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mmu_ciChka_556
Basic information of circular RNA
PanCircBase ID:
mmu_ciChka_556
mm39_Chr. Position ID:
chr19|3942791|3943347|+
Gene name:
Chka
Transcript:
ENSMUST00000128694.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
12
Exon/intron offsets:
0
Genomic length:
556
Exon/intron sizes in nt:
556
Flanking exon/introns:
chr19:3942791-3943347
Splice length:
556
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTTTCAGGGGTAATTCTCCCAACTGCAATGAAGAGCTGTGGTGTGTGAGCTTGATTTGGGCATTTGGTGACCTAGTGGCACCAGGGCAGTGTAGCCTCACTCCAGGGCCATAGGAGCTGTCCTTGACATGAGACTCTTTCTTGGGGCAGGTCCTTCTCATACTAGGATGATTCTCCTTTAGGTGGGAGGTTTGGTAATGATGCCATGAGGCAAAGACAAGAAACATTTGGATATTTAAAGCAGGTTTTCAAGTCAGCACGTTGGCTCAGCAGGTGAAGGCTTCTGCCACCAAGCTTTTGATGAGTAATCTAGTACCCACATGGTGGAAGGAGAACTGTCCCTTGCAAGTTGTCCCTTGACCTCTACACATGCTATGTGGCATGAGTATGCCCTGACAAATGAAATGAAATTTTAAAAATCTGACATGACCGGATGATCAAAGATGGCATCAGAGACACAGGTGTGGGTTTTGCTGCCATGGTGGTCCACAGCAGCACAGACGGTCCGGTCAGCCTGGCTACATAGTGAAGTACTTTGTTCGGTCTCTTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACAGGTGTGGGTTTTGCTG
59.9
GCTCACACACCACAGCTCTT
60.53
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACAGGTGTGGGTTTTGCTG
59.9
AAGCTCACACACCACAGCTC
60.53
153
PCR template sequence:
AGACACAGGTGTGGGTTTTGCTGCCATGGTGGTCCACAGCAGCACAGACGGTCCGGTCAGCCTGGCTACATAGTGAAGTACTTTGTTCGGTCTCTTCCAGGTAAGTTTCAGGGGTAATTCTCCCAACTGCAATGAAGAGCTGTGGTGTGTGAGCTTGATTTGGGCATTTGGTGACCTAGTGGCACCAGGGCAGTGTAGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-17-5p(1), mmu-miR-511-3p(1), mmu-miR-370-3p(1), mmu-miR-324-3p(1), mmu-miR-377-3p(1), mmu-miR-300-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGGTCTCTTCCAGGTAAGTTTCAGGG
siRNA sets
TGAAACTTACCTGGAAGAG, AACTTACCTGGAAGAGACC, GAAACTTACCTGGAAGAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CICHKA_556_ORF_1
1.1729
-0.190942679
0.045394105
114
ORF sequence:
ATGGCATCAGAGACACAGGTGTGGGTTTTGCTGCCATGGTGGTCCACAGCAGCACAGACGGTCCGGTCAGCCTGGCTACATAGTGAAGTACTTTGTTCGGTCTCTTCCAGGTAA
Peptide sequence:
MASETQVWVLLPWWSTAAQTVRSAWLHSEVLCSVSSR
IRESfinder result
IRESfinder score
0.498730665
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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