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

>Osa03LNT0209600.1

TTGCAAAGAGACATGGAAAACTCTAAAGGACAGACTGTTGTGCTCAGCACTGGTTTGAAGGACAAAAATCGTGCTACGGATATGATGGATGATGCTGATGAGGAGGAAGAGGAGGCGGCATTAGAAGATTTCAGGATTTCTGAGGATGATGAGGATGAGGATGAGGATGAAGGGGAAGATGAAGAAGTGGAGCATTTTGGCTTATAAGGTGGGATGAGCCAGGTGCGGTTCATGCCATAGGAGCAAATGAGTGATGACACATAGGAGAGCCTGGCATACAACGTGACTGAACGTAGCGTTTACTTGACGGTGTTTAGGAGAACCTAGTCATGCCTGGTGTTTCTTTCCAGGTGATTAAAACGGAAATGAAATTGTCAATATCATATCAGTAGGGGTGGCTGATTGCTAGTCTGTAAATCGACTCTTCTCTGGGTCAATCTCGTATGCTCATGTCGGCAATGTATGCCACGATTCTATAAAACTTGATATTGAACTTCTGTTTCCTACAGCTGCAATGCCCAAAGTTCATCGCAAATTCTTGGCGAGAGAAGGAAAGCTAAAAATCTGTTCGGTTGTAGTTCCATATAACCTTAGCCGGAAGAGGACCCTCTGACTTTCTTCCTTCTGACTTTGAGTCACTGATACGTGAGTTTATTGGGTAGAGGGTCCACATATCAATGATATAAGTTAAATATAAGTAGGTTAGAGCATCTCTAACAGTCTATCCAAATTTGACTGTCCAAATGTCTATTTGGCCAACTCTCCATTTAATTTAGCAAGTCAAATTGTCTTTTACTCCAACAGCCA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.221129
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0209600.1 3 11174474 G A
Osa03LNT0209600.1 3 11176318 G A
Osa03LNT0209600.1 3 11177845 A C
Osa03LNT0209600.1 3 11177875 T C
Osa03LNT0209600.1 3 11175191 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa03LNT0209600.1 DTM_#DNAt_MULE_japo_Os0053 Chr3 + 11175051 11176266 1215
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0209600.1 osa-miR414 Cleavage 1.5 7.673 1 21
Osa03LNT0209600.1 osa-miR414 Cleavage 3.0 14.628 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0209600.1 3 qBM-3 Physiological trait Source activity RG369 RG745
Osa03LNT0209600.1 3 qGY-3 Morphological trait Seed RG369 RG745
Osa03LNT0209600.1 3 nan Morphological trait Seed RM251 RM554
Osa03LNT0209600.1 3 nan Morphological trait Seed RM251 RM554
Osa03LNT0209600.1 3 qLVG3 Resistance or Tolerance Cold tolerance RM251 RM282
Osa03LNT0209600.1 3 ccs3 Physiological trait Source activity RM282 RM251
Osa03LNT0209600.1 3 dcf3 Physiological trait Source activity RM282 RM251
Osa03LNT0209600.1 3 qLEI3 Resistance or Tolerance Submergency tolerance RM7249 RM3803
Osa03LNT0209600.1 3 qLEI3 Resistance or Tolerance Submergency tolerance nan nan
Osa03LNT0209600.1 3 qGL3-1 Physiological trait Eating quality nan nan
Osa03LNT0209600.1 3 qOE3-1 Physiological trait Eating quality nan nan
Osa03LNT0209600.1 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0209600.1 3 nan Physiological trait Eating quality RZ574 RZ284
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