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mmu_circIca1l_565
Basic information of circular RNA
PanCircBase ID:
mmu_circIca1l_565
mm39_Chr. Position ID:
chr1|60052978|60067395|-
Gene name:
Ica1l
Transcript:
ENSMUST00000027172.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,1892,8758,14248
Genomic length:
14417
Exon/intron sizes in nt:
19,91,24,73,169
Flanking exon/introns:
chr1:60049393-60052978|chr1:60067395-60081955
Splice length:
565
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TTACTCCATGGATTCCTCTGAGCAACTCAGAGCAGAAGATAACCAGTCAGTAGTGAGCAGAATGCAGAAGAACTACTGGAGAACTAAACAAGTCTTTATCAAAGCGACGGGAAAGAAGGAGGACGAGCATGTGGTTGCATCCGATGCAGAACTGGACGCTAAGTTGGAGGTTTTTCACTCCATCCAGGAGACATGCAATGAACTTGTGAAGATAGTTGAGAAATACCAGCTAAGACTCAACGTTATATCAGAGGAAGAAAATGAACTAGGACTCTTTTTAAAGTTTCAAGCAGAGCGGGATTCGACTCAAGCTGGCGAAATGATGGATGCTGCTGGCAAGGCCCTCTGTTCTTCAGCCAAGCAAAGATTGGCCTTGTGTACTCCCCTGTCTCGTCTTAAGCAAGAAGTGGCAACATTCAGTCAGAGGGCCATTTCTGACACCTTGGTGACCATTAACCGCATGGAGCGGGCCCGCACAGAGTACAGAGGAGCCCTGCTGTGGATGAAAGATGCATCGCAGGAACTTGACCCAGACACCTTCAAACAAATGGAAAAGTTCAGAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCACAGAGTACAGAGGAGCC
59.83
TCTGCTCACTACTGACTGGT
57.71
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCACAGAGTACAGAGGAGC
60.18
TCTGCTCACTACTGACTGGT
57.71
154
PCR template sequence:
GCGGGCCCGCACAGAGTACAGAGGAGCCCTGCTGTGGATGAAAGATGCATCGCAGGAACTTGACCCAGACACCTTCAAACAAATGGAAAAGTTCAGAAAATTACTCCATGGATTCCTCTGAGCAACTCAGAGCAGAAGATAACCAGTCAGTAGTGAGCAGAATGCAGAAGAACTACTGGAGAACTAAACAAGTCTTTATC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
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-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGTTCAGAAAATTACTCCATGGAT
siRNA sets
ATGGAGTAATTTTCTGAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCICA1L_565_ORF_1
0.9452
0.21792304
0.865359058
621
ORF sequence:
ATGCATCGCAGGAACTTGACCCAGACACCTTCAAACAAATGGAAAAGTTCAGAAAATTACTCCATGGATTCCTCTGAGCAACTCAGAGCAGAAGATAACCAGTCAGTAGTGAGCAGAATGCAGAAGAACTACTGGAGAACTAAACAAGTCTTTATCAAAGCGACGGGAAAGAAGGAGGACGAGCATGTGGTTGCATCCGATGCAGAACTGGACGCTAAGTTGGAGGTTTTTCACTCCATCCAGGAGACATGCAATGAACTTGTGAAGATAGTTGAGAAATACCAGCTAAGACTCAACGTTATATCAGAGGAAGAAAATGAACTAGGACTCTTTTTAAAGTTTCAAGCAGAGCGGGATTCGACTCAAGCTGGCGAAATGATGGATGCTGCTGGCAAGGCCCTCTGTTCTTCAGCCAAGCAAAGATTGGCCTTGTGTACTCCCCTGTCTCGTCTTAAGCAAGAAGTGGCAACATTCAGTCAGAGGGCCATTTCTGACACCTTGGTGACCATTAACCGCATGGAGCGGGCCCGCACAGAGTACAGAGGAGCCCTGCTGTGGATGAAAGATGCATCGCAGGAACTTGACCCAGACACCTTCAAACAAATGGAAAAGTTCAGAAAA
Peptide sequence:
MHRRNLTQTPSNKWKSSENYSMDSSEQLRAEDNQSVVSRMQKNYWRTKQVFIKATGKKEDEHVVASDAELDAKLEVFHSIQETCNELVKIVEKYQLRLNVISEEENELGLFLKFQAERDSTQAGEMMDAAGKALCSSAKQRLALCTPLSRLKQEVATFSQRAISDTLVTINRMERARTEYRGALLWMKDASQELDPDTFKQMEKFRK
IRESfinder result
IRESfinder score
0.537792001
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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