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mmu_circNotch1_513
Basic information of circular RNA
PanCircBase ID:
mmu_circNotch1_513
mm39_Chr. Position ID:
chr2|26370235|26371705|-
Gene name:
Notch1
Transcript:
ENSMUST00000028288.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,750,1347
Genomic length:
1470
Exon/intron sizes in nt:
15,62,34,123
Flanking exon/introns:
chr2:26370068-26370235|chr2:26371705-26374279
Splice length:
513
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTGCTGGACAGAACTGTGAAGAAAATGTGGATGACTGTCCAGGAAACAACTGCAAGAATGGGGGTGCCTGTGTGGACGGCGTGAATACCTACAATTGCCGCTGCCCACCGGAGTGGACGGGTCAGTACTGTACAGAGGATGTGGACGAATGTCAGCTCATGCCCAATGCCTGCCAGAATGGCGGAACCTGCCACAACACACACGGCGGCTACAACTGTGTGTGTGTCAATGGGTGGACTGGCGAGGACTGCAGTGAGAACATTGATGACTGTGCCAGTGCCGCCTGTTTCCAGGGTGCCACTTGCCACGACCGTGTGGCTTCCTTCTACTGCGAATGTCCGCATGGGCGCACAGGTCTGCTGTGCCACCTCAACGATGCGTGCATCAGCAACCCCTGCAACGAGGGCTCCAACTGTGACACCAACCCTGTCAACGGCAAAGCCATCTGCACCTGCCCCTCGGGGTACACAGGGCCAGCCTGCAGCCAGGACGTGGATGAGTGTGCTCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAACCCTGTCAACGGCAAAG
59.97
ACCCCCATTCTTGCAGTTGT
59.81
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGTGACACCAACCCTGTCA
59.82
ACCCCCATTCTTGCAGTTGT
59.81
166
PCR template sequence:
AACTGTGACACCAACCCTGTCAACGGCAAAGCCATCTGCACCTGCCCCTCGGGGTACACAGGGCCAGCCTGCAGCCAGGACGTGGATGAGTGTGCTCTGGGTTTTGCTGGACAGAACTGTGAAGAAAATGTGGATGACTGTCCAGGAAACAACTGCAAGAATGGGGGTGCCTGTGTGGACGGCGTGAATACCTACAATTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-101a-3p(1), mmu-miR-328-3p(1), mmu-miR-101b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGTGTGCTCTGGGTTTTGCTGGACA
siRNA sets
CAAAACCCAGAGCACACTC, TGTCCAGCAAAACCCAGAG, GTCCAGCAAAACCCAGAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNOTCH1_513_ORF_1
1.2201
0.355968028
0.990916496
864
ORF sequence:
ATGCCCAATGCCTGCCAGAATGGCGGAACCTGCCACAACACACACGGCGGCTACAACTGTGTGTGTGTCAATGGGTGGACTGGCGAGGACTGCAGTGAGAACATTGATGACTGTGCCAGTGCCGCCTGTTTCCAGGGTGCCACTTGCCACGACCGTGTGGCTTCCTTCTACTGCGAATGTCCGCATGGGCGCACAGGTCTGCTGTGCCACCTCAACGATGCGTGCATCAGCAACCCCTGCAACGAGGGCTCCAACTGTGACACCAACCCTGTCAACGGCAAAGCCATCTGCACCTGCCCCTCGGGGTACACAGGGCCAGCCTGCAGCCAGGACGTGGATGAGTGTGCTCTGGGTTTTGCTGGACAGAACTGTGAAGAAAATGTGGATGACTGTCCAGGAAACAACTGCAAGAATGGGGGTGCCTGTGTGGACGGCGTGAATACCTACAATTGCCGCTGCCCACCGGAGTGGACGGGTCAGTACTGTACAGAGGATGTGGACGAATGTCAGCTCATGCCCAATGCCTGCCAGAATGGCGGAACCTGCCACAACACACACGGCGGCTACAACTGTGTGTGTGTCAATGGGTGGACTGGCGAGGACTGCAGTGAGAACATTGATGACTGTGCCAGTGCCGCCTGTTTCCAGGGTGCCACTTGCCACGACCGTGTGGCTTCCTTCTACTGCGAATGTCCGCATGGGCGCACAGGTCTGCTGTGCCACCTCAACGATGCGTGCATCAGCAACCCCTGCAACGAGGGCTCCAACTGTGACACCAACCCTGTCAACGGCAAAGCCATCTGCACCTGCCCCTCGGGGTACACAGGGCCAGCCTGCAGCCAGGACGTGGATGAGTGTGCTCTG
Peptide sequence:
MPNACQNGGTCHNTHGGYNCVCVNGWTGEDCSENIDDCASAACFQGATCHDRVASFYCECPHGRTGLLCHLNDACISNPCNEGSNCDTNPVNGKAICTCPSGYTGPACSQDVDECALGFAGQNCEENVDDCPGNNCKNGGACVDGVNTYNCRCPPEWTGQYCTEDVDECQLMPNACQNGGTCHNTHGGYNCVCVNGWTGEDCSENIDDCASAACFQGATCHDRVASFYCECPHGRTGLLCHLNDACISNPCNEGSNCDTNPVNGKAICTCPSGYTGPACSQDVDECAL
IRESfinder result
IRESfinder score
0.187984478
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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