top of page
mmu_circCdc42bpa_2228
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc42bpa_2228
mm39_Chr. Position ID:
chr1|179889354|179941679|+
Gene name:
Cdc42bpa
Transcript:
ENSMUST00000097453.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
6,7,8,9,10,11,12,13,14,15,16,17,18,19,20
Exon/intron offsets:
0,3176,5361,7507,10555,12780,22582,32154,32591,39235,44257,47364,49474,49955,52233
Genomic length:
52325
Exon/intron sizes in nt:
94,201,249,80,167,123,134,243,111,248,106,125,106,149,92
Flanking exon/introns:
chr1:179867765-179889354|chr1:179941679-179945231
Splice length:
2228
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGACATCAAACCTGACAATATATTGATGGATATGAATGGACATATTCGTTTAGCAGATTTTGGTTCTTGTCTGAAGCTGATGGAAGATGGAACGGTCCAGTCCTCGGTGGCAGTTGGAACTCCAGATTATATTTCTCCGGAAATCCTTCAGGCTATGGAAGACGGAAAAGGCAGATATGGACCAGAGTGTGACTGGTGGTCCTTGGGGGTCTGTATGTATGAGATGCTTTACGGAGAAACACCATTCTATGCAGAGTCTCTGGTGGAGACATATGGAAAAATTATGAATCACAAAGAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAAAGATCTTATTCGAAGACTCATTTGTAGTAGAGAACATCGACTTGGCCAAAATGGAATAGAAGACTTTAAGAAGCATCCATTCTTCAGTGGAATTGATTGGGATAACATTCGGAATTGTGAAGCACCTTACATCCCAGAAGTTAGTAGCCCGACAGATACGTCAAATTTTGATGTGGATGACGACTGTTTAAAAAATTCTGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGAAGTGAATCATTTGGAACAACAACTTGAAGAAGCTAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAGGAACTAGTCCAGGCTAGTGAGCGATTAAAAAACCAATCCAAAGAGCTGAAAGATGCACACTGTCAGAGGAAACTGGCCATGCAGGAATTCATGGAGATCAATGAGCGACTAACAGAATTGCACACCCAAAAGCAGAAACTTGCTCGCCATGTCCGAGATAAGGAAGAAGAGGTGGACCTGGTGATGCAAAAAGCTGAGAGCTTAAGGCAGGAGCTGCGCAGAGCAGAAAGAGCCAAGAAAGAGCTGGAAGTTCACACCGAAGCTCTAATTGCTGAAGCATCAAAGGACAAGAAGCTCCGAGAGCAGAGCGAACATTATTCTAAGCAACTGGAAAACGAGTTGGAGGGCCTGAAGCAAAAACAAATTAGTTACTCACCAGGAATATGCAGCATAGAACATCAGCAAGAGATAACTAAACTGAAAACTGACTTGGAAAAGAAAAGTATCTTTTATGAAGAAGAAATTTCTAAAAGAGAAGGAATTCACGCAAGTGAGATTAAAAACCTGAAGAAGGAGCTGCATGACTCAGAAGGCCAGCAGCTTGCTCTCAACAAAGAGATTCTGGTTTTAAAAGACAAATTGGAAAAAACCAGGAGAGAAAGTCAAAGTGAAAGGGAAGAATTTGAAAATGAGTTCAAACAACAATATGAACGGGAAAAAGTATTATTAACTGAAGAGAATAAAAAGTTAACGAGTGAACTCGATAAGCTGACTTCACTGTATGAGAGCTTAAGTTTGCGCAACCAGCACTTAGAAGAAGAAGTCAAAGATCTAGCAGATAAGAAGGAATCAGTTGCCCACTGGGAAGCCCAAATCACAGAGATAATTCAGTGGGTGAGCGATGAGAAGGATGCACGAGGCTATCTTCAGGCCTTAGCTTCTAAAATGACTGAAGAGTTGGAAGCATTAAGAAATTCCAGCTTGGGGACACGAGCAACAGATATGCCCTGGAAAATGCGTCGTTTTGCAAAACTGGACATGTCGGCTAGACTAGAGTTGCAGTCTGCTCTGGATGCAGAAATAAGAGCTAAGCAGGCCATCCAGGAAGAGCTGAATAAAGTCAAAGCATCTAACATCTTAACAGAATGTAAACTGAAAGATTCAGAGAAGAAGAACTTGGAACTGTTGTCCGAAATCGAGCAGCTGATAAAGGACACTGAAGAGCTTAGATCTGAAAAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGTCCGAAATCGAGCAGCT
60.04
CCGTTCCATCTTCCATCAGCT
60.13
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTGTCCGAAATCGAGCAGC
59.9
CCGTTCCATCTTCCATCAGCT
60.13
151
PCR template sequence:
ACAGAATGTAAACTGAAAGATTCAGAGAAGAAGAACTTGGAACTGTTGTCCGAAATCGAGCAGCTGATAAAGGACACTGAAGAGCTTAGATCTGAAAAGGAGACATCAAACCTGACAATATATTGATGGATATGAATGGACATATTCGTTTAGCAGATTTTGGTTCTTGTCTGAAGCTGATGGAAGATGGAACGGTCCAG
