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

>Osa04LNT0286900.1

GTCCAATTTAGTAAACAGAAGTCGCTTGAGGATCATGCACAAGGCATCGGAATACAGATAAAAAATTTGAAAATGGTGTTTAAATGTGATTTTAAGTTCTTTACACTTAGCTTCTCACAACATAATATCCTGAATTGCCTCAATTCAACCATTTATGACGGTTTTCAGTCATACTTTATGCTTGTCAAAGGTGGTCTTCTGGAACATCTCTTTTAGGACACCACATACTGACATACATTTATGAAAAAGAAGTGCTGCATCAAAATTGACATCGGAAACCTCTACTTTTGGCCTAAATTAGCGTGCCTTTGAGTTCCTTACAGTTAAAAAGGGCAGGTCTAGTATATCTTCATAGTCTAGACGTAAATAAGATTCAACAAATTAACTTAGTAGTATAGACTATATAATTGTACTGTTTAATATTAGAGTATATGGTAGTTAGAGTCATATTAGGATATGATTGATTTATGTGGATTTTTTCCATATCTGTAATCCTTCCTTATCTCATGTATCTATATACTGGCCCCTGAGGCTCTAATACCATGTTAAATATAATACTTCCTTATCTCTACCCTATTTATTTCCTATATATGCGGGCTCCTAAGGCTCAATAGAATGTGTCCAATATTCGCAGTAATCTCCTCTTCCTATACTATTCAACATTTATTTACCTGATCATTTTTGCTGAACCAAATCCAAGACTGTCATGAAATAGGCTTGTCATGTACTTCTTCTGTGCAAGGCACAAAAGCTCTGAGCTGTTGTATATAGGGGGCAGGTATGCTTCCCCATTCCCATCTTTGTGTTTATTCCATAATTCGACAAACTTCTTGTGGAAAAAATTCCATGAATCTTCAATTGTCTTCAAGATCC

Coding Potentia
Explanation CPC Score
noncoding -1.16792
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0286900.1 4 34158015 G T
Osa04LNT0286900.1 4 34158848 A T
Osa04LNT0286900.1 4 34158856 T A
Osa04LNT0286900.1 4 34158877 C A
Osa04LNT0286900.1 4 34158895 T C
Osa04LNT0286900.1 4 34158998 A G
Osa04LNT0286900.1 4 34159002 A G
Osa04LNT0286900.1 4 34161486 A G
Osa04LNT0286900.1 4 34159311 T C
Osa04LNT0286900.1 4 34158933 A G
Osa04LNT0286900.1 4 34159290 A G
Osa04LNT0286900.1 4 34160621 C A
Osa04LNT0286900.1 4 34160779 C T
Osa04LNT0286900.1 4 34160855 C T
Osa04LNT0286900.1 4 34159362 T G
Osa04LNT0286900.1 4 34159436 T C
Osa04LNT0286900.1 4 34161477 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa04LNT0286900.1 DTM_#DNAt_MULE_japo_Os0229 Chr4 + 34160402 34160932 530
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0286900.1 osa-miR5532 Translation 4.0 13.729 1 22
Osa04LNT0286900.1 osa-miR160a-5p Cleavage 5.0 18.822 1 21
Osa04LNT0286900.1 osa-miR160c-5p Cleavage 5.0 18.822 1 21
Osa04LNT0286900.1 osa-miR1873 Cleavage 3.0 8.132 1 24
Osa04LNT0286900.1 osa-miR2921 Translation 3.0 13.537 1 24
Osa04LNT0286900.1 osa-miR5488 Translation 3.5 11.659 1 21
Osa04LNT0286900.1 osa-miR5492 Translation 3.5 16.56 1 21
Osa04LNT0286900.1 osa-miR5494 Cleavage 5.0 9.317 1 21
Osa04LNT0286900.1 osa-miR160b-5p Cleavage 5.0 18.822 1 21
Osa04LNT0286900.1 osa-miR160d-5p Cleavage 5.0 18.822 1 21
Osa04LNT0286900.1 osa-miR160e-5p Cleavage 5.0 18.822 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0286900.1 4 np4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0286900.1 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0286900.1 4 np4 Morphological trait Seed RG143 RG214
Osa04LNT0286900.1 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0286900.1 4 nan Morphological trait Panicle/flower RG143 RG214
Osa04LNT0286900.1 4 nan Physiological trait Source activity RG143 RG329
Osa04LNT0286900.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0286900.1 4 nan Morphological trait Panicle/flower RG620 RG214
Osa04LNT0286900.1 4 QGn4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0286900.1 4 QGwp4 Physiological trait Source activity RG143 RG214
Osa04LNT0286900.1 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0286900.1 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