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mmu_circIca1l_522
Basic information of circular RNA
PanCircBase ID:
mmu_circIca1l_522
mm39_Chr. Position ID:
chr1|60049267|60061809|-
Gene name:
Ica1l
Transcript:
ENSMUST00000027172.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,3711,5603,12469
Genomic length:
12542
Exon/intron sizes in nt:
126,199,124,73
Flanking exon/introns:
chr1:60047065-60049267|chr1:60061809-60067226
Splice length:
522
Other database IDs:
circAtlas: mmu-Ica1l_0021
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTTCACTCCATCCAGGAGACATGCAATGAACTTGTGAAGATAGTTGAGAAATACCAGCTAAGACTCAACGTTATATCAGAGGAAGAAAATGAACTAGGACTCTTTTTAAAGTTTCAAGCAGAGCGGGATTCGACTCAAGCTGGCGAAATGATGGATGCTGCTGGCAAGGCCCTCTGTTCTTCAGCCAAGCAAAGATTGGCCTTGTGTACTCCCCTGTCTCGTCTTAAGCAAGAAGTGGCAACATTCAGTCAGAGGGCCATTTCTGACACCTTGGTGACCATTAACCGCATGGAGCGGGCCCGCACAGAGTACAGAGGAGCCCTGCTGTGGATGAAAGATGCATCGCAGGAACTTGACCCAGACACCTTCAAACAAATGGAAAAGTTCAGAAAAGTACAGAATCAAGTGAGAAACAGCAAAGATTCTTTTGACAAGTTAAAGAAGGATGTCTGCCAGAAAGTGGACTTGCTGGGAGCTAGTCGCTGCAATATGCTGTCTCACTCACTCACTACCTACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAAAGTGGACTTGCTGGGAG
59.93
AACGTTGAGTCTTAGCTGGT
56.8
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAAAGTGGACTTGCTGGGA
58.86
AACGTTGAGTCTTAGCTGGT
56.8
140
PCR template sequence:
AGATTCTTTTGACAAGTTAAAGAAGGATGTCTGCCAGAAAGTGGACTTGCTGGGAGCTAGTCGCTGCAATATGCTGTCTCACTCACTCACTACCTACCAGGTTTTTCACTCCATCCAGGAGACATGCAATGAACTTGTGAAGATAGTTGAGAAATACCAGCTAAGACTCAACGTTATATCAGAGGAAGAAAATGAACTAG
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
CACTACCTACCAGGTTTTTCACTCCA
siRNA sets
GAGTGAAAAACCTGGTAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCICA1L_522_ORF_1
0.9317
0.231324404
0.979412843
894
ORF sequence:
ATGATGGATGCTGCTGGCAAGGCCCTCTGTTCTTCAGCCAAGCAAAGATTGGCCTTGTGTACTCCCCTGTCTCGTCTTAAGCAAGAAGTGGCAACATTCAGTCAGAGGGCCATTTCTGACACCTTGGTGACCATTAACCGCATGGAGCGGGCCCGCACAGAGTACAGAGGAGCCCTGCTGTGGATGAAAGATGCATCGCAGGAACTTGACCCAGACACCTTCAAACAAATGGAAAAGTTCAGAAAAGTACAGAATCAAGTGAGAAACAGCAAAGATTCTTTTGACAAGTTAAAGAAGGATGTCTGCCAGAAAGTGGACTTGCTGGGAGCTAGTCGCTGCAATATGCTGTCTCACTCACTCACTACCTACCAGGTTTTTCACTCCATCCAGGAGACATGCAATGAACTTGTGAAGATAGTTGAGAAATACCAGCTAAGACTCAACGTTATATCAGAGGAAGAAAATGAACTAGGACTCTTTTTAAAGTTTCAAGCAGAGCGGGATTCGACTCAAGCTGGCGAAATGATGGATGCTGCTGGCAAGGCCCTCTGTTCTTCAGCCAAGCAAAGATTGGCCTTGTGTACTCCCCTGTCTCGTCTTAAGCAAGAAGTGGCAACATTCAGTCAGAGGGCCATTTCTGACACCTTGGTGACCATTAACCGCATGGAGCGGGCCCGCACAGAGTACAGAGGAGCCCTGCTGTGGATGAAAGATGCATCGCAGGAACTTGACCCAGACACCTTCAAACAAATGGAAAAGTTCAGAAAAGTACAGAATCAAGTGAGAAACAGCAAAGATTCTTTTGACAAGTTAAAGAAGGATGTCTGCCAGAAAGTGGACTTGCTGGGAGCTAGTCGCTGCAATATGCTGTCTCACTCACTCACTACCTACCAG
Peptide sequence:
MMDAAGKALCSSAKQRLALCTPLSRLKQEVATFSQRAISDTLVTINRMERARTEYRGALLWMKDASQELDPDTFKQMEKFRKVQNQVRNSKDSFDKLKKDVCQKVDLLGASRCNMLSHSLTTYQVFHSIQETCNELVKIVEKYQLRLNVISEEENELGLFLKFQAERDSTQAGEMMDAAGKALCSSAKQRLALCTPLSRLKQEVATFSQRAISDTLVTINRMERARTEYRGALLWMKDASQELDPDTFKQMEKFRKVQNQVRNSKDSFDKLKKDVCQKVDLLGASRCNMLSHSLTTYQ
IRESfinder result
IRESfinder score
0.575240919
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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