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mmu_circBrd8_1261
Basic information of circular RNA
PanCircBase ID:
mmu_circBrd8_1261
mm39_Chr. Position ID:
chr18|34740827|34747623|-
Gene name:
Brd8
Transcript:
ENSMUST00000003876.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
12,11,10,9,8,7,6,5
Exon/intron offsets:
0,643,2030,2635,3357,5262,5441,6673
Genomic length:
6796
Exon/intron sizes in nt:
281,210,145,219,137,65,81,123
Flanking exon/introns:
chr18:34740544-34740827|chr18:34747623-34747800
Splice length:
1261
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ACGGAAACGGGGTGAAAAAGGAGAAGTGGTAGAAACTGTTGAAGATGTTATTGTTCGCAAACTGACTGCTGAGAGAGTTGAAGAACTGAAGAAAGTCATAAAGGAGACACAGGAGAGATACAGGCGTCTGAAAAGAGATGCAGAACTAATCCAAGCCGGGCACATGGACAGCAGACTGGATGAGCTCTGCAATGACATTGCAATGAAAAAGAAATTGGAAGAGGAAGAGGCTGAAGTAAAAAGGAAGGCCACCGATGCTGCGTACCAGGCGCGACAAGCAGTGAAAACGCCTCCTCGAAGGTTACCGACTGTGATGGTCCGCTCTCCTGTAGACTCTGCCTCCCCAGGAGGTGATTACCCACTTGGAGACTTGACTCCAACCACTATGGAAGAGGCTACCTCTGGGGTAACCCCTGGGACTTTGCCGAGTACCCCAGTCACCTCGTTTCCTGGGATTCCTGACACCCTTCCTCCAGGCTCTGCACCCTTAGAAGCCCCCATGACCCCAATAACAGATGATTCACCCCAGAAAAAGATGCTTGGACAGAAAGCAACTCCACCCCCCTCCCCTCTGCTGTCAGAGCTCTTGAAGAAGGGCAGCCTCCTGCCTACTAGCCCCAGACTGGTGAATGAGAGTGAAATGCCTGTACCCCCTGGCCATCTGAACAGCACAGGGGTTCTCTTGGAGGTAGGAGGGGTTCTTCCCATGATACATGGTGGGGAGATACAGCCAACAACCAGTGCTGTGGCGGCCTCCCCGGCTGCCTCAGGTGCTCCCACTCTTTCCCGGCTTTTAGAAGCTGGGCCCACACAGTTCACCACTCCTCTTCCTTCCTTCACTACTGTTGCCAGTGAGCCGCCAGTTAAGCTTGTGCCACCCCCTGTAGAGTCTGTGTCCCAGGCTACCATTGTCATGATGCCCGCGCTGCCAGCACCATCCTCTGCTGCGGCTGTCTCCACTTCTGAAAGTGGAGCTCCAGTGAGCCAGCCTGAGCCCTGTGTACCCCTGGAAGCTGTGGGGGATCCACATACTGTGACTGTTTCCATGGATAGCAATGAAATCTCCATGATCATTAATTCCATCAAAGAAGAGTGTTTCCGCTCAGGGGTAGCAGAGGCTCCTGGTGGATCAAAGGCTCCAAGCATAGATGGGAAGGAAGACTTGGATCTAGCGGAGAAGATGGATATTGCTGTGTCTTACACAGGTGAAGAGTTGGACTTTGAAACAGTTGGAGACATCATTGCCATCATTGAGGACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATCTAGCGGAGAAGATGGA
60.16
TCTCAGCAGTCAGTTTGCGA
59.61
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATCTAGCGGAGAAGATGG
58.76
TCTCAGCAGTCAGTTTGCGA
59.61
172
PCR template sequence:
