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mmu_circUsp4_927
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp4_927
mm39_Chr. Position ID:
chr9|108237293|108248258|+
Gene name:
Usp4
Transcript:
ENSMUST00000035237.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
4,5,6,7,8,9,10
Exon/intron offsets:
0,2466,2742,5735,6666,7724,10806
Genomic length:
10965
Exon/intron sizes in nt:
127,146,62,141,118,174,159
Flanking exon/introns:
chr9:108233740-108237293|chr9:108248258-108249760
Splice length:
927
Other database IDs:
CIRCpedia: MMU_CIRCpedia_2302, circAtlas: mmu-Usp4_0007
circAtlas: hsa-USP4_0016, CIRCpedia: HSA_CIRCpedia_138277
Human Ortholog IDs:
Mature spliced Sequence:
GTTGTGGAGCATGGCCTGTTTGTCAAGCACTGCAAAGTGGAAGTGTATTTGCTGGAGCTGAAGCTCTGTGAGAACAGTGACCCCACCAATGTGCTAAGTTGCCATTTTAGCAAAGCAGACACCATTGCAACTATTGAGAAGGAGATGAGGAAGCTCTTCAACATCCCTGCAGAACGTGAAACACGGCTTTGGAACAAATACATGAGCAACACCTATGAGCAGTTGAGCAAGCTAGACAACACTATCCAGGATGCTGGGCTGTACCAGGGTCAGGTGCTAGTAATTGAGCCCCAAAATGAAGATGGCACATGGCCCCGGCAGAGCCTGCAGTCAAAATCAAGCACTGCACCTAGCAGAAATTTCACTACCTCTTCAAAACCATCCGCAAGTCCCTATTGCTCAGTGTCTGCCTCTCTCATTGCAAATGGTGATAGCACTAACAGCTCTGGGATGCACAGCTCCGGTGTCAGCAGGGGTGGATCTGGCTTCTCTGCTTCGTATAATTGCCAGGAGCCCCCATCACCTCATATACAGCCTGGCCTCTGTGGACTTGGAAACCTGGGGAACACTTGCTTCATGAACTCTGCTCTGCAGTGCCTGAGCAACACTGCCCCACTGACTGAGTACTTTCTCAAAGATGAGTATGAGGCCGAGATCAACCGAGACAACCCTCTGGGGATGAAAGGGGAGATTGCAGAGGCCTATGCAGAGCTCATCAAGCAGATGTGGTCTGGAAGGGACACTCACGTGGCACCACGGATGTTCAAGACGCAAGTGGGACGTTTTGCCCCTCAGTTTTCTGGCTACCAACAGCAAGACTCCCAGGAGCTGCTAGCCTTTATTCTAGACGGACTGCACGAGGACCTGAACCGCGTAAAGAAGAAGCCTTACCTGGAGCCCAAGGACGCCAATGGGCGACCAGATGCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACCTGAACCGCGTAAAG
60.04
TAGCACATTGGTGGGGTCAC
59.96
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGACCTGAACCGCGTAAAGA
60.04
TAGCACATTGGTGGGGTCAC
59.96
163
PCR template sequence:
GCTGCTAGCCTTTATTCTAGACGGACTGCACGAGGACCTGAACCGCGTAAAGAAGAAGCCTTACCTGGAGCCCAAGGACGCCAATGGGCGACCAGATGCGGTTGTGGAGCATGGCCTGTTTGTCAAGCACTGCAAAGTGGAAGTGTATTTGCTGGAGCTGAAGCTCTGTGAGAACAGTGACCCCACCAATGTGCTAAGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-let-7c-5p(1), mmu-miR-196a-5p(1), mmu-miR-709(1), mmu-miR-324-5p(1), mmu-let-7d-5p(1), mmu-miR-370-3p(1), mmu-miR-98-5p(1), mmu-miR-690(1), mmu-miR-296-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCGACCAGATGCGGTTGTGGAGCATG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP4_927_ORF_1
0.9597
0.303908131
0.999958122
1710
ORF sequence:
