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mmu_circItch_1189
Basic information of circular RNA
PanCircBase ID:
mmu_circItch_1189
mm39_Chr. Position ID:
chr2|155020961|155048301|+
Gene name:
Itch
Transcript:
ENSMUST00000029126.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
7,8,9,10,11,12,13,14,15,16,17
Exon/intron offsets:
0,1512,3116,4693,6388,10395,13084,20293,23165,24239,27251
Genomic length:
27340
Exon/intron sizes in nt:
46,158,196,96,175,70,85,129,73,72,89
Flanking exon/introns:
chr2:155015991-155020961|chr2:155048301-155050978
Splice length:
1189
Other database IDs:
circAtlas: mmu-Itch_0049
Human Ortholog IDs:
Mature spliced Sequence:
GTACTACACAGAATGATGATGGCTGCAGAACCAGAGATGATACAAGAGTGAGCACAAATGGATCAGAGGACCCTGAGGTTGCAGCGTCAGGGGAAAACAAGAGGGCCAATGGGAACAATTCTCCGTCCCTTTCAAATGGTGGTTTTAAGCCTTCTAGACCTCCTAGACCTTCGAGACCACCTCCACCCACCCCACGAAGACCAGCTTCTGTCAATGGCTCACCATCCACGAATTCTGACAGTGATGGATCTAGTACAGGCTCCTTGCCACCAACAAATACAAATGTAAATACAAGTACATCTGAAGGAGCAACATCTGGATTAATAATTCCTCTTACTATATCTGGAGGCTCGGGCCCTAGGCCTCTGAATACTGTAAGCCAAGCTCCCCTACCACCTGGGTGGGAGCAGAGAGTAGACCAGCATGGGCGTGTTTACTATGTAGACCATGTTGAAAAGCGAACAACATGGGATAGACCAGAACCTCTACCTCCTGGCTGGGAACGGCGTGTGGACAATATGGGACGTATTTATTATGTTGATCATTTCACAAGAACCACAACATGGCAGAGGCCAACCTTGGAATCTGTCCGGAACTATGAACAGTGGCAGCTACAGCGTAGTCAGCTTCAGGGAGCAATGCAGCAGTTTAACCAGAGATTCATCTATGGGAATCAAGATTTGTTTGCTACATCACAAAACAAAGAATTTGATCCGCTTGGTCCGTTGCCCCCTGGATGGGAGAAGAGAACTGATAGCAACGGCAGAGTGTATTTTGTCAACCACAACACTCGGATTACTCAGTGGGAAGACCCCAGAAGCCAAGGTCAGTTAAATGAAAAGCCCTTACCAGAAGGCTGGGAAATGAGATTCACAGTGGATGGAATTCCATATTTTGTGGACCACAATAGAAGAGCAACTACTTATATAGATCCACGAACGGGAAAATCAGCCTTAGACAATGGGCCCCAGATAGCCTATGTGCGGGACTTCAAGGCAAAAGTTCAGTATTTCCGGTTCTGGTGCCAGCAACTGGCCATGCCACAGCATATAAAGATCACAGTGACAAGAAAAACATTGTTTGAGGATTCCTTTCAGCAGATCATGAGCTTCAGCCCGCAAGACCTGAGAAGACGTTTGTGGGTGATTTTCCCAGGAGAAGAAGGTTTAGATTATGGAGGTGTAGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGCAAGACCTGAGAAGACGT
60.04
ACCTCAGGGTCCTCTGATCC
60.03
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCAAGACCTGAGAAGACGT
60.04
CCTCAGGGTCCTCTGATCCA
60.03
151
PCR template sequence:
CCTTTCAGCAGATCATGAGCTTCAGCCCGCAAGACCTGAGAAGACGTTTGTGGGTGATTTTCCCAGGAGAAGAAGGTTTAGATTATGGAGGTGTAGCAAGGTACTACACAGAATGATGATGGCTGCAGAACCAGAGATGATACAAGAGTGAGCACAAATGGATCAGAGGACCCTGAGGTTGCAGCGTCAGGGGAAAACAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
23
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(2), mmu-miR-127-5p(2), mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-30e-5p(1), mmu-let-7c-5p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-328-3p(1), mmu-miR-184-3p(1), mmu-miR-203-3p(1), mmu-miR-30d-5p(1), mmu-let-7d-5p(1), mmu-miR-30b-5p(1), mmu-miR-431-5p(1), mmu-miR-22-3p(1), mmu-miR-98-5p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-669d-5p(1), mmu-miR-670-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGGTGTAGCAAGGTACTACACAGAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITCH_1189_ORF_1
0.4871
0.068948083
0.699858103
687
ORF sequence:
ATGGGACGTATTTATTATGTTGATCATTTCACAAGAACCACAACATGGCAGAGGCCAACCTTGGAATCTGTCCGGAACTATGAACAGTGGCAGCTACAGCGTAGTCAGCTTCAGGGAGCAATGCAGCAGTTTAACCAGAGATTCATCTATGGGAATCAAGATTTGTTTGCTACATCACAAAACAAAGAATTTGATCCGCTTGGTCCGTTGCCCCCTGGATGGGAGAAGAGAACTGATAGCAACGGCAGAGTGTATTTTGTCAACCACAACACTCGGATTACTCAGTGGGAAGACCCCAGAAGCCAAGGTCAGTTAAATGAAAAGCCCTTACCAGAAGGCTGGGAAATGAGATTCACAGTGGATGGAATTCCATATTTTGTGGACCACAATAGAAGAGCAACTACTTATATAGATCCACGAACGGGAAAATCAGCCTTAGACAATGGGCCCCAGATAGCCTATGTGCGGGACTTCAAGGCAAAAGTTCAGTATTTCCGGTTCTGGTGCCAGCAACTGGCCATGCCACAGCATATAAAGATCACAGTGACAAGAAAAACATTGTTTGAGGATTCCTTTCAGCAGATCATGAGCTTCAGCCCGCAAGACCTGAGAAGACGTTTGTGGGTGATTTTCCCAGGAGAAGAAGGTTTAGATTATGGAGGTGTAGCAAGGTACTACACAGAATGA
Peptide sequence:
MGRIYYVDHFTRTTTWQRPTLESVRNYEQWQLQRSQLQGAMQQFNQRFIYGNQDLFATSQNKEFDPLGPLPPGWEKRTDSNGRVYFVNHNTRITQWEDPRSQGQLNEKPLPEGWEMRFTVDGIPYFVDHNRRATTYIDPRTGKSALDNGPQIAYVRDFKAKVQYFRFWCQQLAMPQHIKITVTRKTLFEDSFQQIMSFSPQDLRRRLWVIFPGEEGLDYGGVARYYTE
IRESfinder result
IRESfinder score
0.577539021
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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