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mmu_circIca1l_449
Basic information of circular RNA
PanCircBase ID:
mmu_circIca1l_449
mm39_Chr. Position ID:
chr1|60049267|60054994|-
Gene name:
Ica1l
Transcript:
ENSMUST00000027172.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,5,4
Exon/intron offsets:
0,3711,5603
Genomic length:
5727
Exon/intron sizes in nt:
12,61,99,124
Flanking exon/introns:
chr1:60047065-60049267|chr1:60054994-60061736
Splice length:
449
Other database IDs:
circAtlas: mmu-Ica1l_0004
Human Ortholog IDs:
Mature spliced Sequence:
TTATATCAGAGGAAGAAAATGAACTAGGACTCTTTTTAAAGTTTCAAGCAGAGCGGGATTCGACTCAAGCTGGCGAAATGATGGATGCTGCTGGCAAGGCCCTCTGTTCTTCAGCCAAGCAAAGATTGGCCTTGTGTACTCCCCTGTCTCGTCTTAAGCAAGAAGTGGCAACATTCAGTCAGAGGGCCATTTCTGACACCTTGGTGACCATTAACCGCATGGAGCGGGCCCGCACAGAGTACAGAGGAGCCCTGCTGTGGATGAAAGATGCATCGCAGGAACTTGACCCAGACACCTTCAAACAAATGGAAAAGTTCAGAAAAGTACAGAATCAAGTGAGAAACAGCAAAGATTCTTTTGACAAGTTAAAGAAGGATGTCTGCCAGAAAGTGGACTTGCTGGGAGCTAGTCGCTGCAATATGCTGTCTCACTCACTCACTACCTACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGACTTGCTGGGAGCTAG
60.11
CATTTCGCCAGCTTGAGTCG
59.9
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGACTTGCTGGGAGCTAG
60.11
GCATCCATCATTTCGCCAGC
60.32
148
PCR template sequence:
AGATTCTTTTGACAAGTTAAAGAAGGATGTCTGCCAGAAAGTGGACTTGCTGGGAGCTAGTCGCTGCAATATGCTGTCTCACTCACTCACTACCTACCAGTTATATCAGAGGAAGAAAATGAACTAGGACTCTTTTTAAAGTTTCAAGCAGAGCGGGATTCGACTCAAGCTGGCGAAATGATGGATGCTGCTGGCAAGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-328-3p(1), mmu-miR-381-3p(1), mmu-miR-136-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CACTACCTACCAGTTATATCAGAGGA
siRNA sets
ATATAACTGGTAGGTAGTG, CTCTGATATAACTGGTAGG, TCTGATATAACTGGTAGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCICA1L_449_ORF_1
0.9279
0.212842614
0.552551057
399
ORF sequence:
ATGATGGATGCTGCTGGCAAGGCCCTCTGTTCTTCAGCCAAGCAAAGATTGGCCTTGTGTACTCCCCTGTCTCGTCTTAAGCAAGAAGTGGCAACATTCAGTCAGAGGGCCATTTCTGACACCTTGGTGACCATTAACCGCATGGAGCGGGCCCGCACAGAGTACAGAGGAGCCCTGCTGTGGATGAAAGATGCATCGCAGGAACTTGACCCAGACACCTTCAAACAAATGGAAAAGTTCAGAAAAGTACAGAATCAAGTGAGAAACAGCAAAGATTCTTTTGACAAGTTAAAGAAGGATGTCTGCCAGAAAGTGGACTTGCTGGGAGCTAGTCGCTGCAATATGCTGTCTCACTCACTCACTACCTACCAGTTATATCAGAGGAAGAAAATGAACTAG
Peptide sequence:
MMDAAGKALCSSAKQRLALCTPLSRLKQEVATFSQRAISDTLVTINRMERARTEYRGALLWMKDASQELDPDTFKQMEKFRKVQNQVRNSKDSFDKLKKDVCQKVDLLGASRCNMLSHSLTTYQLYQRKKMN
IRESfinder result
IRESfinder score
0.554246235
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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