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mmu_circLarp4b_990
Basic information of circular RNA
PanCircBase ID:
mmu_circLarp4b_990
mm39_Chr. Position ID:
chr13|9186814|9201260|+
Gene name:
Larp4b
Transcript:
ENSMUST00000188211.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
4,5,6,7,8,9,10,11
Exon/intron offsets:
0,376,6975,8603,10622,13047,14086,14236
Genomic length:
14446
Exon/intron sizes in nt:
148,147,79,137,104,111,54,210
Flanking exon/introns:
chr13:9173998-9186814|chr13:9201260-9208158
Splice length:
990
Other database IDs:
circBase: mmu_circ_0004864, CIRCpedia: MMU_CIRCpedia_34053, circAtlas: mmu-Larp4b_0013
circAtlas: hsa-LARP4B_0036, CIRCpedia: HSA_CIRCpedia_2591
Human Ortholog IDs:
Mature spliced Sequence:
GTCCCAACAACTAAGGTTTCAGAGCTAAACCCTAATGCAAAGGTATGGGGGACTCATATGTTACATTTGGAAGCGAGTAGTGCAGCTGTTGGTGTGAATGCTGCGTGGGAAGAGGCTCCCGGCCATCCTACAGACTGTGACCAGCAGGTTCTAGGATTGGATGCCAATGGTGATGGCGACAAAAGTCGAGAGAATGCAGCGCTCCCGGACGCACAGGAGGCAGAGCAGACAGACATGAGCACTCTGGCTCTGGACCATTCAGAATATGAACCTCTGCCTGAGAACAACGATACGGGAGGAAATGAGTCTCAACCAGAAAGCCAGGAAGACCCTCGGGAAGTACTTAAAAAAACATTGGAATTCTGCTTATCTAGGGAGAATCTTGCTAGCGACATGTACCTTATATCCCAGATGGACAGTGATCAGTATGTGCCAATTACAACGGTAGCTAACCTTGACCATATCAAGAAACTCAGTACTGATGTGGATTTGATTGTTGAAGTGCTAAGATCTTTACCTTTAGTCCAAGTGGATGAGAAGGGAGAGAAAGTAAGGCCAAATCAGAACCGGTGCATAGTAATACTGCGTGAGATATCGGAGTCTACCCCCGTGGAAGAAGTAGAAGCACTATTTAAAGGAGATAATTTACCAAAATTTATAAACTGTGAATTTGCCTATAATGATAATTGGTTTATTACCTTTGAAACAGAAGCTGATGCACAGCAGGCTTACAAATACCTTCGAGAAGAAGTCAGAACTTTCCAAGGAAAGCCAATTAAGGCGCGGATAAAAGCAAAGGCAATAGCGATAAACACATTTTTGCCAAAGAATGGATTTAGACCTCTGGACATGAACCTTTATACCCAGCAGCGCTATGCTACATCGTTTTACTTACCTCCAGTGTACAGTCCCCAGCAGCAGTTCCCTCTGTACAGCCTGATCACCCCCCAGACGTGGTCAACAACACATAGCTATCTTGATCCACCCTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGTACAGCCTGATCACCCC
59.82
AACAGCTGCACTACTCGCTT
59.97
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGCAGTTCCCTCTGTACA
59.68
AACAGCTGCACTACTCGCTT
59.97
166
PCR template sequence:
CTTACCTCCAGTGTACAGTCCCCAGCAGCAGTTCCCTCTGTACAGCCTGATCACCCCCCAGACGTGGTCAACAACACATAGCTATCTTGATCCACCCTTGGTCCCAACAACTAAGGTTTCAGAGCTAAACCCTAATGCAAAGGTATGGGGGACTCATATGTTACATTTGGAAGCGAGTAGTGCAGCTGTTGGTGTGAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-1198-5p(2), mmu-miR-210-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-103-3p(1), mmu-miR-211-5p(1), mmu-miR-382-3p(1), mmu-miR-411-3p(1), mmu-miR-96-5p(1), mmu-miR-107-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGATCCACCCTTGGTCCCAACAACTA
siRNA sets
TAGTTGTTGGGACCAAGGG, GTTGTTGGGACCAAGGGTG, TTGTTGGGACCAAGGGTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLARP4B_990_ORF_1
1.1081
0.155572002
0.999987432
1923
ORF sequence:
