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

>Osa04LNT0252000.3

GTACATAACCGTTATACACCTTAATAGAAACCATTAGTTCTTGAAAACACACAAGAAAGCCATGCTCATCATTAATTTACTACATCCGACATAAGCAAGCAGTTCAATAACACAGGAAGTGTATAGTTTATTTTTCAGCTGGTTAGACTGAGTTCTGGCAGATTCAGGCTGAGAAGATCATTATCCTCAATCAGTTGCTCTCAGTTGCATCCAGGCTCCATAGTGTCCTTAGGAATCACAACCAAGAACGTAGCCCTGTAGGTTGGCCTCCTGCAGGTTGGGCTGCAGTGGCTGAAGCTTTGTACTACTCATGAAGCTGAGGTGAAAGCTGCAGTGCTGTCATGGAAGACTCGGCATCCTGACAGTACATCTGGCTGCTGCACACATCCCACAATGGAAATGGCTTTGGATTGACCATCGAAGCTGCCTGGGTCTGCTCACCAATCAGGTTCTTTTGACAAGCACAAACAAGTTACTCGATAGAGAATCCGTGACATAATTTCACTTGAGGATAAATCCTTGTGCCGAGTTGGAATTGGCACAGATAATTGCTCGTCTCCTGGAATTGGCATCTCCTTTTGGAATGGAGAGAGAGAGATCATAACTTGGTAGTTTAAACTAGTGTAGTAAGGTAGGATAGTACAATACTGAACAAGTGTATCCTTTTGTTAGGTCGTACCCGGTTGCACATCTCAAGAAGCTGCTGATAACGTAGCTGTTGCTTCCTTAGACGAACTTTGTACAGAGAGAACTCAATCTTCTGCTCAAAATTACTCAAATCTGCGGAGATCTCGAGGAATCCTATATGTGGATGTATCAATTTCCAAAATCTCAAGCGGAAGATGAATAGTCTAGCTTTTAAGCTGAGAAGTTTCAACTTTCGACGCTTCTGGCAGTTCCAGATTGCATCTACTTAACAATCATGAGAAACAAAAACTGCTGATTGGTCAATGTGGTCACCAATATAGGCTGCAACTTGATGATGCACATGATCCTTGAAAAATGCCACAACAGTTACACATTTGCGGCTTTACCCATAAAAATAGCATTGTCCAACACAGTACAGCCCATCTATTGAAGTAGTATTCAAATGGATATTAACTTACAGCTTCTTTTCAAGCTTTTTTTGTTATCTCACTGGCCGCAAGCTCCTTTTTCTTCTCATAATCCTTCTTAGACAGACCCTCTCAATCTTCTATCCCTGCAGTTGTAAAAATATGAAGTATACAATGTTCTTCAGGATACTTACAAATATGCTTCCACAAGGCTTCTCCAAATTAGCTCAGTCATCCTTTATTTTGCAGTTATCTCATCAAGCTTCAGAAGGATCCTTTCATTTCCAAAATTTTTTCACCTCCAACTGCAAACTGATGAACACTGCCATTCAGCTCCATCCAACTGCAACCTTTCTTCTTCCACGTCCCCTGGACTTCCATTACTCCCCTTACCTCCTTAACATCATTCCAGTTTCCATATTCTGCATATATATTTGATAAGAGCACTTGTGCTCCACCATGATTAGGGTCCAACTCCAAAATTTTCTTTGCAGCAAACGTGCCGAGCTCAAGATCACCATGCATCCGGCATGCTGCTAACAAAGATCCCCAAATGACCACATTTGGTCTTAAGTGCATGGACTGTATCAGGTCAGCAGCTTGTCCAAGAAGTTTTGCTCTTCCCAAAAGATCCACCATACAACCGTAGTGCTCATGCATGGGCTCAATCCTGTATTGCTGGACCATAATTTTGAACAATAAACGGCCTTCTTCAACTAAACCAGCATGACAGCAAGCATAGAGCAACCCAAGAAATGTCACTCCATTGGGTTGAATCCCTTCACTTTTCATGTTCTCAAAAAGGGTTAAGGCGGATCTTCCATCACCATGCATAGCAGATGCAGTAATTATGCTTGTCCAGGTGACAACATTCTTTTGAGGCATTGCATTGAAGACATCCAAGGCAAGAGTTAAACTCCCACATTTGGAGAACATATCAATAAGAGCATTTCCGATGGGTAATATCTTACACATGCTATGATTCTCCACGAAGGAATGGATACATCTAGCTTTTTCAAGGGCACCAACATTAGCACATGCAGATATTACACTCAGCATGGTAATTTCATCAGGTTTGACACCACTCCGTTGCATATCATGGAACAAATTCAGCGCTTCCATAGGTTTGCTGCTTTCAGCATATCCTGCTATCATAGCACTCCAAGATACCACGTCCTTCGCTGGCATTCCATTGAATATGGAGTGAGCAATCTCAACTTTTCCATTCTTGGCGTATCCATACACCATGGTGGTTGATAATACAATTTCCTTTTCTGACACCCTATTGTACAGCTTTTCAGCCATTTCCATGTCTGCACAACTAGCATACATGTTCATGAGAGCACAGCTGACTTGAGCATCAATAAGAGTATCTGACACCAACATGTATGAGTGGATAGCCTTTCCAAATCTCAAGTTTCTTGTATGAGCACAAGTTGAAAGGACAGTAGCAATAATCACTTGATCAGGAACAACTCTTGATCTCTTCATGCTATGAAAAAGCAACAGGGCTTCTTCATAGTTTCGGGCCTGACAATAAAATGTAGAGGACAACTTTCCGATGCTTGTTCAACATATCATTGGAAGAAGGATCCAGATTGGCCTGATCCCGAGTTTCATTTTGAGTCTTTTTCTTTGCGGCAACTGTTTCAAAATAAACACTTCAAATCAATAGCAGGACCTTCTTTCTTTTCATATTTCAGACTGTTGTGGCTCGATGACGGCGGATGAGTGCTCGACCCATCGGCGCTCCAGGGGAAACCACTTGAGCACCCTCCCGTCCGACACGCCCGTGTACGGGCCGTCGCCGTCGCCGTCGCCGTCGAACGCCACGCTCTCCGGCCCAACCGCGCCGCTGGAGTCCACGGTGATCAGCACGTCGTCGCTCCGGGACCGGGAGTCCAGGGACAAGAACAACGCCGCCGCCACCGCCACGGCGGCCGCGAGCACCACGAGGCTGGCGTCGGCGCGTCAGCGCACAGCGCACTGCCCTGCCGCCGCCGCCTGCTGCCCGCCTCGCCCCCGCGTCGCGAATCGCCAGCCGCCGTTTGGGGAGGGGGAAGGGGAAGAATCGAAGAAAGGAGCTGGAATGGGCTGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.961827
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0252000.3 4 8085016 A T
Osa04LNT0252000.3 4 8085138 G A
Osa04LNT0252000.3 4 8085466 G A
Osa04LNT0252000.3 4 8084882 T C
Osa04LNT0252000.3 4 8083806 A G
Osa04LNT0252000.3 4 8084747 T A
Osa04LNT0252000.3 4 8085071 G C
Osa04LNT0252000.3 4 8085829 A G
Osa04LNT0252000.3 4 8086081 T C
Osa04LNT0252000.3 4 8088384 T C
Osa04LNT0252000.3 4 8088389 A G
Osa04LNT0252000.3 4 8088391 A G
Osa04LNT0252000.3 4 8088431 T C
Osa04LNT0252000.3 4 8088790 G A
Osa04LNT0252000.3 4 8089490 G A
Osa04LNT0252000.3 4 8089612 A C
Osa04LNT0252000.3 4 8089623 G A
Osa04LNT0252000.3 4 8090473 C A
Osa04LNT0252000.3 4 8085286 A C
Osa04LNT0252000.3 4 8087811 G A
Osa04LNT0252000.3 4 8088204 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0252000.3 osa-miR5542 Translation 4.0 5.598 1 21
Osa04LNT0252000.3 osa-miR5834 Translation 4.0 9.083 1 21
Osa04LNT0252000.3 osa-miR6253 Translation 3.5 6.317 1 22
Osa04LNT0252000.3 osa-miR6253 Translation 5.0 20.355 1 22
Osa04LNT0252000.3 osa-miR164a Translation 3.5 18.324 1 21
Osa04LNT0252000.3 osa-miR164b Translation 3.5 18.324 1 21
Osa04LNT0252000.3 osa-miR166k-5p Cleavage 4.5 14.561 1 21
Osa04LNT0252000.3 osa-miR393b-3p Translation 4.0 14.618 1 21
Osa04LNT0252000.3 osa-miR164f Translation 3.5 18.324 1 21
Osa04LNT0252000.3 osa-miR1857-5p Cleavage 4.0 22.306 1 21
Osa04LNT0252000.3 osa-miR1857-5p Cleavage 4.5 14.117 1 21
Osa04LNT0252000.3 osa-miR1862e Translation 5.0 20.882 1 24
Osa04LNT0252000.3 osa-miR2873b Cleavage 4.5 17.669 1 21
Osa04LNT0252000.3 osa-miR5497 Translation 4.0 14.208 1 21
Osa04LNT0252000.3 osa-miR5506 Cleavage 5.0 21.248 1 21
Osa04LNT0252000.3 osa-miR1847.1 Cleavage 5.0 10.166 1 21
Osa04LNT0252000.3 osa-miR1861n Cleavage 4.5 14.975 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0252000.3 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0252000.3 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252000.3 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252000.3 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0252000.3 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0252000.3 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
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