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

>Osa01LNT0032600.1

AGTCAATAGTTTCGTTCAAAGAAGAGTCAATAGTGAAACAGGAAAGGACACGTTAAAGGGTATAGATTATGGGTACTAAATGTCAGTGGTTTGAGTAGTGTGACACAACAAACACCACCACTATAGTATACATAAGCAGGCTTTACTATCCCATCCGTGCTTCTTCCAAAAGAAACATCAAAAATACATCGATGTTTCTAAGCTGCTAGTCCTCAAAGCAATGCGTGACCAAACAAACGCTACTCCTGCTTCATCTTTGATTCAGGCTGGTAGCATGGATGCAGCAACACATGGATGCACAAGAGCCAGCAGGGAAGATGGACAAGAAATACATACAGATATGTCGCGCTGCTCCATTCCCACAAGAACTCCATCCACAGCCAGAAATCACCAACAATGTCTACTGTCCATGATCCCTTGGATAGACCTTTCATGATAAGAAATGCAGCTGGAGGGAAACCCAAGACGGTGAGAAGTATGTTTGAGGCCAACAATACTGTGCGAGGTAGGAAATTCATCTCGAGCTGTGCCCTCAGCGGTCGAGAAAACAAGCACATTGGGATCAATATCAGAGCCCCAAGCTGAGCAGTAGCAAAATTTATGATCGACATAAGCCCCATTCCTATGGTGATGGAAGTGATCATCGTAGCTTTTAGAAGCTTCCATTCCACACCAGCACGGGATGGAGAGCCAAACATTGCATACAGGATGATCAATATAGTGATGGAGAGAACGGCCCAAATCACTGCATACTGTATTGGCATAGCACCAGGAATTTGGCTAATGTAGTATGGGAGTAAAGAAACAAGTACTGCCCAAAATTGGATGATAAGTAGTACTCTTGCAGATTTAAGCCATTTCCACGATCCACCCTCCATTTGCAGGTCATCAGCATTACCCTTTGTTTTACATTCATCCTCCAATTTCCCCTTGGTTTTACTACCACCAGCAAGAGCAGCAGCAACTATTGGGAGGGGTGCCAGGAGTAATGCAAACGGAATCATATATACACCAACTGAAATGAACTTGCTTGGGGCTGTAAGGAAATACAGGAAAAACGATTGATGGAACTTCTCGAGCAGGTTATTTACAGAGCGCACCACCCCTTCAGTTAACCTTCCACCCCTGAGAAGAAATGAAGATTTAGCATTCTCGTTTTTAAGATGAAATGCTGGTGCAAATTCTAAAGAAACTGCATCAACTTGATAGTCACGGAAAGCACCATGAGAACCTGTGGGCACTCCAAGAGCCTGGTTATACATAGAACTAGCAAGGTTTGCAGTACCCTCCACATAATCAGGAACGGTCACGTCAAGCTTCCAGTCAGGATTTATTTTTCTCAACAAACTCCCAAGATTTTGAAATACTTCAGCAATAACCCTAAGCCATGAAGAGCTCAACAAGGAATTAAATGTCTCGACATTCACGCGAAAACCTTGTCTATGAACAGCTAAATAGTGCACCACATTCAGAAGGTCCAAGTTTGGCATTTGGCCATTAGATGCCTCTGCATACATCGTGACACTATCTCTATCACCATATTTCCTGGTTTCTCCAACTTTAAATATGAGTGCAGCAGCCATTGTTCCAGCACGTTTGAAAGCCATAAGTTCTGCCTTTTCTGCAGTGCCATCAGGTTTATATAAAATTTGATTTGCACCATAGATCTTGGTATCCAAATTCACTGGGTGACTCAGAAACATAGGATTATGATACTGATTTAACCATGAAGAGACCGCAGAGTACTCTCCAAATTGTGAGTCTGCAGACAGCCAGACAATATCCTTTGATAGCCATGCAGCTCGACTTAGGAGGGAGAAGACAGAGAATCCAAGTGCAAGTGATAATAATTCATTTGGTGTAACTTTCTGAGAATTATAAGGAGTAACCAGTACAATTGCTTCTTTGCCATCACCTCGTGGAGCCCGTATAATGCCAACTGTGTTAATGCCAAAGTTGGTGTAGGTTCCATTGGGTTTGGCTGCCATATTATTTGTCATGGATGTAAAGAACTTCAGAGGATGAAAACATTTGCTGTCAGGGAGGAACTCATGGTAATACACTTCTGCTCCCAGATTTTTTGTTTGTTGTGCTATGAATTTTGGGATCTCCGTTGTTCCACCTCTTGATTCCCCAATTGCAGCTTCAATTCCCTTCGCAAATCTGTTTGCTTCCTGGACATCCTCAGTAGAAAATAATGTATTCGCAGAGCCGGGTATAAGAGCGTTCTCTGATAGGTACGTGTTCTTGGCAAGCGAAGGGAGGAAGAGGAGCGCGATTATGCCCGCCGTACAACACACAGCGCTGAAGAGTATGTGGTGCGACGCGAGGAATACCCCGAGGCGGACAATGAGGCGCGGCTTCGGTTTTGCCTCCTCCTTAGCTGACGACGCCATGGCAGCAACTTGGTTCAGGTCTGGAGACCGGGAGACTAATCTTGGAGCGGCACAGATCCTGTCTACCCTCGCCGCGCGGGGCAGGATCCCATCAAAAACTGCCACAGAGCTGGACCTCCGCCTCCGCGTGAGCTTCCACAAGTAGATATGCCGATGGAGAGCAGCGGGAGCGGGAGCCACCAGCGGTTCTCCCGGCTGGGGAAGGGATGCGGCTCCGGCGAAGTGGCTTGGTGGGCAAGACGAGCGGATGCGGCGTGGCCAGGGCTCCGCGGCGGCGGAGGCGGAGGAGGAGAGAAGGCGAGCGAAGCGGGCGGCGAGGGGAAGCTGCTCCGTCCTACCTGCTCGCCGGAGGTGGGCGGGGGGTGCCGGCGAGTGGTCGCCGGTGGGTCGCCGCCTCGCTGGAGATCGCGGCGAACCGGCGAGTGAAGGAGATGGGGGAGGGGCAGGCCTGGCCGCGGGCCGTCAGAAGTAAATGGGTCCAGAGAGAAACCGGCT

