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

>Osa01LNT0032400.1

GGAGTATTATGGCTATAATAACCTGTAAAGTTTTCAAAAAAGAAAATCACCAGAACCATTAGCACATTTTAATCCTATACAAAAAGAGCTCCTTTGTATAAATATATATGCACTGTAGGAGAATCTCCTACAATATTTACTTTTAAAAAAAAGCTCCTTTAAGGTCTCCTTTGGAGCAGAAAGAGAACACATCTGCTGTTCTCCTTGACAACTAAAGTATGACAAGCAGAGTCCTTTCCATCACCTCACCAAGATTCCTTTGCACCTGAGTACCTGACATAACAAAACATAACTCCATGCTCGAGAACCGGCTCTAATCATTTCCTTTTTTTTTTCTGTTCTTGCTTTCTTCCTGCAGGGCCATGAAGATAAGCTATTGGTCACGGTTTTGAGATCCATCAAGTTCATTGCTCAACATATGGTGAAGAAGAATATCAACCATGGTCCCCTTTGTCCTCACACGCACAGATCGCCGCCTGTTTCTTCCTTCCAAAGTAGGATCCTGGATATCAGCTTCGCCATCTTTCTCCAGTTCCATCTCAGCAAAAAATGCCTCCAACACAAATGCTACAATCAGATTAAGCAGCAGTAATACTGAAATGAGGTAAAAGCTGACAAAATAAATCAGGCTCCAATAACTTCCAGTCAATTGCCTGTAGCTCTCCATCCAAGCTTGCCAATTGCCCATCACTAACAAATTGAACAGAGTTACCATACCACTTGGATAGTCATTGAAGTTAAAAAGAAGATAGTCGTTACTGAAGAGATCGGTTTCTTCTAGTGTTGGATTTCCTGCATACACAATGCCCCCAAATATCTGCAAACCAAGGGAGCAGTAAATGCAAAGGGTGCAGAATACAATCCCCAAATATGGCATCAAGCTAGACATCAGAGTAAAGAATGTTGCAACAAATGCTCTGAAACGCCGAACTTGCAACAGAATTCTTGTCAAGCGTAACATCCTTCCAAGAAGAAGGTACCGAATCCATTCTCCATTTGAAAGAAAAGAAAGCTTCGATGGGAAGGCAAATGTTAGAGTCTCTCCAATAAATATAGTCCAAGTAAGCACAAAATCAAACTTGTTTTGACCTTCCATCCAGTAGGCACCAAATCCTAATGAAAATATTTTGAGTGCCATCTCTATAACGTAAATCCATCCAAAGACAAACTCAACTTCTTGCCACACTTTCTGCGAGGAGCTGTTTTCTATATCCAGCGTTGTTTCAATAATGACAGCGACTAGATTCATCAGAAGAACAAAAATAACAATATACTCAAACAGTGGGCTCCGCACAAAAGATTTCAACCATTCACACAGTGCTGAATGATAGAAAGATGGATACTTCTCGAGATAGGATGGAGGTGGTTCTTTCTGGAATTTTATTGCAATGGTATTGCACAGTGTAGCAAATTCTTCAGAGGTAACCTTAAAATCACCACTCTGATCAAGCTCGGCAAAAATTAATTCAAAATCTTCCCTTGAGGTTTTAGGTAACGATCTACAAAAGGAGGCACCATTCTGTGAGACCCATAACTGATCCAGGAGCTAGCAGGAATTTGGTAAAATGCAAGGATAACATCTGTCGTCATCAACTTTGGAGGGGAAGGGATGTCTCCCTACCATGTTATGATAATAAGCAAAACTAACTTACACTTACAAACCATTAAGTTGTTGGTTCAATAAAATCAATAAATGCAAAACCGAAAAGTGGACAGCATGATATGCTGCAATTGTAAGAACCATGTTCTAGGCTTCTAGATATTAATTTGACATTTTCTACACAATTAATTCTGCTGATTTCTGATATATGTTATGAATGTCAAAATAATGGAGCAAAACTGAAATAATGTAATTTGGAATAGCATTGAGATTGTAATAACGAAAGCAGACACCCATTCTGACCTGTGTTCTCTTCGAGATGGCATGTCATCTAATGAGTATTCAAGTACCAGTGCATCATCATAAAAATGGATATTTGGCTCTACAGACCAGTAAGGATGCCCATCTTCCAAAGGCAGTCACGTCATTGTTTAAAGGGTTTTTCTTTTGCTTACCATTTGCATGAGTTAGTTACCCTTTTCAGTTTTCAGTGTAAGGATAAAAAAAAAAAGACCTTCCTTAATGGATCGGCCACTTTCACAGATAGCATCAAGCTTGCACGGAAGTGGGGCAATTAGAGACTTCTTATACCCTTGGCATGGACATGGAGTTAATTTTGTTGGCATCTGGGTTGGGTGGGATCTCCTTCAGCACGTTTGCTAACCACTTTACCTACTATGGATTTAATTTTGAAGATTGGTTTCATGCATGACAGATATTGATTTTGACTGACTTAAGATTCCTTCAGGAAATGGAGGAACATCTCCACAAAAAAGATTGTAAAAATAAACTTACTACCCATAAAATGCAGTGTTTACATTCCTTGAGGATGTACCGGGAGGTACTGTATTTTCAGTGTAAATTTTTGGTACCTCCCTTGTGTTGAGGTACTTGAAGGTAGCACAAATTTAAGTTGAGGTACCTGTATTTGTTGAGCTCATCTAGTAATGATAGGCACTGTTCTTTGTTGAGATAACCCTGACCAGTAGCATCAATGATACCAAATGCCTTCTCTAGTATACTTTTCCTTGTACAGTCTGCCTGAGAAACTTGCTTTGCTAGCTGCTCCTTAAAGCTATCATAAATGACAGCAAGAATTAAATTTGTTAGGAAGTAAACTCCCAAAAGTACGTAGACAATAAAAAATAGTGAGGACCAACGAGAGCTCTTATAAGCAGGAACCCATACATCAGGATTATTGGAGGTGGTGAAGAGAATAAACATCTGATATAACGTGGTACCATATGACGAGAAAACAGTCTTTCCTTGTGGTGTATCCTCAAATGTTACATAAGCTAGCCAGCTTGCGAATAAGAGGAACAATAGTGAAAGGGCCAAAACATTAAGGTATGTCCCAACCATACCAACCAGTGTAACAGCACACATTCGCAGTTCCCTGATATTCATTATTAGAAACGCAACACGGATGTAAGGAGCTACTCTGAAAGGTTGGGGACTAAATGCAAACACCAGTATGTCACATGCTAAGATGAAGAGAAGAAGAACCTTCAGTTTATTTATTGTGTTCTTCCAGAATAGGTTTAAACCTTCATAGGACAGTGGATAGAAGATATCCATTACAAGAATAACAAGTGTGAGCCCCTCATATATGAGAGATTCAGTTTTGCTCAAGTATGGCAACTGCCCCAGAAAGTAAAGATCCCTTTGATCACAAGCATGTTGAGAATATCCCCGGCACCAGAGAGGCTTCTCGAGAAAATTCAAAAGAATCAAAGCAAATAGGTTAAGTGACCACAGCCAATCCAACCGGAGATACACAAAATAGAATCTCATAGCCCTCTCAAACCTTGTGTCATTCAAGACATCCTCAGGGATACCCACACCATCTTCTGCGAGGTCGACGAGGGCGGCCGCCTTCTGGTACCGGTTGCCGTAGGCGAGGGCGTCCGAGCGGCGCTGGTACTGCCTCGAGCCCCTCCACCCGCCGCCGCCGCCGCTGGTGTGGCTGCCGGTGCCGGACGACCCGGAGCCGTGGGAATGGGATATGTGCTCCGCCGCCTCCGCGATCAGAGGCGCCTTCGCCTCCCTCATCTCTCCCCTCTCCCTCATCTCTCCCCCTCTCCCTCTCCCTCGAGTGTGAGTGGATGCAGATGTGCAGGGAGAGATCTGGAACCGCGAGCGGAAGCGGAAGTAGAAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.979202
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0032400.1 1 27915935 A G
Osa01LNT0032400.1 1 27907244 C T
Osa01LNT0032400.1 1 27907047 C T
Osa01LNT0032400.1 1 27907707 G A
Osa01LNT0032400.1 1 27908019 A G
Osa01LNT0032400.1 1 27909166 G A
Osa01LNT0032400.1 1 27911792 A C
Osa01LNT0032400.1 1 27912847 A G
Osa01LNT0032400.1 1 27913273 C T
Osa01LNT0032400.1 1 27914212 C T
Osa01LNT0032400.1 1 27916341 A G
Osa01LNT0032400.1 1 27916682 A G
Osa01LNT0032400.1 1 27917071 C G
Osa01LNT0032400.1 1 27918764 A C
Osa01LNT0032400.1 1 27919702 A C
Osa01LNT0032400.1 1 27919727 C G
Osa01LNT0032400.1 1 27908195 C G
Osa01LNT0032400.1 1 27919616 A G
Osa01LNT0032400.1 1 27907294 A C
Osa01LNT0032400.1 1 27910437 C A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0032400.1 DTM_#DNAt_MULE_japo_Os1019 Chr1 - 27919494 27919620 126
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0032400.1 osa-miR5788 Cleavage 5.0 16.0 1 21
Osa01LNT0032400.1 osa-miR5822 Translation 4.0 16.098 1 21
Osa01LNT0032400.1 osa-miR5079b Cleavage 4.5 12.069 1 22
Osa01LNT0032400.1 osa-miR156k Cleavage 4.5 14.01 1 21
Osa01LNT0032400.1 osa-miR1429-3p Cleavage 3.5 16.367 1 21
Osa01LNT0032400.1 osa-miR1431 Cleavage 3.5 14.457 1 21
Osa01LNT0032400.1 osa-miR1881 Cleavage 5.0 17.358 1 24
Osa01LNT0032400.1 osa-miR827 Translation 4.0 17.647 1 21
Osa01LNT0032400.1 osa-miR2090 Translation 4.5 8.641 1 22
Osa01LNT0032400.1 osa-miR2864.1 Translation 3.5 12.069 1 21
Osa01LNT0032400.1 osa-miR5079a Cleavage 4.5 12.069 1 22
Osa01LNT0032400.1 osa-miR5155 Translation 5.0 16.265 1 24
Osa01LNT0032400.1 osa-miR5340 Cleavage 4.5 17.735 1 23
Osa01LNT0032400.1 osa-miR5492 Cleavage 4.5 12.106 1 21
Osa01LNT0032400.1 osa-miR5509 Translation 5.0 11.178 1 21
Osa01LNT0032400.1 osa-miR1862f Cleavage 5.0 14.399 1 20
Osa01LNT0032400.1 osa-miR1862g Cleavage 5.0 14.399 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0032400.1 1 nan Morphological trait Seed CDO118 CDO455
Osa01LNT0032400.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0032400.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0032400.1 1 yld1.1 Physiological trait Source activity RM5 RG462
Osa01LNT0032400.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0032400.1 1 nan Morphological trait Root RM3475 RM3494
Osa01LNT0032400.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0032400.1 1 QPh1b Resistance or Tolerance Submergency tolerance RZ527 RZ154
Osa01LNT0032400.1 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