ATGAGGAAGCTCTTCAACATCCCTGCAGAACGTGAAACACGGCTTTGGAACAAATACATGAGCAACACCTATGAGCAGTTGAGCAAGCTAGACAACACTATCCAGGATGCTGGGCTGTACCAGGGTCAGGTGCTAGTAATTGAGCCCCAAAATGAAGATGGCACATGGCCCCGGCAGAGCCTGCAGTCAAAATCAAGCACTGCACCTAGCAGAAATTTCACTACCTCTTCAAAACCATCCGCAAGTCCCTATTGCTCAGTGTCTGCCTCTCTCATTGCAAATGGTGATAGCACTAACAGCTCTGGGATGCACAGCTCCGGTGTCAGCAGGGGTGGATCTGGCTTCTCTGCTTCGTATAATTGCCAGGAGCCCCCATCACCTCATATACAGCCTGGCCTCTGTGGACTTGGAAACCTGGGGAACACTTGCTTCATGAACTCTGCTCTGCAGTGCCTGAGCAACACTGCCCCACTGACTGAGTACTTTCTCAAAGATGAGTATGAGGCCGAGATCAACCGAGACAACCCTCTGGGGATGAAAGGGGAGATTGCAGAGGCCTATGCAGAGCTCATCAAGCAGATGTGGTCTGGAAGGGACACTCACGTGGCACCACGGATGTTCAAGACGCAAGTGGGACGTTTTGCCCCTCAGTTTTCTGGCTACCAACAGCAAGACTCCCAGGAGCTGCTAGCCTTTATTCTAGACGGACTGCACGAGGACCTGAACCGCGTAAAGAAGAAGCCTTACCTGGAGCCCAAGGACGCCAATGGGCGACCAGATGCGGTTGTGGAGCATGGCCTGTTTGTCAAGCACTGCAAAGTGGAAGTGTATTTGCTGGAGCTGAAGCTCTGTGAGAACAGTGACCCCACCAATGTGCTAAGTTGCCATTTTAGCAAAGCAGACACCATTGCAACTATTGAGAAGGAGATGAGGAAGCTCTTCAACATCCCTGCAGAACGTGAAACACGGCTTTGGAACAAATACATGAGCAACACCTATGAGCAGTTGAGCAAGCTAGACAACACTATCCAGGATGCTGGGCTGTACCAGGGTCAGGTGCTAGTAATTGAGCCCCAAAATGAAGATGGCACATGGCCCCGGCAGAGCCTGCAGTCAAAATCAAGCACTGCACCTAGCAGAAATTTCACTACCTCTTCAAAACCATCCGCAAGTCCCTATTGCTCAGTGTCTGCCTCTCTCATTGCAAATGGTGATAGCACTAACAGCTCTGGGATGCACAGCTCCGGTGTCAGCAGGGGTGGATCTGGCTTCTCTGCTTCGTATAATTGCCAGGAGCCCCCATCACCTCATATACAGCCTGGCCTCTGTGGACTTGGAAACCTGGGGAACACTTGCTTCATGAACTCTGCTCTGCAGTGCCTGAGCAACACTGCCCCACTGACTGAGTACTTTCTCAAAGATGAGTATGAGGCCGAGATCAACCGAGACAACCCTCTGGGGATGAAAGGGGAGATTGCAGAGGCCTATGCAGAGCTCATCAAGCAGATGTGGTCTGGAAGGGACACTCACGTGGCACCACGGATGTTCAAGACGCAAGTGGGACGTTTTGCCCCTCAGTTTTCTGGCTACCAACAGCAAGACTCCCAGGAGCTGCTAGCCTTTATTCTAGACGGACTGCACGAGGACCTGAACCGCGTAAAGAAGAAGCCTTACCTGGAGCCCAAGGACGCCAATGGGCGACCAGATGCG
Peptide sequence:
MRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQNEDGTWPRQSLQSKSSTAPSRNFTTSSKPSASPYCSVSASLIANGDSTNSSGMHSSGVSRGGSGFSASYNCQEPPSPHIQPGLCGLGNLGNTCFMNSALQCLSNTAPLTEYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDTHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFILDGLHEDLNRVKKKPYLEPKDANGRPDAVVEHGLFVKHCKVEVYLLELKLCENSDPTNVLSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQNEDGTWPRQSLQSKSSTAPSRNFTTSSKPSASPYCSVSASLIANGDSTNSSGMHSSGVSRGGSGFSASYNCQEPPSPHIQPGLCGLGNLGNTCFMNSALQCLSNTAPLTEYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDTHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFILDGLHEDLNRVKKKPYLEPKDANGRPDA
IRESfinder result
IRESfinder score
0.478212585
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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