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-93-5p(1), mmu-miR-375-3p(1), mmu-miR-223-3p(1), mmu-miR-18a-5p(1), mmu-miR-217-5p(1), mmu-miR-132-3p(1), mmu-miR-212-3p(1), mmu-miR-382-5p(1), mmu-miR-383-5p(1), mmu-miR-466d-3p(1), mmu-miR-1198-5p(1), mmu-miR-129-5p(1), mmu-miR-539-5p(1), mmu-miR-466b-3p(1), mmu-miR-1904(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGATCTGAAAAGGAGACATCAAACCT
siRNA sets
TTTGATGTCTCCTTTTCAG, GTTTGATGTCTCCTTTTCA, ATGTCTCCTTTTCAGATCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC42BPA_2228_ORF_1
0.9783
0.173949795
0.999998272
2229
ORF sequence:
ATGGATATGAATGGACATATTCGTTTAGCAGATTTTGGTTCTTGTCTGAAGCTGATGGAAGATGGAACGGTCCAGTCCTCGGTGGCAGTTGGAACTCCAGATTATATTTCTCCGGAAATCCTTCAGGCTATGGAAGACGGAAAAGGCAGATATGGACCAGAGTGTGACTGGTGGTCCTTGGGGGTCTGTATGTATGAGATGCTTTACGGAGAAACACCATTCTATGCAGAGTCTCTGGTGGAGACATATGGAAAAATTATGAATCACAAAGAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAAAGATCTTATTCGAAGACTCATTTGTAGTAGAGAACATCGACTTGGCCAAAATGGAATAGAAGACTTTAAGAAGCATCCATTCTTCAGTGGAATTGATTGGGATAACATTCGGAATTGTGAAGCACCTTACATCCCAGAAGTTAGTAGCCCGACAGATACGTCAAATTTTGATGTGGATGACGACTGTTTAAAAAATTCTGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGAAGTGAATCATTTGGAACAACAACTTGAAGAAGCTAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAGGAACTAGTCCAGGCTAGTGAGCGATTAAAAAACCAATCCAAAGAGCTGAAAGATGCACACTGTCAGAGGAAACTGGCCATGCAGGAATTCATGGAGATCAATGAGCGACTAACAGAATTGCACACCCAAAAGCAGAAACTTGCTCGCCATGTCCGAGATAAGGAAGAAGAGGTGGACCTGGTGATGCAAAAAGCTGAGAGCTTAAGGCAGGAGCTGCGCAGAGCAGAAAGAGCCAAGAAAGAGCTGGAAGTTCACACCGAAGCTCTAATTGCTGAAGCATCAAAGGACAAGAAGCTCCGAGAGCAGAGCGAACATTATTCTAAGCAACTGGAAAACGAGTTGGAGGGCCTGAAGCAAAAACAAATTAGTTACTCACCAGGAATATGCAGCATAGAACATCAGCAAGAGATAACTAAACTGAAAACTGACTTGGAAAAGAAAAGTATCTTTTATGAAGAAGAAATTTCTAAAAGAGAAGGAATTCACGCAAGTGAGATTAAAAACCTGAAGAAGGAGCTGCATGACTCAGAAGGCCAGCAGCTTGCTCTCAACAAAGAGATTCTGGTTTTAAAAGACAAATTGGAAAAAACCAGGAGAGAAAGTCAAAGTGAAAGGGAAGAATTTGAAAATGAGTTCAAACAACAATATGAACGGGAAAAAGTATTATTAACTGAAGAGAATAAAAAGTTAACGAGTGAACTCGATAAGCTGACTTCACTGTATGAGAGCTTAAGTTTGCGCAACCAGCACTTAGAAGAAGAAGTCAAAGATCTAGCAGATAAGAAGGAATCAGTTGCCCACTGGGAAGCCCAAATCACAGAGATAATTCAGTGGGTGAGCGATGAGAAGGATGCACGAGGCTATCTTCAGGCCTTAGCTTCTAAAATGACTGAAGAGTTGGAAGCATTAAGAAATTCCAGCTTGGGGACACGAGCAACAGATATGCCCTGGAAAATGCGTCGTTTTGCAAAACTGGACATGTCGGCTAGACTAGAGTTGCAGTCTGCTCTGGATGCAGAAATAAGAGCTAAGCAGGCCATCCAGGAAGAGCTGAATAAAGTCAAAGCATCTAACATCTTAACAGAATGTAAACTGAAAGATTCAGAGAAGAAGAACTTGGAACTGTTGTCCGAAATCGAGCAGCTGATAAAGGACACTGAAGAGCTTAGATCTGAAAAGGAGACATCAAACCTGACAATATATTGA
Peptide sequence:
MDMNGHIRLADFGSCLKLMEDGTVQSSVAVGTPDYISPEILQAMEDGKGRYGPECDWWSLGVCMYEMLYGETPFYAESLVETYGKIMNHKERFQFPAQVTDVSENAKDLIRRLICSREHRLGQNGIEDFKKHPFFSGIDWDNIRNCEAPYIPEVSSPTDTSNFDVDDDCLKNSETMPPPTHTAFSGHHLPFVGFTYTSSCVLSDRSCLRVTAGPTSLDLDVSVQRTLDNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEEIEKLRKQVAEVNHLEQQLEEANSVRRELDDAFRQIKASEKQIKTLQQEREELNKELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQKQKLARHVRDKEEEVDLVMQKAESLRQELRRAERAKKELEVHTEALIAEASKDKKLREQSEHYSKQLENELEGLKQKQISYSPGICSIEHQQEITKLKTDLEKKSIFYEEEISKREGIHASEIKNLKKELHDSEGQQLALNKEILVLKDKLEKTRRESQSEREEFENEFKQQYEREKVLLTEENKKLTSELDKLTSLYESLSLRNQHLEEEVKDLADKKESVAHWEAQITEIIQWVSDEKDARGYLQALASKMTEELEALRNSSLGTRATDMPWKMRRFAKLDMSARLELQSALDAEIRAKQAIQEELNKVKASNILTECKLKDSEKKNLELLSEIEQLIKDTEELRSEKETSNLTIY
IRESfinder result
IRESfinder score
0.524144934
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page