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

>Osa03LNT0221100.2

CAAATTTATAAGTTACTGATGTAATTAACTCCCAACGGTAAGTTTTGTTAGGCAGAACAAAGTATAAATCATCTGATAATATTCTGGTCTCAAGAAATATAAAGCCCAGAAAAATGGGTCAGGAGAGGACAAAAAAACCTCTTCCACATCAGAAGCATGACATAGATGACCCATCAAAACTACTTGAAGCTCAGCTCAAATATCACAATTCTCGCTCTGAAACAAGTTTTTGGAATGCTTGTGACGACAAAACCAGCCCTTCTAACGAATAGGGTGGTACTGTGCTGATACTCGTTTCGGTGGAAGCTTACGGAGGATGAATAGGACAAGAGCAGAGGGCAGTATCTCCGTTAACATATAGTAAAAGAAATCCAGTATTGGATGATCCAAAACCTCAAGAGATAGATCAGGATCAAATGATGACATCGCCACCACAATGCATCTTATCAAGAAACATGTGAAGCAAATTGCTGTCACAGTCCCAACCTCATAGAGCTTCTTTCTGCGGCCCTTTGATTCAATCGGAAAACGCCTCAGCATGAAAAATAGCCTTCCACCATAAATTAAGAATCCCAAAAGAGCTAAGAATGAGACAACTGATATAAAAATTTTGCTCACAGGCTCTAGCAGAGGACTATCATTTGTCCCAAGGTATATCCAAATACAAACCTGGATTACATATATAACACCATTAACTGCCATGTATATAATCCTTAGCTTGTCAGTGGGAAGATTCTTAGCCTGATGGTATATTTCTGCCCAGAACAGCACAAGTAGCGTGTATGTCGAGAAAAATAGAAGACCAGGAAGATCCAATAACACCAAAGTATACACTTTTGTTTGAAAAAGGAACACTTGAGCATGAAATCCAAACACGACAGCACGAACTCCGTTTACAACAAAGTTCATCAGATGGAAAACCTTCTGGGTAGTCCAACCAAATTCAGGCACTCGCAACTGAATTCTGATCAATTGAACCTTCAAAAGGAAAGAAATTGTGGCCACTCATCATCTTGGAAGTTCAATTAAAGGTAAAATCACCATAAGATAATAATAAAATAATGTCAATTACCACATCAATGACATGTTGATATATACATAAATGGAACTAAACTTTATTCCGCTGTCCAAATAAATCCTAACATGTTCCCAGCCAAATACATAAATGTTATATAGGTAACACTCCACATCAATAATGACAAAACAAGGTTCGTACAAGGTTGATTGCACAATTTAGAAAAGAGTGAAGTACATGGGCGGTCTCTAAACTTGTGCCAGTGTGTCATCTAGGTCCCTGAACTCCTAAAATGCATTTTTAGGTCCCTTAACTTGCCATGTGTGTTATATAGGTCCAAACGGGTTCTAACCCACTCGATGCGCTGACGTGGCAATGCCACGGTGACACCTCCGTGTTAGTGGAATCCACATGTCAAGCATATATAAAAAATAAAATTAAAAACCATATTTTCTCCTCTTAGGTAGACAGAAAAAAAAGATAAAAATTCTAAGGTAGAGAGGAGAAAATATGTTTTTCTACTTATATTTTTTTCTATGTGACTGACACGTGGGTCCAACTAACACGTATGAACTATCGTGGCATGCCACATCAGCGCATGGAAGGGGTTGGAGCTCATTTGAACCTATATGACACCCCAAAACAAGTTCGAGGACACGAAAATGCATTTTGAGAGTTTAGGGACCTAGATGACACACCCGCACAAGTTTAGAGACCGCTCGTGCACTTCACTCTTTAGAAAACATTAGTGCAAAAAAATGTAACTATAGGAAGATAGCAATAGCAGTCTCCTCACTTTTCAGTAAGTGTAGGATCTCTTTGAAATGAAAAAGCCATCTGCTTAGATCACATGAAATGTATACTCCACAAGACAGCATAAACATTTTCATTGAACCAACTGAACTCAAAAGGATTAAGAAATGGAAAAACCATCTGCCTTTATCTCACGAAACATATACATATTCACTTAACCAACTATTATCTCACGAAACATATACATATTCACCTAACCAACTAAAGTCAAAGGAAACTTAATGTGTGACCGTGTGAGAAAAAGAGTCCTGCACAATGCAGTGCCATATGAGCTTCTTGGACTAAAACACGAGTGCATAACAATACCAAAGCAGTATTCCCTCCAGCGCGACGGCGGAGACGAGCGCGTAGGCGGCGGAGAGGGAGAAGAAGGCGCCGTCCTGCCACGCCGGCGACCCGTTCACCTCCTCCCACCAACCCCGCAGCGCCAGCGCCAGCGCCACGGCAGCCATCTCCGGCGTACCCGCGAGCGCCGTCGCCGTCGGCAGGGACGGCGAGGGGACCAGCTTCCTCATCTCCGATCTCCCACCTCTGTCTCTATCGCCGTGTCGTGGTGCGGGCGTCAGCGAGAGAGGCGATAGCTCCTCTTCCTCCTCCCTCCTCCGCCTCCTGGGAAGGAAAGATCGAGTCGAGGAGATTAGGCAGGCGGCGTCTCCGTCTCGAAA

