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mmu_circUsh2a_1433
Basic information of circular RNA
PanCircBase ID:
mmu_circUsh2a_1433
mm39_Chr. Position ID:
chr1|188147874|188179063|+
Gene name:
Ush2a
Transcript:
ENSMUST00000124358.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
14,15,16,17,18,19
Exon/intron offsets:
0,15029,21134,27336,28765,31019
Genomic length:
31189
Exon/intron sizes in nt:
1,84,16,41,59,49,52,61,000
Flanking exon/introns:
chr1:188132579-188147874|chr1:188179063-188183930
Splice length:
1433
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTTTTACAGTTCTCCCAGCAATGCCACTGGCTGCCTGCCATGCTTATGCCACACAGCTGGTGCTGTGAGCCACATCTGTAATAGTGTCACGGGACAGTGCTCTTGCCATGACCCCTCAACCACTGGGCGTAGCTGTCACCAGTGTCAAGAAAGTTACTTTAGATTTGATCCCCTGACTGGAAGATGCAGGCCTTGTCACTGTCATGTAGCAGGAGCCTCGAATGGAACTTGTGATGCAGTCACAGGCCAGTGTTTCTGCAAAGAGTTTGTCACTGGCTCAAAATGTGACACTTGTGTTCCTGGTGCAAGCCACTTGGACGTCAACAATCTATTAGGCTGCAGCAAAACTCCATCTCAGCAACCTCCACCCAGAGGATGGGTTCAGAGTTCTTCTACCATCAATGTGTCCTGGAGTCCACCCGAGTGCCCAAATGCTCACTGGCTTACATACACTCTGTTCAGGAATGGCTCTGAGATCTACACAACTGAAGATGAACACCCGTACTATACTCAGTACTTCTTAGACACTAGTCTGTCACCACACACAGCATATTCATATTATATAGAGACCTCCAATGTGCACAGTTCGACAAGGAGCATACCTGTCATTTATGAGACAAAGCCAGAGGTCTCAGAAGGACACTTGAACTTGACTCACATCATTCCTGTGGGCTCGGACTCCATTACACTTACCTGGACTGGACTCTCCAACAGCTCTGATCCTGTGGCAAAATATGTTTTATCATGCACACCTGTGGACAGCACTGAGCCCTGTGTCTCCTATGAAGGTCCAGAAACCTCAGCTACCATCTGGAATCTGGTTCCATTCACCCAGTACTGTTTTTCTGTCCAGGGCTGTACTAATGAGAGCTGTTTCTACAGCTTGCCTATTATAGTAACCACAGCCCAAGCACCTCCTCAAACGCAGGGGCCACCTACAGTATGGAAAATCAGTCCCACAGAACTCAGAATAGAATGGTCTCCTCCAGTGGACTCAAATGGTATAATTATAAGCTATGAGTTATACATGAGGAGATGGCTGTCCACCGAAGAAAGCCTAGTGTTTGAGAGCCACGGTTTGGTCAGTTCTCACTCAGCTTTACAGTCGGTCAATCCGAGTAAGAACCTGCTCCAGCAGCCCCAAGCCAGCACGTTCATCTCTGGCTTGGAGCCACACACAGAGTATGCATTTAGGGTCTTGGCTGTGAATATGGCTGGCAGGGTGTCGTCTGCCTGGGCCTCAGAAAGAACGGGGGAATCAGTACCCGTATTCATGGCCCCTCCTTCAGTCTCTCCACTCTCACCACACTCCCTCAGTGTCTCCTGGGAGAAGCCAGCAGAAAACTTTACAAGAGGAGAAATTATAGGGTACAAGATCAGCATGGTTTCTGAACATTTCCCTCTACACGATGTTCCAGTCATGTGCTCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGGTACAAGATCAGCATGGT
58.8
TGTGGCTCACAGCACCAG
59.89
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGCAGAAAACTTTACAAGAG
58.46
GCTGTGTGGCATAAGCATGG
59.9
158
PCR template sequence:
GCCAGCAGAAAACTTTACAAGAGGAGAAATTATAGGGTACAAGATCAGCATGGTTTCTGAACATTTCCCTCTACACGATGTTCCAGTCATGTGCTCAAAGGCTTTTACAGTTCTCCCAGCAATGCCACTGGCTGCCTGCCATGCTTATGCCACACAGCTGGTGCTGTGAGCCACATCTGTAATAGTGTCACGGGACAGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
21
Interacting miRNAs (#binding sites)
mmu-miR-673-5p(2), mmu-miR-574-5p(2), mmu-miR-23b-3p(1), mmu-miR-134-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-31-5p(1), mmu-miR-101a-3p(1), mmu-miR-122-5p(1), mmu-miR-29a-3p(1), mmu-miR-146a-5p(1), mmu-miR-217-5p(1), mmu-miR-203-3p(1), mmu-miR-320-3p(1), mmu-miR-23a-3p(1), mmu-miR-143-3p(1), mmu-miR-24-3p(1), mmu-miR-382-3p(1), mmu-miR-297a-5p(1), mmu-miR-1904(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGTGCTCAAAGGCTTTTACAGTTC
siRNA sets
AACTGTAAAAGCCTTTGAG, ACTGTAAAAGCCTTTGAGC, TGTAAAAGCCTTTGAGCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSH2A_1433_ORF_1
0.9452
0.070098021
0.538619725
474
ORF sequence:
ATGAGGAGATGGCTGTCCACCGAAGAAAGCCTAGTGTTTGAGAGCCACGGTTTGGTCAGTTCTCACTCAGCTTTACAGTCGGTCAATCCGAGTAAGAACCTGCTCCAGCAGCCCCAAGCCAGCACGTTCATCTCTGGCTTGGAGCCACACACAGAGTATGCATTTAGGGTCTTGGCTGTGAATATGGCTGGCAGGGTGTCGTCTGCCTGGGCCTCAGAAAGAACGGGGGAATCAGTACCCGTATTCATGGCCCCTCCTTCAGTCTCTCCACTCTCACCACACTCCCTCAGTGTCTCCTGGGAGAAGCCAGCAGAAAACTTTACAAGAGGAGAAATTATAGGGTACAAGATCAGCATGGTTTCTGAACATTTCCCTCTACACGATGTTCCAGTCATGTGCTCAAAGGCTTTTACAGTTCTCCCAGCAATGCCACTGGCTGCCTGCCATGCTTATGCCACACAGCTGGTGCTGTGA
Peptide sequence:
MRRWLSTEESLVFESHGLVSSHSALQSVNPSKNLLQQPQASTFISGLEPHTEYAFRVLAVNMAGRVSSAWASERTGESVPVFMAPPSVSPLSPHSLSVSWEKPAENFTRGEIIGYKISMVSEHFPLHDVPVMCSKAFTVLPAMPLAACHAYATQLVL
IRESfinder result
IRESfinder score
0.657239816
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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