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

>Osa04LNT0286500.2

GGTCAATATATTATTGAAGAGATTCAGAATAACGTTGCATCAGAAGTGGCAATGAGTGAGCGATATTAGGCGGTGTAAATGTCAAGTCACCATGCTGGTTTGAGAAATAGCTGAAGAAGAGAAAGAAAAAAAATGGTACGATTACTTTAATCTTTCTTAAGACAAGATATGGCCACGGGCTCATGCTGACTAGACTACTACTCCCGTCCCTTAATATAAAGGATTTTGATATTTTTCTTGCACTGTTTGACCACTCGTCTTATTCAAAAAAATTTGCGCAAATATAAAAAACGGAAAGTTGTGCTTAAAGTATTTTGGATAATAAAGTAAGTCACAAACAAAATAATAATTCCAAAATTTTGTGGATAAGATGAATGGTCAAACAGTGCGAGTAAAATGTCAAAATCCCTTATATTAAGGGACGGAGGGAGTACGTCAGAACTGACCAGAGAATAGACATAGAAAGGTGTCTTGTTGCATTGCGATCAGCCGATCAAGGGAGAAAGGGAGCAGCTACAGGGCCAACAGGTGAAATATGTCGCAGCTGGTTGATCAGCTGGTGCATCCCTCCTGGATGGGCATGGGCAAGCCCATCTCCTAGGTAACTGAAACTTTATTAAATTTGAGGTCCAGATGCTGAGTGAATCAATAGTCATGTTGGATCAGTCGATTATTCATGGAAAGTTGTGATGTATACATTCTCTGACTCACGACGATAATTTTCTTCCTGGTAGACCTGTGGATATTTTATAGTTAAAAGTAACGGGATATTTTTGCTAAATCCTGGCTGGTAATCGAAATTCAGCATGTTTTCTACATGTCCTGATTGTAAGTTTCCAAAAGAGAATTGCTAGTTCAACAGCAGTGCATTAGGAATCTACTTGCCCTTACTTTCATTTGGCATTAAATTATGACAGGCTCAGGTTTTCTCTCACTAAAACAAACAAGAACTGATGGCCACTGAGGCATAACTTAAATGTCTAAAATGACAAATCTGAATGCCCTTCGAGAGTAAAAACATACCGTGGCAGCTCAAGGTAGTTCAAGTAGAAGACAGAACGAGTGTGAAGTCTGTGTAATTTGCTGAACTAGATAGCCCTTCACCTTTATGGCCTCAATCAGTTATCTGAAAAAGCTCTGTTTTGCTTTACTCTGCTTTTCTTGATAGCACTATTACGTTGAAGTTCACCGAGTTGGGAATGTTGTGCATGGTGGCCTTAATGATATTCACAGCATCCTGCAGTAAGCTTTTAGAGGATGATGGGCCATGATTTATTGGTCCAGGCTTCATACCATCAAGCTCATAGAGTGTTCCATCACATTCGACAAAACATATATAATGCTCTTCAACGTCATCAGATAGCTTTGTGTCACCGGCACTGGCAGCCGATAAGTGAGCTCTTGCCATGTCATCATCCTTCTCAAGAAACACAGCACGCTCGTATGAAGTCATGCCAGATGTTGATTTGATAAACATGTCCAAGAAAGAATTCTCCGACAAACTGATTTCTGAATATGCATTTCCAACAGCATGAAGTAGCGCAATAGTTCCACAAGCATTTCCTAGTGATTCAATTTGTTTTATGAAAAACAAAGTTTCCTTCTCTCCAGTAATTAAAAGATGCTGTGAAGGATTACTTGCATCCTGCACCGAAGTAGGGCTAAGTGTGTAAATCAAGTAAAGGCTGAAACCCATAATAGTACTAAGCTAGTAAATGTACATTAAAAAGAGAGAGATTCTTTACACACATTTCACAGAAACAATCAACATGTCCATATATCATCATAAAAAAACACATTTAATTATTGGTTGAGATGCGTATATCACAGAGTAGTTGAACTATAAATGCATAGAGCCATAGAGGTTCTATTACCCTTTTATATAAGATTATGCACCTAACAACCAGGGAATATCTGACAGAATATATAAATGGAGATATTAAATAGTGAACCTTCTGCCCCAATTATAGCTTATTAGAGATGTCAAACATACATAACAAAGGTCATGGCCATTTTATCTCTCCTCAACAGGTCAAACATGCCACAAAACTAGTTTTTGGGCACTCTTGTGAAGCAATGGGGGTATAGTAACAACATTAAAACAATCACTGAAGCACCTCAGTGATCTCATGTCTATACAGCATATGAAGCACTGAAGTCTGGAACTTGTACATTAATCTGGAGAGATTTCAATGATGACAAAGAGATATAGTGTTCAATGGTCCTTTTTGAGAAGAACAACTCCTGAAAATGATATTTAAGAGTACTGACGTGGGTGTAGCATCGAATTTAGTCGAGCACACGGAAGCCAAGTCAAAAAAATTGAGACACGCGACCTAACCGGCTATGCGAAGGAACAGATATAAGCTCCAACTTGACCCTCACAGCAGTATACATAGTTTCAGTTAAGACACATCGCAAGATGATCATTGATCATCCACTTATATTGGAGTTACACGGTTGTAGAAGGCAAATCAGGAAACATTATGCATTTGTATGGGTGAGCGGAGATCGAGCCCCTGATTTTTCTCAAAACTCGCGAAACAGAAAACAAATTCTGGAGCAAAGTGATGAATGCACCTGGGTTGGATCGGGGAAGCAGAAGACGACGGCGAGCACAGGCTGGGGCACCATCTCCAGCGCATCGGCGTCGAGGCTGTACACGTCGTGGAACTCCGCCACGTCCTCCGGGACACCCAGCGACCACATGAGCTGGTTGAATACGTCGGGGCTCGACTCGAGCGGCGGCCATCTCTCGCCGGGGGAGACCGGAACCGGCGGCGCGGCGGCGGAGGGCACCGCTGCCATGGGGGATTCGCCGGGGAAACCTCGCCGCCGTCGGCCTGGAAACCTCGGGCCAGTACTCCAGTAGTAGGG

