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mmu_circC2cd5_347
Basic information of circular RNA
PanCircBase ID:
mmu_circC2cd5_347
mm39_Chr. Position ID:
chr6|143007478|143018420|-
Gene name:
C2cd5
Transcript:
ENSMUST00000171349.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
10,9,8
Exon/intron offsets:
0,5303,10790
Genomic length:
10942
Exon/intron sizes in nt:
1,09,86,152
Flanking exon/introns:
chr6:142995965-143007478|chr6:143018420-143023988
Splice length:
347
Other database IDs:
circAtlas: mmu-C2cd5_0005
circAtlas: hsa-C2CD5_0002, CIRCpedia: HSA_CIRCpedia_7972
Human Ortholog IDs:
Mature spliced Sequence:
GATTCCCTTCAATGAGGATCCCAACCCCAATACTCACTCATCAGGACCCTCAACCCCTCTGAAAAACCAAACTTATTCCTTTTCACCTTCCAAGTCCTACAGTCGGCAGTCCTCTTCTTCTGACACAGATTTGAGTTTGACACCCAAGACTGGAATGGGCAGTGGGAGTGCTGGAAAAGAAGGGGGGCCCTTTAAAGCCCTTTTACGGCAACAGACGCAGTCGGCGTTGGAACAGCGGGAGTTCCCGTTCCTCACCCTGACGGCCTTCCCCCCTGGACTTCTTGTGCACGTCGGTGGCGTTGTCAGTGCACGCTCTGTGAAGCTTTTAGATCGGATCCACAACCCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGGACTTCTTGTGCACGT
60.53
TTTCAGAGGGGTTGAGGGTC
58.94
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCTGGACTTCTTGTGCAC
60.89
TTCAGAGGGGTTGAGGGTCC
60.84
141
PCR template sequence:
TTCCTCACCCTGACGGCCTTCCCCCCTGGACTTCTTGTGCACGTCGGTGGCGTTGTCAGTGCACGCTCTGTGAAGCTTTTAGATCGGATCCACAACCCTGGATTCCCTTCAATGAGGATCCCAACCCCAATACTCACTCATCAGGACCCTCAACCCCTCTGAAAAACCAAACTTATTCCTTTTCACCTTCCAAGTCCTAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-296-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCCACAACCCTGGATTCCCTTCAAT
siRNA sets
ATTGAAGGGAATCCAGGGT,GAAGGGAATCCAGGGTTGT,TTGAAGGGAATCCAGGGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCC2CD5_347_ORF_1
0.7934
0.175136752
0.226584804
255
ORF sequence:
ATGGGCAGTGGGAGTGCTGGAAAAGAAGGGGGGCCCTTTAAAGCCCTTTTACGGCAACAGACGCAGTCGGCGTTGGAACAGCGGGAGTTCCCGTTCCTCACCCTGACGGCCTTCCCCCCTGGACTTCTTGTGCACGTCGGTGGCGTTGTCAGTGCACGCTCTGTGAAGCTTTTAGATCGGATCCACAACCCTGGATTCCCTTCAATGAGGATCCCAACCCCAATACTCACTCATCAGGACCCTCAACCCCTCTGA
Peptide sequence:
MGSGSAGKEGGPFKALLRQQTQSALEQREFPFLTLTAFPPGLLVHVGGVVSARSVKLLDRIHNPGFPSMRIPTPILTHQDPQPL
IRESfinder result
IRESfinder score
0.691963975
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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