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

>Osa01LNT0025400.1

GGTTATCCGACTTCAAAGTATGAGGTGTTAGATGGACTTTTACTGAGGGTATATTGACTTCTCCCTATATAGTAATTTAGTAACACCAAGCAAACTACATTAAGAGACCATGGAGCAACAGCATCACTCTTGTTCTACACACTTTCACTGCAGCAACACCACAAATTAAACCTGAATACATCAGAGTTGCTACTGCTCCCTAATTCAGTCTGTTATTTTGGTGTTCGCGTTACAGAAAAAGGCTCAACTTGTGTCCACAGAACCTGCACCTTTCTCCTCAAGCTTATCCATGGCTGATGCCAAATAGTTGTCACAGTAACCAGGTGGCTCATAGATAAAGCAAGAGATCACGTCTCGCAGTGTCACGACACCAACAACCTCGAAGTCACCGTCCACGACGTATATCCGGTGGGTTATTCTTGATGCAATGCTGTCAATCACGCTGCCAAGAGAAGCGTCAGGCGAACAGGTGAGAGGTGGCTTCACCAGGCCGTTCCCTGAATCAGAAACGGTGGAACCTATGGTCTTCATGAACTCCATGACAGTAAGTTGCCTGAAATTCGAAAACAAGTCAGGCCTAAGTAACAAAAAGCGAATATCCCTTATGCTCACACTGCCAACAAGTTTTTTGTTGGGACCTTCTACTACAGGCACACCACCAATTTTGTTGTCCTTCATGCACTTAAAAGCTTCCAAGATTAGATCACCACTGTTAACAGTGATAACCTCATCAAGTGACATAAATGGAAGTCCCAAGTCCGAGAGAGGGAGCGCTGAAATATAATCAAACCAATCCCTTCCTTTGCACTGCTGAAGTCCTTTAACAACACCAGTCTGAGTAATGAAGTTCTTAATAATTGGCTTATCAGGCTCAATCACTGGGACATTCCTTAACCTGTACTTGGATAGCAACAGTAATACAGTAAGCATTGAAGTGTCCAGTGTAATGGGGACAAAAGGAGACCAGCGGTAGGATTCTACAATTGATCGAACTGTAGTTGATTTGAAAGGTTCTTGCTGAAGCAGAACTTTGTAGAAATCTTCTCCTAAATGATCAGCAGCAGTTAGTCCATCCTTTGCCACACCCTTTTCTGCTGTTAACCCACCAGCAACAGCAGCCCCTACTGCAGCGGCAGTCAAGCCAGCAACAGCTGCAGGACCAGTTGCACCCAATGCTGCCACTCCCACTGCACCGACAGCACCCATTCCAACTCCTGCTGCGGTTGCTGACCCAGCTGATAGAGCAACGGCGGCAATCTCAGCATTTTCTAGAACCCAGAGGATGATAGCCGAGTAATCAATGATGCCAAGGTACCTCCCTTTCCAATCAGCCGGAGCTCCACATTCCGGATTTAGCACTGGCGCTGCCCTAATGTTGTGTTTGGAGAGAATTCTCACAGCGTCAAGAACGGAAGTGTCTCCTGGAATTTCAATCACTCGGCCATTAGGAACATCAGGAAAAGACGAGACAGGAATCTGAGCAAAGGCAGCAGTGAGCGATTCTTGCAAAGAGAGGGGCAGCTTCTTCTTGGACTGTATAGTGTCAAAATACGCATCACAGCTTGGGAATTTCACGGTTTCATCAGGTCGATCCATTTCGGGCGAAGTGGCGGAAGCAGCTGGGACTTCCGCCGGCGTCGGTTGCTCGCGGGAGGGGAAGGGGATCGATCGGGGCGCTGCTCCGCTCGGCGGCGGCGGCGCGAACCGCGGCGATTGCTGGAAACCGTGGGCGGCGGCGGCAATCCAGGAGGAGGAGGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.929608
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0025400.1 1 22820304 C T
Osa01LNT0025400.1 1 22821517 A T
Osa01LNT0025400.1 1 22821605 G A
Osa01LNT0025400.1 1 22821690 A G
Osa01LNT0025400.1 1 22822068 T G
Osa01LNT0025400.1 1 22822308 C A
Osa01LNT0025400.1 1 22822771 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0025400.1 osa-miR5533 Cleavage 4.0 18.258 1 21
Osa01LNT0025400.1 osa-miR167h-3p Cleavage 5.0 13.807 1 21
Osa01LNT0025400.1 osa-miR2921 Cleavage 5.0 14.231 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0025400.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0025400.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0025400.1 1 nan Resistance or Tolerance Drought tolerance RM129 RM5
Osa01LNT0025400.1 1 nan Morphological trait Root RM23 RM306
Osa01LNT0025400.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0025400.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0025400.1 1 qNVB-1-1 Morphological trait Culm/leaf R2159 C178
Osa01LNT0025400.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0025400.1 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0025400.1 1 qVB-1 Morphological trait Culm/leaf RZ776 RZ744
Osa01LNT0025400.1 1 qVB-1 Morphological trait Culm/leaf RZ776 RZ744
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