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mmu_ciCerkl_1462
Basic information of circular RNA
PanCircBase ID:
mmu_ciCerkl_1462
mm39_Chr. Position ID:
chr2|79285432|79286894|-
Gene name:
Cerkl
Transcript:
ENSMUST00000153602.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
1
Exon/intron offsets:
0
Genomic length:
1462
Exon/intron sizes in nt:
1462
Flanking exon/introns:
chr2:79223529-79286894
Splice length:
1462
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAATTATGATTCCTATTTTTTACTCTCCCGAGAATAAAAGCAATAATTGAAGAGCTGTACCTTGGTACTTTGCATGCGCACATTTGTGGAGTCGGTTGTCCCTATATTTGAGATCAGTGTCCCTCCTCGTAATTGCCCACAAGTACTCGCACGTAATGAGTCCCAGCACTCAAGTACCCCCTGCAGGCTTTCTAATTACATTTAATTTTTAATAGTATAGAAGCTTTTAGAATGTTTGGGGAGGGGAGTAACTGTAATTATTTGTAAGCGGTTATTTGAAAGTCCCCAAAGCAAACAACCACTTCCAGTTCTCACTTATTCAGGGGAGAAAAGGAGAGAAAGAGAAAAACAAAACAAAACAAAACAAACAAACAAAAACACCTGCTGCCCATAGTTTTATTTGGTGTACAGATATTTAGGCTCATCGTGCATATGAAACTATCTATTTCAGGAGAATGTAGTACTGGAAAACCGATTGGACTCTGAAATAGCTTAGCTGAAATGTAGGGAGAGGGGGAGAAAAGGAAGGAAATTTTCCTGCTACCTGTTACTGTCCCAGAGGCGGCCAAGTCCCCATGCTGGGGCCAGACATTCAGTTGTTTTACTAAAGGCTTTTTACAGTTCTTATGAGAAGCAGCACCTTCACCATTGCCAGTCGCTGACCATTGTAATTACTCCATCTTTTAAAGGGAGGTTTGAGGCGAACTTTGAAAAGCCCCAATAAAGAGCGGGCGGCCCTTTCAATGGGCTGTTTATTAGAGAGGAGCCTTTTGCACCTGATCCCCAGCGCGTGGGAGAGCCTCGCCTGGGAGCCAGAGCTTTTGTACAAGGTGGGAATTTAGCGGGGGCGTGGGGGGGGGGTGGTGAGGCAAAGAAAGAAAGGCAAGAGAGGGATGGAAGACTTGTGCCCACTTCTGTGGCCAAATGTGTTGTCGATAGGAAAATAATTTGATGGAAACTACCTTTCCTCCTCTGTGCATTGGCTCTCCCTTCCATATAATCTTCTTTAAAAATTGGGGTCAGTGCTAGGAAATTACGTAATGGCTTTTCAATTTATTTAAACCTCTAAGTAGTGCGAAGCCAGAGCAGAGATGAGTTCAGAGTATTCCATTTCCAAACTCATCGTTTTTGTGAGTTGGGAGTGACTTGGGACACAGTCAGAAAACCATGCACTCTGTACGCATTTCCACACAGGGCACCTGGCCAGATAATTGCCCTGCACACAGTTGAGCTGATCACTAGGAAAGGCACCCATAGCCACTCATGACAGGCCTAGTGGTACCTACTACGCAGCACCGAGGTACAGACACGCCAGCATGAAGCACTGCGTTTAACTTTTCCTGGAGGCATCCATTTTGCAGTGGACTCCTGTGTATTTCTATTTGTGTGCATTTCTGTAGGATTAGGGAGAGGGAGCTGAAGGCTTATCCAGCTTTTAAATATAGCGGGTGGATTTCCCCC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAGGGAGAGGGAGCTGAAGG
59.74
ACTCCACAAATGTGCGCATG
59.76
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAGGGAGAGGGAGCTGAAGG
59.74
GACTCCACAAATGTGCGCAT
59.48
152
PCR template sequence:
TGGACTCCTGTGTATTTCTATTTGTGTGCATTTCTGTAGGATTAGGGAGAGGGAGCTGAAGGCTTATCCAGCTTTTAAATATAGCGGGTGGATTTCCCCCGTAATTATGATTCCTATTTTTTACTCTCCCGAGAATAAAAGCAATAATTGAAGAGCTGTACCTTGGTACTTTGCATGCGCACATTTGTGGAGTCGGTTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-196a-5p(2), mmu-miR-384-3p(2), mmu-miR-5101(2), mmu-miR-140-5p(1), mmu-miR-106a-5p(1), mmu-miR-221-3p(1), mmu-miR-320-3p(1), mmu-miR-182-5p(1), mmu-miR-224-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-350-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGGATTTCCCCCGTAATTATGATTC
siRNA sets
ATAATTACGGGGGAAATCC, GAATCATAATTACGGGGGA, AATCATAATTACGGGGGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.790810918
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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