Coding Potentia
Explanation CPC Score
noncoding -1.17697
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0221100.2 3 20421626 T A
Osa03LNT0221100.2 3 20421702 C T
Osa03LNT0221100.2 3 20423660 A G
Osa03LNT0221100.2 3 20423891 A G
Osa03LNT0221100.2 3 20424566 T A
Osa03LNT0221100.2 3 20424317 C T
Osa03LNT0221100.2 3 20425868 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa03LNT0221100.2 DTM_#DNAt_MULE_japo_Os0229 Chr3 - 20424010 20424517 507
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0221100.2 osa-miR7695-5p Cleavage 4.5 23.298 1 24
Osa03LNT0221100.2 osa-miR399h Cleavage 5.0 13.237 1 21
Osa03LNT0221100.2 osa-miR399k Cleavage 5.0 13.237 1 21
Osa03LNT0221100.2 osa-miR435 Cleavage 4.0 11.12 1 20
Osa03LNT0221100.2 osa-miR1850.1 Translation 3.5 19.419 1 21
Osa03LNT0221100.2 osa-miR2095-3p Cleavage 4.5 11.667 1 20
Osa03LNT0221100.2 osa-miR2905 Cleavage 4.5 19.291 1 21
Osa03LNT0221100.2 osa-miR1863b.2 Translation 5.0 16.037 1 23
Osa03LNT0221100.2 osa-miR5153 Cleavage 1.5 24.131 1 24
Osa03LNT0221100.2 osa-miR5338 Cleavage 4.5 17.582 1 21
Osa03LNT0221100.2 osa-miR5339 Cleavage 4.5 18.515 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0221100.2 3 qGL-3 Morphological trait Seed R19 C1677
Osa03LNT0221100.2 3 qLWR-3 Morphological trait Seed R19 C1677
Osa03LNT0221100.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0221100.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0221100.2 3 ccf3b Physiological trait Source activity RM16 RM282
Osa03LNT0221100.2 3 ccfs3 Physiological trait Source activity RM16 RM282
Osa03LNT0221100.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0221100.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0221100.2 3 qDLR3 Resistance or Tolerance Other soil stress tolerance RM338 RM2453
Osa03LNT0221100.2 3 nan Morphological trait Shoot/Seedling RZ284 RZ403
Osa03LNT0221100.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0221100.2 3 sho2 Morphological trait Dwarf nan nan
Osa03LNT0221100.2 3 nan Morphological trait Panicle/flower RZ403 RZ452
Osa03LNT0221100.2 3 An5(t) Morphological trait Panicle/flower C1677 R19
Osa03LNT0221100.2 3 qGW-3 Morphological trait Seed G332 C80
Osa03LNT0221100.2 3 gw3.1 Morphological trait Seed RZ672 RZ474
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
Osa03LNT0221100.2 osa-MIR5153 92.308 208 1 206 4.14e-80 294
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus