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mmu_ciNotch1_1009
Basic information of circular RNA
PanCircBase ID:
mmu_ciNotch1_1009
mm39_Chr. Position ID:
chr2|26356631|26357640|-
Gene name:
Notch1
Transcript:
ENSMUST00000028288.5
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
26
Exon/intron offsets:
0
Genomic length:
1009
Exon/intron sizes in nt:
1009
Flanking exon/introns:
chr2:26356627-26357640
Splice length:
1009
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTGCTCCAGCTCCTGCTGTTGTGGGCTGTTTCCCAGTGTGTCCCTGGGTTCTCTAACCAGCTTAACCCTGGAGGTGTAACCTCAGGGGAGGTAGTATTCACCTTATTTTATAGTCAGAAAGCACCTGGGATGAAGAGGGCATCCCTCTGATGAGGACTTGGCAGGCCTCAGGGTTTGCCCAGATGTGATTTTCAGGCCCCACTGTGTACCAGGTGTTGGAGACCAAGCTGATTAAAGCCTCCAGGGTGTCCCCTGGGGCTAAGTCATCCTAGACCAATCCTGACCCTCAGTCACTACAGCCCTTATCCCTACTACAGAGGAGGCAGTGAGGGGTACAGAAGGGCACTGTTGCTGAGCCTGGAAGGCTGAGGAGCCGAGGGAGGCACAAATAAGAGCATCTCCTGGATGCTGCACAGAGCCATCTGGGGATGGGCAGGGAAGCACCAGCCAGGCATTTGGAGGTTCCAGGAGCCTTCGCTGTTGGGCATCTGCCTGGTGGCACCTCAGTGTCTCCTGACCCCAGTGGTTCCTGGTCCTGGTTTTCTTGTCGTGGGACTGTGGTGAAGGTCAGAAATTAATTGTTTCCTGGAGGCTGTTAGAATCCTGTTTCTGAGAGGCCAGTGACTGAGAGTTGGTGACTTGGCTGGCATGAGAGAGCTGACTCTCTGGCATCTGAGCCTGCTGTCACCTCAAGCTACACCATAGGGAGTCACAACTGCATCCTTGCAGTTCTGTGGGGCCCCAGGCACTGCTCTCAAGAGGGCATTGGATGCCTAAAGACTATTCTTTGAAGTAAGGAAAAGGGGTGCTGTGCACCTAAGGGGCAAGGCTAGACAGTGGAATGACCCCCGCTGAGTGCTAAACACTGGGGCAGCAGGGAGAGTGTCCCATTGCGGGGCTGTCGTCTGATAAGCCCTGTGGGTCAGGGTGATGGGCTAGGGAGTCAGAGCTGGTGTGTAGGCAGTGTACTGGGGTGTATCTAATCTCACTGTGCCATGTGTGTTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGATAAGCCCTGTGGGTCAG
59.09
GAGAACCCAGGGACACACTG
59.96
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGATAAGCCCTGTGGGTCA
59.09
GAGAACCCAGGGACACACTG
59.96
157
PCR template sequence:
CTGATAAGCCCTGTGGGTCAGGGTGATGGGCTAGGGAGTCAGAGCTGGTGTGTAGGCAGTGTACTGGGGTGTATCTAATCTCACTGTGCCATGTGTGTTCGTGAGTGCTCCAGCTCCTGCTGTTGTGGGCTGTTTCCCAGTGTGTCCCTGGGTTCTCTAACCAGCTTAACCCTGGAGGTGTAACCTCAGGGGAGGTAGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-351-5p(2), mmu-miR-484(2), mmu-miR-199a-5p(1), mmu-miR-18a-5p(1), mmu-miR-125b-5p(1), mmu-miR-214-3p(1), mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-125a-5p(1), mmu-miR-183-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCATGTGTGTTCGTGAGTGCTCCAG
siRNA sets
CTGGAGCACTCACGAACAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CINOTCH1_1009_ORF_5
0.6565
-0.117035509
0.020296057
93
ORF sequence:
ATGTGTGTTCGTGAGTGCTCCAGCTCCTGCTGTTGTGGGCTGTTTCCCAGTGTGTCCCTGGGTTCTCTAACCAGCTTAACCCTGGAGGTGTAA
Peptide sequence:
MCVRECSSSCCCGLFPSVSLGSLTSLTLEV
IRESfinder result
IRESfinder score
0.58107426
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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