ATGTTACATTTGGAAGCGAGTAGTGCAGCTGTTGGTGTGAATGCTGCGTGGGAAGAGGCTCCCGGCCATCCTACAGACTGTGACCAGCAGGTTCTAGGATTGGATGCCAATGGTGATGGCGACAAAAGTCGAGAGAATGCAGCGCTCCCGGACGCACAGGAGGCAGAGCAGACAGACATGAGCACTCTGGCTCTGGACCATTCAGAATATGAACCTCTGCCTGAGAACAACGATACGGGAGGAAATGAGTCTCAACCAGAAAGCCAGGAAGACCCTCGGGAAGTACTTAAAAAAACATTGGAATTCTGCTTATCTAGGGAGAATCTTGCTAGCGACATGTACCTTATATCCCAGATGGACAGTGATCAGTATGTGCCAATTACAACGGTAGCTAACCTTGACCATATCAAGAAACTCAGTACTGATGTGGATTTGATTGTTGAAGTGCTAAGATCTTTACCTTTAGTCCAAGTGGATGAGAAGGGAGAGAAAGTAAGGCCAAATCAGAACCGGTGCATAGTAATACTGCGTGAGATATCGGAGTCTACCCCCGTGGAAGAAGTAGAAGCACTATTTAAAGGAGATAATTTACCAAAATTTATAAACTGTGAATTTGCCTATAATGATAATTGGTTTATTACCTTTGAAACAGAAGCTGATGCACAGCAGGCTTACAAATACCTTCGAGAAGAAGTCAGAACTTTCCAAGGAAAGCCAATTAAGGCGCGGATAAAAGCAAAGGCAATAGCGATAAACACATTTTTGCCAAAGAATGGATTTAGACCTCTGGACATGAACCTTTATACCCAGCAGCGCTATGCTACATCGTTTTACTTACCTCCAGTGTACAGTCCCCAGCAGCAGTTCCCTCTGTACAGCCTGATCACCCCCCAGACGTGGTCAACAACACATAGCTATCTTGATCCACCCTTGGTCCCAACAACTAAGGTTTCAGAGCTAAACCCTAATGCAAAGGTATGGGGGACTCATATGTTACATTTGGAAGCGAGTAGTGCAGCTGTTGGTGTGAATGCTGCGTGGGAAGAGGCTCCCGGCCATCCTACAGACTGTGACCAGCAGGTTCTAGGATTGGATGCCAATGGTGATGGCGACAAAAGTCGAGAGAATGCAGCGCTCCCGGACGCACAGGAGGCAGAGCAGACAGACATGAGCACTCTGGCTCTGGACCATTCAGAATATGAACCTCTGCCTGAGAACAACGATACGGGAGGAAATGAGTCTCAACCAGAAAGCCAGGAAGACCCTCGGGAAGTACTTAAAAAAACATTGGAATTCTGCTTATCTAGGGAGAATCTTGCTAGCGACATGTACCTTATATCCCAGATGGACAGTGATCAGTATGTGCCAATTACAACGGTAGCTAACCTTGACCATATCAAGAAACTCAGTACTGATGTGGATTTGATTGTTGAAGTGCTAAGATCTTTACCTTTAGTCCAAGTGGATGAGAAGGGAGAGAAAGTAAGGCCAAATCAGAACCGGTGCATAGTAATACTGCGTGAGATATCGGAGTCTACCCCCGTGGAAGAAGTAGAAGCACTATTTAAAGGAGATAATTTACCAAAATTTATAAACTGTGAATTTGCCTATAATGATAATTGGTTTATTACCTTTGAAACAGAAGCTGATGCACAGCAGGCTTACAAATACCTTCGAGAAGAAGTCAGAACTTTCCAAGGAAAGCCAATTAAGGCGCGGATAAAAGCAAAGGCAATAGCGATAAACACATTTTTGCCAAAGAATGGATTTAGACCTCTGGACATGAACCTTTATACCCAGCAGCGCTATGCTACATCGTTTTACTTACCTCCAGTGTACAGTCCCCAGCAGCAGTTCCCTCTGTACAGCCTGATCACCCCCCAGACGTGGTCAACAACACATAGCTATCTTGATCCACCCTTG
Peptide sequence:
MLHLEASSAAVGVNAAWEEAPGHPTDCDQQVLGLDANGDGDKSRENAALPDAQEAEQTDMSTLALDHSEYEPLPENNDTGGNESQPESQEDPREVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRPNQNRCIVILREISESTPVEEVEALFKGDNLPKFINCEFAYNDNWFITFETEADAQQAYKYLREEVRTFQGKPIKARIKAKAIAINTFLPKNGFRPLDMNLYTQQRYATSFYLPPVYSPQQQFPLYSLITPQTWSTTHSYLDPPLVPTTKVSELNPNAKVWGTHMLHLEASSAAVGVNAAWEEAPGHPTDCDQQVLGLDANGDGDKSRENAALPDAQEAEQTDMSTLALDHSEYEPLPENNDTGGNESQPESQEDPREVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRPNQNRCIVILREISESTPVEEVEALFKGDNLPKFINCEFAYNDNWFITFETEADAQQAYKYLREEVRTFQGKPIKARIKAKAIAINTFLPKNGFRPLDMNLYTQQRYATSFYLPPVYSPQQQFPLYSLITPQTWSTTHSYLDPPL
IRESfinder result
IRESfinder score
0.559855924
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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