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

>Osa01LNT0041300.3

GGCACATAATATGACCACCTTGTATATATACGGAAAATTTTATCCAGATACACGTGTAACCTATTATTTACGCAATTACACTGTCTGCAAAACAGCTCTATCAGGTTACATTCTCAGAACTGACAAAATTGTTCCAGCTGCATGATCTTCAGTGCTTGGCACTCATGCAGCATTTTGCAGACTCACTATTAACCTCTCTTCAAGGCAAGTGCTTTATCAACATTCTATTGGTAAACCATTTACCTGAGACTTTTGTTAACAGAAATATCAAACCATGTCTGACTTATCTTGCTGGCCTGCGTGTTGAACATGCTATTCTTGAAGCTTTTTTGTCTTCCTTTTTGGCATACCACTCACCATGTCTGACTTATCTTGCAATCTTGCGCCTTGCAATCCATTATCCTTGCAGAAACGGACTGCCAAAGATTGAGAAGGGGCAGCTGGGGGGAAATCTTCAGCTGGCATTGCAAATGGACGAACCATTTTATCAAATTTGTCCAAGGTGAGATATGATCCAACTTCCTGCAATCTTTCTGGCTCCATAATTTTCATAGTGTGATCATCAGGTAGCAATGAATCTTTTCCATGTTCGCTCTGTAAGGAACTTATATCTGCACCACGACTATATGTCATTTCTATGCGAAACCTTTTTGGGTCTTCCAAAGAAACCTCTGTATTCTCGAACATACGCAATACAATGTAACTCATGTAGTCAAGTTCCCTTGTTTTAAACAGATTATCTAGAGCATTTTTGCAAACAAGACTTTCTTCTCCATCCATAGATTCATCAAAATTGCAGTATCGAAGTACATTCATTAGAGAATGTATATGTGATTCTGATGTAAAATAGAGCCTTGTTCGAACACGTCGTTCAGGTTCCATCACATTGGCATATTTTGGATCCAAGCAGTATTTGGTTTCTTTGTGCGAATCATCAAGATCAATTGACTTCTTGTTTGAGTTAGGTCTATCAAAACCCTCATTCTTAACATCCCCATAGTAACCCCTATCCTTCCGTTTTGAAGAAGGCACTATTGTTGGATCATGGCATGCATTAGATTCACCACCAGCAGCAGCAACCTCTCGTCTGGTGTTATGCAGGTCAATCAGAATCTTGCCCAACAAACGGCGTGCAATCTTTGAACCAATTTTGAGTTTCTGCTTCGCATTTATTCCATACTCATTTGGAATTACACCATCAGCTAGTGACTGAGAAACTCTGAAGAGATCACTCAAACCATTAAGTTTGAGATGTGAGTTATGAAGGAGGTCATACCTGTCAAGTATACTGTTAGAAATAGATGAGGTGAAGAGATATGCTGGAACAAAGAAATGTTTTTGAAACTTGAGAAAATGCTTTTGTTTCGAACAAAAGCATCACGTGATTTTTAAAATAATTGCAAGAAGCCTTGAATTGCAAAAAAGAGAGAGCAGATGAACACTTGCAAAAAAAGCAAAATGAAGTTATTTTGGGCAAATTTTATCTGTCTTTGAGATCGTCAACATTGTGAACTTTCCAGTGATCCACTAGCAAACTTTCAGGTAAGCTTTAGGAAATATTTGAGACTTTGATAGTCATGTTTTTTTTTTTTTGAAACCAATAGTCATGGTTTTCTTATGAAAATAAGAAATTTATTTTCCTACGGCTGGGCTGTTTCGCTGAACATTCTTGTTGATTCCCTAGGTCACAGCCCCTAAGGCCTAAACAGCATGGAAAGCAGCTGGGCAAATCAAGGTCAGGCCCTCTCATGGCCAAGTTTCGAGGCACAATTTGGTATGCTAATTTGCATGTTCATTCAGAAAAGCAAATTCGAATGAAGTTGACAATTGACAAAGATCTTATGGAAGAGCATGATACAATCATATAATAGGCATCCAGGGCCCAGCTATTTTGTGAAGAGAAATAGAAGCATCTGGAGATGGTAACATGGTTACCCACTTGCAAGAGTCATATATATCAGGTATTTGCGTAGTGTCAAAACGTTTTTTTCTTTCGTTGTAGAGATCCCTCTCTAGTTTCTTCCAACGGGCAAACATCAAAAGGAAGCTCTCGCTGCCACAAGGCAATCCAGAAGCAATGCGGTCCATATCAATTGCTGTTTTCCCTAGTGCCTTTGCTTGATCATAAGGATGACTTGGTGAGTCACTATCTGTCACAGCCTCTTCATCTTCATTGTCAGAAAGCAGCTTCACTTGTGCAGTTATTTCCTTGGTCAATTGAGCCAAATTTGTGAGAAGGTTAGCAGCATTTGGAGGCACTCCAGCTCCATCAACCATCCATGGGAACTCCATAGTCTCACCATTTGCAATTTTTGAAGAAAGGATAATATTGTGCAAACGAGCCTTCGCTTCATCTATCTCAATAGAGCCATCCTGAAGTCCATCAAGCATAGAAGAGTCCTTACTGACAAGTGAAACCAGAATTGGAGTTAACTCCCCCTCCAAATCAAGAAGACCTTTCGCAAAAGCTGCTGCAGACATCTGGACACGACCTTCATCTGAACTGTATATTTTCAGATCATGCCTATATGTACTGTGCAGACGAAGCAATCCTGGTCCTTCACTTGGATACATATTATTTCTGAAGTATCTTCCCAACTCTTCTGCCTGCTTTCTCCCAGCATGAGTTAGAACTCCACCGTACTTGAGAACCATCAGTGCTTCAATTGGATACTCCTCCTTCCCGTTGCCGTTACTTTTAGGAATATGGACCCAATTGGATGGCTTTAACTGCACTTTCCTATAAATACCTGAAAAATGTCCACCCTCTTCTAGAACTGCTCTAACTTGGCGTAGCTTCTCTGCATGCTCAATTTCAGCATCACTATCACTTTCACGGCCAGACCTAGCACGTGGAACAAGGATTCTTGTTGCATCTAATAGATCTTGCAGCTGCAAGGCACTTTTAAGTTTTGCCTCTGCATGGGCCTTTCCTCCATTGTATTTCAACATTAATTTTAAAAGCTTTTCTTCAGTTACCTTCAGCTTCACCTTTTGCTTTGGCGTGCGATCCCCATGGCGTATAACAGCTATGACACAGCGCAGCTCTTCTGATTGCCTAGATATGCCAACAGTTCCCCTTTCTCGATCTCTTACAGCATCAAATGGTTGGACTGGCTCACTGACTTTCCATGGAAGATTAGCAGGAATGGTGGATGAAATATGTGGAGCTTTATCATCGAGAAACATTTTCCTCAGAATGCATGCAGCATCATCGTAGTACTTGTGTGAGCTTTTCACAAAACTCCAGCCATTGACATCACATACATAAGACCTTGCCTCCCCCAAATCACACCTTAGAAGATCAAAACCACACACCGCTTGTCCGAAGGCTTGGCAAATATTCCTTGCAATTTGTTTCTCAGTAGGGGTTAGTAAAACAGGATAGCGCACCTCTTTTCCATCAGAATTCCTCATAACAACCCCATCTACAACTGGAGATTTGCGGGCTTCAGCATGTGCATATCCTGGCCCAACTGTATAAACCTTGACATCTGTTCCTCCTGTTGGCATGAATTCTTCATAAATGTAAGATCCATCTCGCCTCACCTTCCTAATGTCTGGATAAAATTCACTAGATCGATTGCCAACCTTGCGGAACAGTTCTTTCATTCCTCCACCAGCGGAGCTAGGATAATATATCATTATGTTATGGTCATCTCCATCGATTGGTTTCTCCACAAAAGGCTTGTAAAATCGCTTTCCATGGATCTCAATAAAATCATCTTGCTCAACAAAGTACTTTAACTCTTGGTTAGGGTATTCTCTTCTGACAACAGCATAAGTTGGAACAGGAACTCCGAACAATTTAAGGTGCAGATATTCATAGATGATCTTGCTGCCATCTTTTGGTTTATATACTGTTGAGTACTACTACCTTCTTCAAGAGAAGTTATTTCTTCTAGTTTAAAGGAGGTTAATTTGCATCCCATGATAACTAGCAAGAAATAACACATCTTTAAAGAATCTCATATACTTTGCTGCGATCATGGAGGAGGTATTGGGGATCCAACTCATTGACCAAAAATGGCCTGCGTAAAGCAGCATATTTCTCTGCCTTTTCTAGTGGATACCCAGCCGAGTAAAAGGCAATCAGACAGTCACATAGAGGCCAGCTTTCAATAGGATCTTCAAGAATGATTTTGTCACCAAAAATTATAATCTCGAACTCCCCGAACGCCCGCAGCCTCTCAAGAATCTGCTCCATGGGGGAACACCACACCTTCTTCTCCATGACGCAGACACCAATCTTGATCTTGCCTCCACCGTCACAGCCATCATTCCGCCGCTCCATCCCCTCGCTACCCCTTTCTGTTCTCCGGGAAAGAAGAGATTACAACGGGAAAGGGAGGGTCTGTTTCTTAGGACATTTCGCACCCCCCACAAGGATTCCAAGATTGAAGCTTTTTATGGAGGAGGGCAGGGAGGGACGAAGAGGGTATGTGAGGAGAGTGCACTGTGCAAGGATAAACTTTTCTTCCTTTTTCCCCCTTTATTTTTCAAGGACTACAAGTCTACAATGAGCAGCTCTCTGCGTCTCTCCCCATGCTAGTTATTCTGAATCTCTTCCCATGCTAGTTTATCTCGGATTTGCTCGGAAAGAACCTCCTTTTCATTGCTTTTACTTTTGTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.876168
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0041300.3 1 32911514 T C
Osa01LNT0041300.3 1 32912247 A G
Osa01LNT0041300.3 1 32913109 C T
Osa01LNT0041300.3 1 32913782 T G
Osa01LNT0041300.3 1 32914664 A G
Osa01LNT0041300.3 1 32914673 A C
Osa01LNT0041300.3 1 32915196 T G
Osa01LNT0041300.3 1 32915877 C T
Osa01LNT0041300.3 1 32916660 T C
Osa01LNT0041300.3 1 32917110 T C
Osa01LNT0041300.3 1 32918542 T A
Osa01LNT0041300.3 1 32919072 A G
Osa01LNT0041300.3 1 32919297 A G
Osa01LNT0041300.3 1 32919568 T C
Osa01LNT0041300.3 1 32919992 T C
Osa01LNT0041300.3 1 32920024 T C
Osa01LNT0041300.3 1 32920935 G A
Osa01LNT0041300.3 1 32920990 T C
