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

>Osa03LNT0220600.2

GTGGCATCTCGTGATTTTAAAGGATTGTTAGAAGCATTCATTCTCAACACACAGCCCATGTAGGATGAGCTTATGAACCAATTTAATATCGGTCAAAAACTGAAAGCAACACTACACATATTGCACGCATTGCCAAGGATCGCAACAATAAATACCTCATCATGTTTGCCCCTAGCTCACAGATATGAACAAAGAAAAAGAGAAGACTTAATTTGTCATTGGCAACATGGTGATCAAGCAGGCACATCGCACCGGCGCCTCCCATTTCAGTTATAGCTGGCCAATACGATCCTGAAGCATCTGCATGAGTTTGGGGTTCTGCTCCAAAAGCTTACAAAGCTTGTCACGATCACTCAACAGACTCTGCAAGAAGTAGAGTAGAAGACGTCAAAATCAGTCTGAATAGCTTCTGGAGATGAAAAAAAATGATTTAAATTCATCCCAGAGTCCATCTGCTGTTGTGCACTCTGCCCAATCGGTTGCAAGACAGACTCCTGAGTCTGATGGTAAAATTGTAGTTGTGGAACATGAAGCTGGTTCGGAAACTGCAATGGCACCTGAGGCTGAATAGTATTTAGTGGATATGGCATTGGCTGCTCTTGTGGTTGTTGAAGAGAACCTTGGAATGTTTGAGATGGATGTGGCTGTGGAGGTGGTGGTGGTGGTGCTCGTGGTTGCATTGAGGAAAGAGAAGGCTGGGGATTAGAGACACTCTGTGCAAGGCCAGATGAGAGTTGGATTTGAAGAGGAGTGCCAAAAAATGGAGGAGTTGAAGGCCTACCAATTATATATTGTGATGCAAGTGATGGCAAAGAATTTGAAGCAAGTGCACCACCAGATGCGGGATTTGTCCCTAAAGTTGCATCATTGATAAGGGATGCAGGTGGAGAAGGCTGGAGAACACCAGACCCTCCTTGATTATACAGTGATCCTGGAGGCCCAGAGTCCATTGCAGCATGTTGGGTTGCCAGAACTGGCCGTAGAGGAAGGGGTGACACTGGCCGAGTAGATGAACCAGAGCTGAGGTGTTCCATAGGGATCCTATTTACTGGAAGTGTGCTCCACAAGAACTTGGCATCAACACTTGGCAATGCATTTGATGATGAATCACCGGTGCTTGGTAGGACATTTTCAGTTTGAACCTGATGCCCCACAAATGAAGGCATACAAGCGTCAAAAGACTGCATTAGATAACTAGGAGGAAAAGGTGGTGGCCCATCTCTAGCAATGTAAGATGATGGTTGCCTTTGAATTGAATCAGGATTTTGTAGAGACGTAGAAGAAACTGGTGGGGGCATCGGTGGCAAAGGTGGCTGGCTGTTGTAAAGTGTACGATCATGTCCATGAGATCCAGAGGACACCGAACTCTCAGCCAGCTTATGTGGGCTTCTTTTCCGATGCATATTTGGAGGTAATTGTCGCAGTGTTGCTTGTGCAGCATGTGTGCTATAACCAGGTATAACCTTCAATCCAGTAGTAGGAGAGATAAATGGAGATTCGTCCGCATGATCGGGGAACATGACCTTCTCTGGGCTAGAAACTGAAAATTTTCGCTCAGAAGGGATGTTAGATTCTTGACGGATTGCTGTCTGTGAAGATATGACAGTTTCACAAGCTTCATCACTCTCAGATACAACTGTACCAGAAAACAGATTTATTCCATTCTGCTGATTTTCTGTCTCATCAACAACGGGACCTGGAGAGTTCTCCCCAATAATGACAGGTGGTGATTGCAGACTGTCATCTGGTTGAGGAAAAGGAAGTTTATCATCTGATCCTGACTCCTCATCAAAGATTATGTTGATTTCTTGATCATCATCAAGATCAGCCTTTGGTTGTCTCGGTTTCTCTGGCTTGGTAGAGACATTGTCATCCAAAGTTGCCTTACTTCTTACCTGAGTTGCATCCCCAGATGGCGCTAGAACAGGATTTTGACGTTCCCTCTGTCTTGCCATAAATTCATCTACATGAATGGATGGAGGCCTTCCACTAAGTGCTCCACGTGGAGTAGAACTTACAATATTTGATGCACTGCTTGCACCTTCTATGTTTCTCTCTCTTGCGACATAGTCATCAACATGCATTGAAGGTGGTCTACTTGTGTTCGGTTTCCGCTGGCGGAAAGTGTCTCTACGCGTATGACCTATAGAGGCACTAGGTGTATTTAAACCTCGAGAGAACTGTCCACTAGGTTCATGTGTTTGATTGTCCCTTACACGTCTACTTGCGCTATCTCCTAGTGCCAGTTTTCTCCTGGCAGATTGGCTCGGGATTAGCTGTTTATCAATAGAACAATCAGGCAACTCCCACACCATCCTCTTGCTAAAGTCAGACACTTGGCATCCAAAAGGTTCTGCAAAATCACCAAAAGCCTTCCAAGCATTGGTAAATAAAAGAGCAGGATCATCATTTACTGACACAAAGTCTATGGAAGGCATTAGATGAGAAGTCATGACAATATTGTGGAACACCCCAACTGGTATTGTGCTCTCTTCAAGAACCAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.851817
