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mmu_ciStk40_964
Basic information of circular RNA
PanCircBase ID:
mmu_ciStk40_964
mm39_Chr. Position ID:
chr4|126031638|126032602|+
Gene name:
Stk40
Transcript:
ENSMUST00000116286.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
12
Exon/intron offsets:
0
Genomic length:
964
Exon/intron sizes in nt:
964
Flanking exon/introns:
chr4:126031638-126032602
Splice length:
964
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTGGGGAGCAGGGGGAATTCCTGGGTTTTCCCTCCCCGGCCCTTGCAATAGAAAGGCACCCCTGGCCTGCCTTGTGACCTGCCGTGGGAGCTCCCAGTGCCAGGCAACCATCTGGGCCTCTGGGGTGGCCTCTTCCTGCCCCAGTCACAGTTCTCTCCCTCTCTGACTCACTGGGTTCTCTCTCACCCTTCCTGCTTTTCAGTTTTTACATGATTCATTTATCCCTCTTCTCTCTCCTCCCTGTTCCACAGTAGAGAAAGTGCTGGGCGAGGGGTGGGCACAGAGACATGAGTGCTTAGGCAGCAGCTGTGACAGGTTTCAGGGTGCCCCGAGAGGGAAGCTGGGCCTTCCCTGGGAGCACTGGCCGAGTAGGACCAGGAAGAGCTGTGAGTGGAAGCCCACCCGGTTCCCATTCAGTCCACCCTAGGGCACGTGGGTCCTATTTTTACCTGAGGATCGGAGAAGTACACTGATGTGTCCACGGTCACACAGTGTGGCAGCAGGGGAATTGTGCCTTGATTCCAAAATCCTGCCTTCCCACTAGTCAGGACCTGCCGCTGGAGTCTTCCATCGCCTGCCTAACCCCCACACGTGTCAGCCCCTCAGAGTTCCAGAGACCCTTTGTGAGGAGACACCCTTCACTGCCACTCTACTCACATGCACACACCGCTGCACCCTCCCCCTCGTACACACGTGCTCTACCCTTACCTCATACGCCCCACCACCACACACACGCACCCCACTATGGGGAGGATGCTATGCAGCCTAGAAGGCCAGAGGAAAGGGTTGTGTGTAGCTAGAGCTTCCGGCAGCCACTCACATCAGCCAGCAGGGCCCCCCACTCAGCCTGTAGGAAGATGGCGCTTGAACTGTGGTACCCGGGAAACATGACCTCAGCAGCCACACTGTGCTGGGCTCCCCGAGTGCTTGCTGTCTTCACCTTGCTCTCTCCCCTCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGTACCCGGGAAACATG
59.96
GCCAGGGGTGCCTTTCTATT
60.03
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACTGTGGTACCCGGGAAAC
59.89
GCCAGGGGTGCCTTTCTATT
60.03
163
PCR template sequence:
GCGCTTGAACTGTGGTACCCGGGAAACATGACCTCAGCAGCCACACTGTGCTGGGCTCCCCGAGTGCTTGCTGTCTTCACCTTGCTCTCTCCCCTCACAGGTGAGTGGGGAGCAGGGGGAATTCCTGGGTTTTCCCTCCCCGGCCCTTGCAATAGAAAGGCACCCCTGGCCTGCCTTGTGACCTGCCGTGGGAGCTCCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-125a-5p(1), mmu-miR-342-5p(1), mmu-miR-207(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTCCCCTCACAGGTGAGTGGGGAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CISTK40_964_ORF_1
0.7532
-0.007423887
0.124793766
273
ORF sequence:
ATGGCGCTTGAACTGTGGTACCCGGGAAACATGACCTCAGCAGCCACACTGTGCTGGGCTCCCCGAGTGCTTGCTGTCTTCACCTTGCTCTCTCCCCTCACAGGTGAGTGGGGAGCAGGGGGAATTCCTGGGTTTTCCCTCCCCGGCCCTTGCAATAGAAAGGCACCCCTGGCCTGCCTTGTGACCTGCCGTGGGAGCTCCCAGTGCCAGGCAACCATCTGGGCCTCTGGGGTGGCCTCTTCCTGCCCCAGTCACAGTTCTCTCCCTCTCTGA
Peptide sequence:
MALELWYPGNMTSAATLCWAPRVLAVFTLLSPLTGEWGAGGIPGFSLPGPCNRKAPLACLVTCRGSSQCQATIWASGVASSCPSHSSLPL
IRESfinder result
IRESfinder score
0.705036385
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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