CTTGGATCTAGCGGAGAAGATGGATATTGCTGTGTCTTACACAGGTGAAGAGTTGGACTTTGAAACAGTTGGAGACATCATTGCCATCATTGAGGACAAGACGGAAACGGGGTGAAAAAGGAGAAGTGGTAGAAACTGTTGAAGATGTTATTGTTCGCAAACTGACTGCTGAGAGAGTTGAAGAACTGAAGAAAGTCATA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-27a-3p(2), mmu-miR-298-5p(2), mmu-let-7a-5p(1), mmu-miR-27b-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-223-3p(1), mmu-let-7c-5p(1), mmu-miR-132-3p(1), mmu-miR-709(1), mmu-let-7d-5p(1), mmu-miR-149-5p(1), mmu-miR-98-5p(1), mmu-miR-207(1), mmu-miR-673-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CATTGAGGACAAGACGGAAACGGGGT
siRNA sets
ACCCCGTTTCCGTCTTGTC, TTCCGTCTTGTCCTCAATG, TTTCCGTCTTGTCCTCAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCBRD8_1261_ORF_1
1.102
0.226047424
0.996676033
1113
ORF sequence:
ATGGACAGCAGACTGGATGAGCTCTGCAATGACATTGCAATGAAAAAGAAATTGGAAGAGGAAGAGGCTGAAGTAAAAAGGAAGGCCACCGATGCTGCGTACCAGGCGCGACAAGCAGTGAAAACGCCTCCTCGAAGGTTACCGACTGTGATGGTCCGCTCTCCTGTAGACTCTGCCTCCCCAGGAGGTGATTACCCACTTGGAGACTTGACTCCAACCACTATGGAAGAGGCTACCTCTGGGGTAACCCCTGGGACTTTGCCGAGTACCCCAGTCACCTCGTTTCCTGGGATTCCTGACACCCTTCCTCCAGGCTCTGCACCCTTAGAAGCCCCCATGACCCCAATAACAGATGATTCACCCCAGAAAAAGATGCTTGGACAGAAAGCAACTCCACCCCCCTCCCCTCTGCTGTCAGAGCTCTTGAAGAAGGGCAGCCTCCTGCCTACTAGCCCCAGACTGGTGAATGAGAGTGAAATGCCTGTACCCCCTGGCCATCTGAACAGCACAGGGGTTCTCTTGGAGGTAGGAGGGGTTCTTCCCATGATACATGGTGGGGAGATACAGCCAACAACCAGTGCTGTGGCGGCCTCCCCGGCTGCCTCAGGTGCTCCCACTCTTTCCCGGCTTTTAGAAGCTGGGCCCACACAGTTCACCACTCCTCTTCCTTCCTTCACTACTGTTGCCAGTGAGCCGCCAGTTAAGCTTGTGCCACCCCCTGTAGAGTCTGTGTCCCAGGCTACCATTGTCATGATGCCCGCGCTGCCAGCACCATCCTCTGCTGCGGCTGTCTCCACTTCTGAAAGTGGAGCTCCAGTGAGCCAGCCTGAGCCCTGTGTACCCCTGGAAGCTGTGGGGGATCCACATACTGTGACTGTTTCCATGGATAGCAATGAAATCTCCATGATCATTAATTCCATCAAAGAAGAGTGTTTCCGCTCAGGGGTAGCAGAGGCTCCTGGTGGATCAAAGGCTCCAAGCATAGATGGGAAGGAAGACTTGGATCTAGCGGAGAAGATGGATATTGCTGTGTCTTACACAGGTGAAGAGTTGGACTTTGAAACAGTTGGAGACATCATTGCCATCATTGAGGACAAGACGGAAACGGGGTGA
Peptide sequence:
MDSRLDELCNDIAMKKKLEEEEAEVKRKATDAAYQARQAVKTPPRRLPTVMVRSPVDSASPGGDYPLGDLTPTTMEEATSGVTPGTLPSTPVTSFPGIPDTLPPGSAPLEAPMTPITDDSPQKKMLGQKATPPPSPLLSELLKKGSLLPTSPRLVNESEMPVPPGHLNSTGVLLEVGGVLPMIHGGEIQPTTSAVAASPAASGAPTLSRLLEAGPTQFTTPLPSFTTVASEPPVKLVPPPVESVSQATIVMMPALPAPSSAAAVSTSESGAPVSQPEPCVPLEAVGDPHTVTVSMDSNEISMIINSIKEECFRSGVAEAPGGSKAPSIDGKEDLDLAEKMDIAVSYTGEELDFETVGDIIAIIEDKTETG
IRESfinder result
IRESfinder score
0.509970493
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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