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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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Institute of Life sciences, Bhubaneswar, India

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