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mmu_circBrd3_1178
Basic information of circular RNA
PanCircBase ID:
mmu_circBrd3_1178
mm39_Chr. Position ID:
chr2|27349468|27354205|-
Gene name:
Brd3
Transcript:
ENSMUST00000028282.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,2072,2964,3998,4432
Genomic length:
4737
Exon/intron sizes in nt:
37,22,15,14,81,38,305
Flanking exon/introns:
chr2:27347049-27349468|chr2:27354205-27365153
Splice length:
1178
Other database IDs:
circAtlas: mmu-Brd3_0009
circAtlas: hsa-BRD3_0009
Human Ortholog IDs:
Mature spliced Sequence:
GTGCCTGATTGGGCCCAGAAATGGGATGCCAAGCCTCCACGAGGAGCGCCTCTTTGAGCTGCTGCTGTGACAGCAAGTGACTAAGCTGCCAGAGGATGTCCACTACAGCGGCTGCCCCCACGGGGATCCCGGCAGTCCCGGGCCCCGTGAACCCTCCCCCACCTGAGGTCTCCAACCCCAGCAAGCCCGGGCGAAAGACTAACCAACTGCAGTACATGCAGAATGTAGTGGTGAAGACACTCTGGAAACATCAGTTTGCCTGGCCTTTCTACCAGCCTGTGGATGCAATCAAGCTGAACCTGCCTGATTATCATAAAATAATAAAAAACCCAATGGACATGGGGACTATCAAGAAGAGACTAGAAAATAATTATTATTGGAGTGCCAGTGAGTGTATGCAGGACTTCAACACCATGTTTACAAACTGTTATATTTATAATAAGCCCACAGATGATATAGTGCTAATGGCCCAGGCCTTAGAGAAAATCTTTCTGCAGAAAGTGGCCCAGATGCCTCAGGAGGAAGTTGAACTATTGCCCCCTGCTCCAAAGGGCAAAGGCCGGAAGCCAGCTGCAGGAGCCCAAAATGCAGGTTCCCAACAAGTGGCAGCTGTGTCTTCGGTCTCCCCAGCAACCCCCTTCCAGAACATACCCCCCACCGTGTCCCAGACACCCGTCATTGCCGCTACCCCTGTACCAACCATCACTGCAAACGTCACGTCAGTTCCAGTCCCCCCACCCGCTGCACCGCCTCCTCCTGCGACACCCATCGTCCCTGTGGTCCCTCCCACACCGCCTGTAGTCAAGAAAAAGGGCGTGAAGCGGAAAGCAGACACAACCACACCCACAACATCTGCCATCACTGCCAGCCGGAGTGAGTCTCCCCCACCACTTTCAGAGCCCAAGCAAGCCAAGGTAGTGGCCCGAAGGGAGAGCGGGGGCCGCCCCATCAAACCTCCCAAGAAGGACCTGGAAGATGGTGAGGTCCCACAGCACGCGGGTAAAAAGGGAAAACTGTCCGAGCACCTGCGGCACTGTGACAGCATCCTCCGGGAGATGCTGTCCAAGAAGCATGCTGCCTATGCGTGGCCCTTTTACAAGCCAGTGGACGCGGAGGCGCTGGAGCTGCATGACTACCATGACATCATCAAGCACCCCATGGACCTCAGCACGGTCAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGAGCTGCATGACTACCA
59.46
TGGCAGCTTAGTCACTTGCT
59.6
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGAGCTGCATGACTACC
60.81
TGGCAGCTTAGTCACTTGCT
59.6
152
PCR template sequence:
CTATGCGTGGCCCTTTTACAAGCCAGTGGACGCGGAGGCGCTGGAGCTGCATGACTACCATGACATCATCAAGCACCCCATGGACCTCAGCACGGTCAAAGTGCCTGATTGGGCCCAGAAATGGGATGCCAAGCCTCCACGAGGAGCGCCTCTTTGAGCTGCTGCTGTGACAGCAAGTGACTAAGCTGCCAGAGGATGTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-705(2), mmu-miR-16-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-326-3p(1), mmu-miR-22-3p(1), mmu-miR-96-5p(1), mmu-miR-342-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGCACGGTCAAAGTGCCTGATTGGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCBRD3_1178_ORF_1
1.155
0.319012714
0.998308829
1140
ORF sequence:
ATGTCCACTACAGCGGCTGCCCCCACGGGGATCCCGGCAGTCCCGGGCCCCGTGAACCCTCCCCCACCTGAGGTCTCCAACCCCAGCAAGCCCGGGCGAAAGACTAACCAACTGCAGTACATGCAGAATGTAGTGGTGAAGACACTCTGGAAACATCAGTTTGCCTGGCCTTTCTACCAGCCTGTGGATGCAATCAAGCTGAACCTGCCTGATTATCATAAAATAATAAAAAACCCAATGGACATGGGGACTATCAAGAAGAGACTAGAAAATAATTATTATTGGAGTGCCAGTGAGTGTATGCAGGACTTCAACACCATGTTTACAAACTGTTATATTTATAATAAGCCCACAGATGATATAGTGCTAATGGCCCAGGCCTTAGAGAAAATCTTTCTGCAGAAAGTGGCCCAGATGCCTCAGGAGGAAGTTGAACTATTGCCCCCTGCTCCAAAGGGCAAAGGCCGGAAGCCAGCTGCAGGAGCCCAAAATGCAGGTTCCCAACAAGTGGCAGCTGTGTCTTCGGTCTCCCCAGCAACCCCCTTCCAGAACATACCCCCCACCGTGTCCCAGACACCCGTCATTGCCGCTACCCCTGTACCAACCATCACTGCAAACGTCACGTCAGTTCCAGTCCCCCCACCCGCTGCACCGCCTCCTCCTGCGACACCCATCGTCCCTGTGGTCCCTCCCACACCGCCTGTAGTCAAGAAAAAGGGCGTGAAGCGGAAAGCAGACACAACCACACCCACAACATCTGCCATCACTGCCAGCCGGAGTGAGTCTCCCCCACCACTTTCAGAGCCCAAGCAAGCCAAGGTAGTGGCCCGAAGGGAGAGCGGGGGCCGCCCCATCAAACCTCCCAAGAAGGACCTGGAAGATGGTGAGGTCCCACAGCACGCGGGTAAAAAGGGAAAACTGTCCGAGCACCTGCGGCACTGTGACAGCATCCTCCGGGAGATGCTGTCCAAGAAGCATGCTGCCTATGCGTGGCCCTTTTACAAGCCAGTGGACGCGGAGGCGCTGGAGCTGCATGACTACCATGACATCATCAAGCACCCCATGGACCTCAGCACGGTCAAAGTGCCTGATTGGGCCCAGAAATGGGATGCCAAGCCTCCACGAGGAGCGCCTCTTTGA
Peptide sequence:
MSTTAAAPTGIPAVPGPVNPPPPEVSNPSKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEEVELLPPAPKGKGRKPAAGAQNAGSQQVAAVSSVSPATPFQNIPPTVSQTPVIAATPVPTITANVTSVPVPPPAAPPPPATPIVPVVPPTPPVVKKKGVKRKADTTTPTTSAITASRSESPPPLSEPKQAKVVARRESGGRPIKPPKKDLEDGEVPQHAGKKGKLSEHLRHCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKVPDWAQKWDAKPPRGAPL
IRESfinder result
IRESfinder score
0.401935716
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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