAGCGTCTCCACCCCGTGCGCCCCGATGTACCCCATCCTTCCCCTCGGCTCGCTCGCTCGCTCGTCGGCGGGGAGCTCCTGGTCGGGGGAGGCGTCGGCGGGGAGCAGTGGGGAGCTTGGGGGCGGCGGCGGCGGCGGCGAGATCGCGGAGGCGGAGAAGATGGGGAGCGGCGGATCAGTGATGGCGGCGATGGGTATATTCGAGTCGAAA

Coding Potentia
Explanation CPC Score
noncoding -1.18118
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0332800.2 6 5284687 A G
Osa06LNT0332800.2 6 5279236 C G
Osa06LNT0332800.2 6 5282491 T A
Osa06LNT0332800.2 6 5284578 A C
Osa06LNT0332800.2 6 5284589 T C
Osa06LNT0332800.2 6 5277711 C T
Osa06LNT0332800.2 6 5277429 A T
Osa06LNT0332800.2 6 5281970 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa06LNT0332800.2 DTM_#DNAt_MULE_japo_Os0229 Chr6 - 5281804 5282301 497
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0332800.2 osa-miR1319b Translation 5.0 18.74 1 24
Osa06LNT0332800.2 osa-miR6251 Translation 4.5 12.854 1 21
Osa06LNT0332800.2 osa-miR435 Translation 4.0 12.216 1 20
Osa06LNT0332800.2 osa-miR1427 Translation 4.5 14.61 1 21
Osa06LNT0332800.2 osa-miR1435 Cleavage 3.5 11.421 1 20
Osa06LNT0332800.2 osa-miR1861e Translation 5.0 18.009 1 22
Osa06LNT0332800.2 osa-miR1861g Translation 4.5 18.009 1 22
Osa06LNT0332800.2 osa-miR1861k Translation 5.0 18.009 1 22
Osa06LNT0332800.2 osa-miR1861m Translation 5.0 18.009 1 22
Osa06LNT0332800.2 osa-miR2095-3p Cleavage 4.0 18.764 1 20
Osa06LNT0332800.2 osa-miR2120 Cleavage 5.0 13.922 1 24
Osa06LNT0332800.2 osa-miR2929 Cleavage 4.5 14.686 1 21
Osa06LNT0332800.2 osa-miR5156 Cleavage 4.5 15.561 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0332800.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0332800.2 6 AsTol Resistance or Tolerance Other soil stress tolerance RZ516 RG213
Osa06LNT0332800.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0332800.2 6 nan Morphological trait Seed RG138 RZ398
Osa06LNT0332800.2 6 qRCRJ-6 Physiological trait Source activity RM217 RM402
Osa06LNT0332800.2 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0332800.2 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0332800.2 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0332800.2 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0332800.2 6 nan Morphological trait Seed RG138 RZ398
Osa06LNT0332800.2 6 qRCT6b Resistance or Tolerance Cold tolerance R1954 RM253
Osa06LNT0332800.2 6 hr6 Physiological trait Eating quality RM190 RM253
Osa06LNT0332800.2 6 alk6-1 Physiological trait Eating quality RM190 RM253
Osa06LNT0332800.2 6 Ps-4 Others Others nan nan
Osa06LNT0332800.2 6 rrsd6b Resistance or Tolerance Drought tolerance RM253 RM314
Osa06LNT0332800.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0332800.2 6 QGt6b Physiological trait Eating quality RM253 RM314
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
Osa06LNT0332800.2 6 5279236 Lemma-and-palea-pubescence 8.734972 -
Osa06LNT0332800.2 6 5281882 Panicle-type 10.75035572 -