Osa01LNT0041300.3 1 32923945 C T
Osa01LNT0041300.3 1 32924407 A T
Osa01LNT0041300.3 1 32924762 A G
Osa01LNT0041300.3 1 32924912 A G
Osa01LNT0041300.3 1 32923205 T C
Osa01LNT0041300.3 1 32920379 A T
Osa01LNT0041300.3 1 32922316 A G
Osa01LNT0041300.3 1 32925067 G A
Osa01LNT0041300.3 1 32925633 C G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0041300.3 DTM_#DNAt_MULE_japo_Os3566 Chr1 - 32906535 32906995 460
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0041300.3 osa-miR5791 Cleavage 4.5 14.26 1 21
Osa01LNT0041300.3 osa-miR5804 Cleavage 4.0 13.88 1 21
Osa01LNT0041300.3 osa-miR812v Cleavage 4.5 15.126 1 24
Osa01LNT0041300.3 osa-miR5824 Cleavage 4.0 15.278 1 24
Osa01LNT0041300.3 osa-miR6246 Translation 5.0 19.885 1 23
Osa01LNT0041300.3 osa-miR6256 Cleavage 4.0 14.9 1 22
Osa01LNT0041300.3 osa-miR166e-3p Cleavage 5.0 20.639 1 21
Osa01LNT0041300.3 osa-miR395t Cleavage 4.0 17.765 1 21
Osa01LNT0041300.3 osa-miR395c Cleavage 4.0 17.765 1 21
Osa01LNT0041300.3 osa-miR396c-3p Cleavage 5.0 14.489 1 21
Osa01LNT0041300.3 osa-miR166i-5p Translation 5.0 18.35 1 21
Osa01LNT0041300.3 osa-miR437 Cleavage 5.0 14.943 1 21
Osa01LNT0041300.3 osa-miR437 Translation 4.5 12.926 1 21
Osa01LNT0041300.3 osa-miR528-5p Translation 3.5 17.813 1 21
Osa01LNT0041300.3 osa-miR1869 Translation 5.0 13.549 1 24
Osa01LNT0041300.3 osa-miR2100-5p Cleavage 4.5 17.983 1 22
Osa01LNT0041300.3 osa-miR2101-3p Cleavage 4.5 13.238 1 22
Osa01LNT0041300.3 osa-miR2104 Cleavage 4.0 7.471 1 22
Osa01LNT0041300.3 osa-miR2122 Cleavage 4.0 15.655 1 22
Osa01LNT0041300.3 osa-miR2118e Cleavage 5.0 20.184 1 22
Osa01LNT0041300.3 osa-miR2118r Cleavage 5.0 20.184 1 22
Osa01LNT0041300.3 osa-miR2918 Cleavage 5.0 20.657 1 21
Osa01LNT0041300.3 osa-miR2923 Translation 5.0 12.987 1 22
Osa01LNT0041300.3 osa-miR5149 Cleavage 4.5 12.249 1 22
Osa01LNT0041300.3 osa-miR5152-5p Cleavage 3.5 16.75 1 21
Osa01LNT0041300.3 osa-miR5157a-3p Cleavage 4.0 14.905 1 24
Osa01LNT0041300.3 osa-miR5157b-3p Cleavage 4.0 14.905 1 24
Osa01LNT0041300.3 osa-miR5160 Translation 4.0 15.525 1 22
Osa01LNT0041300.3 osa-miR5491 Cleavage 5.0 17.427 1 21
Osa01LNT0041300.3 osa-miR5499 Translation 4.0 14.626 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0041300.3 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0041300.3 1 An10 Morphological trait Panicle/flower nan nan
Osa01LNT0041300.3 1 qCC-1 Physiological trait Source activity RG541 RG101
Osa01LNT0041300.3 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0041300.3 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0041300.3 1 qLRC-1 Resistance or Tolerance Drought tolerance RM237 RM302
Osa01LNT0041300.3 1 gpy1 Others Others RG541 RG101
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