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mmu_circRnf25_576
Basic information of circular RNA
PanCircBase ID:
mmu_circRnf25_576
mm39_Chr. Position ID:
chr1|74634789|74638299|-
Gene name:
Rnf25
Transcript:
ENSMUST00000135140.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,6,5,4,3,2
Exon/intron offsets:
0,235,2731,2899,3062,3435
Genomic length:
3510
Exon/intron sizes in nt:
138,72,70,68,153,75
Flanking exon/introns:
chr1:74634460-74634789|chr1:74638299-74640483
Splice length:
576
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGTCCTTCCCTCTGAAGTTGAAGTATTAGAGTCTATCTATCTGGATGAGCTACAGGTGATGAAAGGGAATGGCAGCTCTCAAGCCCCTGCCTAGTCACATCCTTCGTTTTCACTTCATCCCCCTGCAGATCACCATGGGAGATCTTTATCACTCTGCACCCTGCCACCGCAGAGGTCCAAGATTCGCAGTTTGTCTGCTTTACTCTGGTTCTTCGGATCCCAGTCCAGTATCCCCACGAGGTTCCACAGATCTCCATCCGTAACCCTCGAGGACTTTCAGATGAGCAGATCCACAAGATCTCACAGGCCCTGGGCCATGTGGCCAAGGAAGGACTAGGCACTGCCATGCTCTATGAACTCATTGAGAAAGGGAAGGAGATTCTCACGGATAACAACATTCCCCATGGCCAGTGTGTCATCTGCCTCTATGGTTTCCAGGAGAAGGAGGCCTTTACCAAAACACCCTGTTACCACTACTTCCACTGCCATTGCCTTGCCAGGTACATCCAGCACATGGAACAAGAGCTGACTACACAGGAACAGGAACAGGAGCGACAGCACGTTGTCACCAAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGCCAGGTACATCCAGCA
60.04
CTTGAGAGCTGCCATTCCCT
59.74
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGGTACATCCAGCACAT
60.11
CTTGAGAGCTGCCATTCCCT
59.74
164
PCR template sequence:
CTTCCACTGCCATTGCCTTGCCAGGTACATCCAGCACATGGAACAAGAGCTGACTACACAGGAACAGGAACAGGAGCGACAGCACGTTGTCACCAAGCAGGGTCCTTCCCTCTGAAGTTGAAGTATTAGAGTCTATCTATCTGGATGAGCTACAGGTGATGAAAGGGAATGGCAGCTCTCAAGCCCCTGCCTAGTCACAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-211-5p(2), mmu-miR-204-5p(2), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-709(1), mmu-miR-34b-5p(1), mmu-miR-207(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TGTCACCAAGCAGGGTCCTTCCCTCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRNF25_576_ORF_1
0.961
0.321635616
0.403069566
246
ORF sequence:
ATGCTCTATGAACTCATTGAGAAAGGGAAGGAGATTCTCACGGATAACAACATTCCCCATGGCCAGTGTGTCATCTGCCTCTATGGTTTCCAGGAGAAGGAGGCCTTTACCAAAACACCCTGTTACCACTACTTCCACTGCCATTGCCTTGCCAGGTACATCCAGCACATGGAACAAGAGCTGACTACACAGGAACAGGAACAGGAGCGACAGCACGTTGTCACCAAGCAGGGTCCTTCCCTCTGA
Peptide sequence:
MLYELIEKGKEILTDNNIPHGQCVICLYGFQEKEAFTKTPCYHYFHCHCLARYIQHMEQELTTQEQEQERQHVVTKQGPSL
IRESfinder result
IRESfinder score
0.685113045
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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