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mmu_circUsh2a_772_1
Basic information of circular RNA
PanCircBase ID:
mmu_circUsh2a_772_1
mm39_Chr. Position ID:
chr1|188447237|188460936|+
Gene name:
Ush2a
Transcript:
ENSMUST00000060479.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
39,40
Exon/intron offsets:
0,13070
Genomic length:
13699
Exon/intron sizes in nt:
1,43,629
Flanking exon/introns:
chr1:188446651-188447237|chr1:188460936-188465629
Splice length:
772
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATTATTCCCCATTCCTTCTGCATCGTTAAGCTACGAAGTGACTGGTCTCCAGCCGTTCACAGTGTATGAGTTTCGGTTGGTTGCCACCAATGGCTTTGGCACTGCATACAGTGCTTGGACTCCGCTCATGACTACAGAGGACAAGCCTGGACCTATAGATGCTCCAATTCTTATCAATGTGAAAGCTAGGATGTTGTCGGTCATCTGGAGGCAGCCTGCAAAGTGCAATGGGGCCATTACCCATTATAACATCTACCTGCATGGCCGTCTCTACTTAACAGTCTCTGGACGAGTCACTAACTATACTGTGGTCCCTCTGCATCCTTACAAGGCCTATCACTTCCAGGTAGAAGCCTGCACCTCCCAAGGGTGCTCTAAGTCACCATCGTCTGAGACTGTGTGGACACTCCCAGGAAATCCAGAAGGCATCCCAAGCCCACAGTTGTTCCCATACACTCCAACATCAATCATAGTAACTTGGCAACCCTCGGCACACCTGGATCTCTTGGTTGAGAACGTTACAATCGAGAGACGAGTCAAAGGGAAAAAGGAAGTTAGGAACCTGGTGACCCTGGCAAGAAGTCAAGCCATGAAGTTTATTGATAATGATCCTGCCCTCCGCCCTTGGACACGCTATGAATACCGGGTTCTGGGGAGCACTCTTGATGGGGGCACAAACAGCAGTGCTTGGGTAGAAGTGACCACAAGACCCTGTCGGCCTTCCGGAGTACAGCCACCCACAGTGCGTGTGCTGGCACCAGATACAGTCGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACAAACAGCAGTGCTTGGG
60.25
TACACTGTGAACGGCTGGAG
59.68
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGACCACAAGACCCTGTCG
60.6
GTGGCAACCAACCGAAACTC
59.97
162
PCR template sequence:
CACAAACAGCAGTGCTTGGGTAGAAGTGACCACAAGACCCTGTCGGCCTTCCGGAGTACAGCCACCCACAGTGCGTGTGCTGGCACCAGATACAGTCGAGATTATTCCCCATTCCTTCTGCATCGTTAAGCTACGAAGTGACTGGTCTCCAGCCGTTCACAGTGTATGAGTTTCGGTTGGTTGCCACCAATGGCTTTGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-32-5p(1), mmu-miR-135a-5p(1), mmu-miR-92a-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-23a-3p(1), mmu-miR-25-3p(1), mmu-miR-676-3p(1), mmu-miR-342-5p(1), mmu-miR-697(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGATACAGTCGAGATTATTCCCCATT
siRNA sets
AATAATCTCGACTGTATCT, GAATAATCTCGACTGTATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSH2A_772_1_ORF_1
0.842
0.144517435
0.883904381
714
ORF sequence:
ATGACTACAGAGGACAAGCCTGGACCTATAGATGCTCCAATTCTTATCAATGTGAAAGCTAGGATGTTGTCGGTCATCTGGAGGCAGCCTGCAAAGTGCAATGGGGCCATTACCCATTATAACATCTACCTGCATGGCCGTCTCTACTTAACAGTCTCTGGACGAGTCACTAACTATACTGTGGTCCCTCTGCATCCTTACAAGGCCTATCACTTCCAGGTAGAAGCCTGCACCTCCCAAGGGTGCTCTAAGTCACCATCGTCTGAGACTGTGTGGACACTCCCAGGAAATCCAGAAGGCATCCCAAGCCCACAGTTGTTCCCATACACTCCAACATCAATCATAGTAACTTGGCAACCCTCGGCACACCTGGATCTCTTGGTTGAGAACGTTACAATCGAGAGACGAGTCAAAGGGAAAAAGGAAGTTAGGAACCTGGTGACCCTGGCAAGAAGTCAAGCCATGAAGTTTATTGATAATGATCCTGCCCTCCGCCCTTGGACACGCTATGAATACCGGGTTCTGGGGAGCACTCTTGATGGGGGCACAAACAGCAGTGCTTGGGTAGAAGTGACCACAAGACCCTGTCGGCCTTCCGGAGTACAGCCACCCACAGTGCGTGTGCTGGCACCAGATACAGTCGAGATTATTCCCCATTCCTTCTGCATCGTTAAGCTACGAAGTGACTGGTCTCCAGCCGTTCACAGTGTATGA
Peptide sequence:
MTTEDKPGPIDAPILINVKARMLSVIWRQPAKCNGAITHYNIYLHGRLYLTVSGRVTNYTVVPLHPYKAYHFQVEACTSQGCSKSPSSETVWTLPGNPEGIPSPQLFPYTPTSIIVTWQPSAHLDLLVENVTIERRVKGKKEVRNLVTLARSQAMKFIDNDPALRPWTRYEYRVLGSTLDGGTNSSAWVEVTTRPCRPSGVQPPTVRVLAPDTVEIIPHSFCIVKLRSDWSPAVHSV
IRESfinder result
IRESfinder score
0.582030113
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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