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mmu_circBdp1_713
Basic information of circular RNA
PanCircBase ID:
mmu_circBdp1_713
mm39_Chr. Position ID:
chr13|100228701|100235737|-
Gene name:
Bdp1
Transcript:
ENSMUST00000038104.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,1220,5344,6292,6759
Genomic length:
7036
Exon/intron sizes in nt:
1,34,13,26,01,10,277
Flanking exon/introns:
chr13:100225955-100228701|chr13:100235737-100240134
Splice length:
713
Other database IDs:
circAtlas: mmu-Bdp1_0027
Human Ortholog IDs:
Mature spliced Sequence:
TGATGAAAAGACTGGTGACAAAAATAATGCTGCAGAGTCCAGCACATTGTCCTCTGCTTCTTCACAGAGAAGAAAGCGAGTGTCAAGCACATCCAGTCTTGTTCAGCCTTCTGGCAGTGCCCCCTCACAGAGTCGCCCCTTATCTACAGTTGATCACGATGCACCACAGCCAAACCCTACTCCAGCTAAAGAGAAGCAGCCGTGTTCAGACAGATACCGAATCTATAAGGCCCGAAAACTGAGGGAGATGTTGAAAGAGGAACTGAGAAAGGAGAAGAAACAATGGAAAAACAAATTTTCTACAAATGAAAGCCAGAGGCCACCAGATCGTTCAAAAATGACTATGAGAGACTTCATATATTACCTTCCAGATAACAATCCAATGACTTCTTCAGTGGAACAAGAAAAGAAACCTGAGAAATCCTTGGCTCCCACCCCAACGAGAGATAGGCAAGAAAATCAGAGCACTCAAGATGCTAATGATAATGAAGACGTGGAAGAGGAGGTGGATGATGGGCCACTTCTGGTTCCTCGAGTAAAAGTGGCAGAAGATGGTTCTATTATTTTAGATGAAGAAAGTTTAACTGTAGAAGTTTTGAGAACAAAAGGCCCCTGCGTCGTTGAAGAGAATGATCCTATATTTGAGCGCGGCTCCACTACTACTTACTCCAGCTTCAGGAAGAACTACTACTCAAAGCCATGGTCCAATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTATATTTGAGCGCGGCT
59.32
GTGCTTGACACTCGCTTTCT
58.78
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATCCTATATTTGAGCGCGGC
59.34
AGCAGAGGACAATGTGCTGG
60.32
140
PCR template sequence:
TGCGTCGTTGAAGAGAATGATCCTATATTTGAGCGCGGCTCCACTACTACTTACTCCAGCTTCAGGAAGAACTACTACTCAAAGCCATGGTCCAATAAAGTGATGAAAAGACTGGTGACAAAAATAATGCTGCAGAGTCCAGCACATTGTCCTCTGCTTCTTCACAGAGAAGAAAGCGAGTGTCAAGCACATCCAGTCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-298-5p(1), mmu-miR-139-5p(1), mmu-miR-218-5p(1), mmu-miR-324-3p(1), mmu-miR-107-3p(1), mmu-miR-705(1), mmu-miR-207(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGGTCCAATAAAGTGATGAAAAGACT
siRNA sets
TTTCATCACTTTATTGGAC, TTTTCATCACTTTATTGGA, TTCATCACTTTATTGGACC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCBDP1_713_ORF_1
0.7821
0.088857331
0.838949007
708
ORF sequence:
ATGTTGAAAGAGGAACTGAGAAAGGAGAAGAAACAATGGAAAAACAAATTTTCTACAAATGAAAGCCAGAGGCCACCAGATCGTTCAAAAATGACTATGAGAGACTTCATATATTACCTTCCAGATAACAATCCAATGACTTCTTCAGTGGAACAAGAAAAGAAACCTGAGAAATCCTTGGCTCCCACCCCAACGAGAGATAGGCAAGAAAATCAGAGCACTCAAGATGCTAATGATAATGAAGACGTGGAAGAGGAGGTGGATGATGGGCCACTTCTGGTTCCTCGAGTAAAAGTGGCAGAAGATGGTTCTATTATTTTAGATGAAGAAAGTTTAACTGTAGAAGTTTTGAGAACAAAAGGCCCCTGCGTCGTTGAAGAGAATGATCCTATATTTGAGCGCGGCTCCACTACTACTTACTCCAGCTTCAGGAAGAACTACTACTCAAAGCCATGGTCCAATAAAGTGATGAAAAGACTGGTGACAAAAATAATGCTGCAGAGTCCAGCACATTGTCCTCTGCTTCTTCACAGAGAAGAAAGCGAGTGTCAAGCACATCCAGTCTTGTTCAGCCTTCTGGCAGTGCCCCCTCACAGAGTCGCCCCTTATCTACAGTTGATCACGATGCACCACAGCCAAACCCTACTCCAGCTAAAGAGAAGCAGCCGTGTTCAGACAGATACCGAATCTATAAGGCCCGAAAACTGA
Peptide sequence:
MLKEELRKEKKQWKNKFSTNESQRPPDRSKMTMRDFIYYLPDNNPMTSSVEQEKKPEKSLAPTPTRDRQENQSTQDANDNEDVEEEVDDGPLLVPRVKVAEDGSIILDEESLTVEVLRTKGPCVVEENDPIFERGSTTTYSSFRKNYYSKPWSNKVMKRLVTKIMLQSPAHCPLLLHREESECQAHPVLFSLLAVPPHRVAPYLQLITMHHSQTLLQLKRSSRVQTDTESIRPEN
IRESfinder result
IRESfinder score
0.570316341
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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