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mmu_circBdp1_319
Basic information of circular RNA
PanCircBase ID:
mmu_circBdp1_319
mm39_Chr. Position ID:
chr13|100206584|100211053|-
Gene name:
Bdp1
Transcript:
ENSMUST00000038104.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
13,12
Exon/intron offsets:
0,4310
Genomic length:
4469
Exon/intron sizes in nt:
1,60,159
Flanking exon/introns:
chr13:100204064-100206584|chr13:100211053-100212012
Splice length:
319
Other database IDs:
circBase: mmu_circ_0004382, CIRCpedia: MMU_CIRCpedia_21, circAtlas: mmu-Bdp1_0016
Human Ortholog IDs:
Mature spliced Sequence:
TAATCAACAAGACATCATGCCACTAGCAAGGGAGTCCTCAGAGTCGTGTGCTGTGGCTTTACCTGTGTGGGAACCCGGTAATACTGCCTCTGCTGACATGGCTCATGCTGAGAGCTCCTGCTCAGAAGGAAGAGGTGCTGACCTGAAGACTGCGGCACCAGAGACTGAACAGACAGAAAATGTCAAACCAAAATCAAGAAGTCGACTACAGAGACCTAAGCCTAATCTGGCAAGGGCAGTTGGGAAGAAATCAGCTGTTTCACAAGACAGACAAGATGAAAGGAACAAGAACTCACCTTCAGAAACTGCAGCTGAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAGGGCAGTTGGGAAGAA
60.83
TAAAGCCACAGCACACGACT
59.89
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAGGGCAGTTGGGAAGAA
60.83
CGGGTTCCCACACAGGTAAA
59.89
167
PCR template sequence:
GCCTAATCTGGCAAGGGCAGTTGGGAAGAAATCAGCTGTTTCACAAGACAGACAAGATGAAAGGAACAAGAACTCACCTTCAGAAACTGCAGCTGAGAAGTAATCAACAAGACATCATGCCACTAGCAAGGGAGTCCTCAGAGTCGTGTGCTGTGGCTTTACCTGTGTGGGAACCCGGTAATACTGCCTCTGCTGACATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
TGCAGCTGAGAAGTAATCAACAAGAC
siRNA sets
CTTGTTGATTACTTCTCAG,TTGATTACTTCTCAGCTGC,TCTTGTTGATTACTTCTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCBDP1_319_ORF_1
0.9203
0.11236638
0.556040068
459
ORF sequence:
ATGTCAAACCAAAATCAAGAAGTCGACTACAGAGACCTAAGCCTAATCTGGCAAGGGCAGTTGGGAAGAAATCAGCTGTTTCACAAGACAGACAAGATGAAAGGAACAAGAACTCACCTTCAGAAACTGCAGCTGAGAAGTAATCAACAAGACATCATGCCACTAGCAAGGGAGTCCTCAGAGTCGTGTGCTGTGGCTTTACCTGTGTGGGAACCCGGTAATACTGCCTCTGCTGACATGGCTCATGCTGAGAGCTCCTGCTCAGAAGGAAGAGGTGCTGACCTGAAGACTGCGGCACCAGAGACTGAACAGACAGAAAATGTCAAACCAAAATCAAGAAGTCGACTACAGAGACCTAAGCCTAATCTGGCAAGGGCAGTTGGGAAGAAATCAGCTGTTTCACAAGACAGACAAGATGAAAGGAACAAGAACTCACCTTCAGAAACTGCAGCTGAGAAG
Peptide sequence:
MSNQNQEVDYRDLSLIWQGQLGRNQLFHKTDKMKGTRTHLQKLQLRSNQQDIMPLARESSESCAVALPVWEPGNTASADMAHAESSCSEGRGADLKTAAPETEQTENVKPKSRSRLQRPKPNLARAVGKKSAVSQDRQDERNKNSPSETAAEK
IRESfinder result
IRESfinder score
0.311976081
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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