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0220600.2 3 19587179 A G
Osa03LNT0220600.2 3 19586265 G A
Osa03LNT0220600.2 3 19586579 T C
Osa03LNT0220600.2 3 19587323 T A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0220600.2 osa-miR5533 Translation 5.0 22.068 1 21
Osa03LNT0220600.2 osa-miR5815 Translation 4.0 20.686 1 24
Osa03LNT0220600.2 osa-miR810a Translation 5.0 12.555 1 21
Osa03LNT0220600.2 osa-miR1426 Cleavage 4.5 19.229 1 21
Osa03LNT0220600.2 osa-miR1876 Cleavage 5.0 14.17 1 24
Osa03LNT0220600.2 osa-miR827 Translation 5.0 23.499 1 21
Osa03LNT0220600.2 osa-miR2921 Cleavage 5.0 24.3 1 24
Osa03LNT0220600.2 osa-miR812n-5p Cleavage 4.5 18.286 1 24
Osa03LNT0220600.2 osa-miR5083 Cleavage 5.0 22.305 1 20
Osa03LNT0220600.2 osa-miR5144-3p Cleavage 4.5 14.495 1 21
Osa03LNT0220600.2 osa-miR5340 Cleavage 5.0 16.323 1 23
Osa03LNT0220600.2 osa-miR5522 Cleavage 5.0 16.648 1 21
Osa03LNT0220600.2 osa-miR417 Cleavage 4.0 11.11 1 21
Osa03LNT0220600.2 osa-miR443 Translation 5.0 12.026 1 22
Osa03LNT0220600.2 osa-miR2921 Cleavage 4.0 16.335 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0220600.2 3 An5(t) Morphological trait Panicle/flower C1677 R19
Osa03LNT0220600.2 3 sho2 Morphological trait Dwarf nan nan
Osa03LNT0220600.2 3 gw3.1 Morphological trait Seed RZ672 RZ474
Osa03LNT0220600.2 3 qGW-3 Morphological trait Seed G332 C80
Osa03LNT0220600.2 3 qGL-3 Morphological trait Seed R19 C1677
Osa03LNT0220600.2 3 qLWR-3 Morphological trait Seed R19 C1677
Osa03LNT0220600.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0220600.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0220600.2 3 ccf3b Physiological trait Source activity RM16 RM282
Osa03LNT0220600.2 3 ccfs3 Physiological trait Source activity RM16 RM282
Osa03LNT0220600.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0220600.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0220600.2 3 qDLR3 Resistance or Tolerance Other soil stress tolerance RM338 RM2453
Osa03LNT0220600.2 3 nan Morphological trait Shoot/Seedling RZ284 RZ403
Osa03LNT0220600.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0220600.2 3 nan Morphological trait Panicle/flower RZ403 RZ452
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