Coding Potentia
Explanation CPC Score
noncoding -1.16619
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0286500.2 4 34075211 C T
Osa04LNT0286500.2 4 34073352 A G
Osa04LNT0286500.2 4 34075463 C A
Osa04LNT0286500.2 4 34075704 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0286500.2 osa-miR5526 Cleavage 4.5 15.898 1 21
Osa04LNT0286500.2 osa-miR5079b Cleavage 3.0 15.036 1 22
Osa04LNT0286500.2 osa-miR5079b Cleavage 4.0 18.345 1 22
Osa04LNT0286500.2 osa-miR167a-3p Cleavage 4.0 17.738 1 22
Osa04LNT0286500.2 osa-miR818a Cleavage 2.5 8.488 1 22
Osa04LNT0286500.2 osa-miR1438 Translation 3.0 10.507 1 22
Osa04LNT0286500.2 osa-miR1853-5p Cleavage 5.0 17.738 1 24
Osa04LNT0286500.2 osa-miR2101-5p Translation 4.0 17.341 1 22
Osa04LNT0286500.2 osa-miR2873a Translation 4.5 11.927 1 24
Osa04LNT0286500.2 osa-miR3979-5p Cleavage 5.0 16.574 1 20
Osa04LNT0286500.2 osa-miR2873b Translation 3.5 15.043 1 21
Osa04LNT0286500.2 osa-miR5079a Cleavage 3.0 15.036 1 22
Osa04LNT0286500.2 osa-miR5079a Cleavage 4.0 18.345 1 22
Osa04LNT0286500.2 osa-miR5516b Cleavage 4.5 15.401 1 21
Osa04LNT0286500.2 osa-miR6252 Cleavage 4.5 8.544 1 23
Osa04LNT0286500.2 osa-miR818b Cleavage 2.5 8.488 1 22
Osa04LNT0286500.2 osa-miR818c Cleavage 2.5 8.488 1 22
Osa04LNT0286500.2 osa-miR818d Cleavage 2.5 8.488 1 22
Osa04LNT0286500.2 osa-miR818e Cleavage 2.5 8.488 1 22
Osa04LNT0286500.2 osa-miR5516a Cleavage 4.5 15.401 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0286500.2 4 np4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0286500.2 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0286500.2 4 np4 Morphological trait Seed RG143 RG214
Osa04LNT0286500.2 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0286500.2 4 nan Morphological trait Panicle/flower RG143 RG214
Osa04LNT0286500.2 4 nan Physiological trait Source activity RG143 RG329
Osa04LNT0286500.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0286500.2 4 nan Morphological trait Panicle/flower RG620 RG214
Osa04LNT0286500.2 4 QGn4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0286500.2 4 QGwp4 Physiological trait Source activity RG143 RG214
Osa04LNT0286500.2 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0286500.2 4 gpps4.1 Resistance or Tolerance Drought tolerance RG214 RG620
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