Coding Potentia
Explanation CPC Score
noncoding -1.03164
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0032600.1 1 28119678 A C
Osa01LNT0032600.1 1 28120075 T G
Osa01LNT0032600.1 1 28120585 T C
Osa01LNT0032600.1 1 28121245 A T
Osa01LNT0032600.1 1 28121415 A G
Osa01LNT0032600.1 1 28122421 C T
Osa01LNT0032600.1 1 28118126 T G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0032600.1 DTM_#DNAt_MULE_japo_Os0098 Chr1 - 28120202 28120574 372
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0032600.1 osa-miR5837.2 Cleavage 5.0 15.915 1 21
Osa01LNT0032600.1 osa-miR160f-5p Translation 4.0 18.684 1 21
Osa01LNT0032600.1 osa-miR814a Cleavage 3.5 15.928 1 22
Osa01LNT0032600.1 osa-miR814b Cleavage 3.5 15.928 1 22
Osa01LNT0032600.1 osa-miR814c Cleavage 3.5 15.928 1 22
Osa01LNT0032600.1 osa-miR1861d Cleavage 5.0 21.958 1 22
Osa01LNT0032600.1 osa-miR1861h Cleavage 4.5 21.958 1 22
Osa01LNT0032600.1 osa-miR1861j Cleavage 4.5 21.958 1 22
Osa01LNT0032600.1 osa-miR2095-3p Cleavage 4.5 19.471 1 20
Osa01LNT0032600.1 osa-miR2096-3p Cleavage 4.0 9.822 1 21
Osa01LNT0032600.1 osa-miR812o-3p Cleavage 4.5 16.191 1 24
Osa01LNT0032600.1 osa-miR5157a-3p Cleavage 3.0 12.365 1 24
Osa01LNT0032600.1 osa-miR5157b-3p Cleavage 3.0 12.365 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0032600.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0032600.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0032600.1 1 yld1.1 Physiological trait Source activity RM5 RG462
Osa01LNT0032600.1 1 nan Morphological trait Root RM3475 RM3494
Osa01LNT0032600.1 1 nan Morphological trait Seed CDO118 CDO455
Osa01LNT0032600.1 1 QPh1b Resistance or Tolerance Submergency tolerance RZ527 RZ154
Osa01LNT0032600.1 1 nan Physiological trait Source activity RG532 RM472
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