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mmu_circChd2_342
Basic information of circular RNA
PanCircBase ID:
mmu_circChd2_342
mm39_Chr. Position ID:
chr7|73143172|73147579|-
Gene name:
Chd2
Transcript:
ENSMUST00000169922.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
14,13
Exon/intron offsets:
0,4282
Genomic length:
4407
Exon/intron sizes in nt:
2,17,125
Flanking exon/introns:
chr7:73141172-73143172|chr7:73147579-73149341
Splice length:
342
Other database IDs:
CIRCpedia: MMU_CIRCpedia_213731, circAtlas: mmu-Chd2_0078
CIRCpedia: HSA_CIRCpedia_350331
Human Ortholog IDs:
Mature spliced Sequence:
GCTCTAAAGCAAAGGCCGAGATTTGTGGCTTTGAAGAAGCAGCCAGCTTATTTAGGAGGGGAGAGTCTGGAGCTCCGAGACTATCAGCTGGAGGGCCTCAACTGGCTGGCTCACTCCTGGTGCAAAAGTAACAGTGTAATCCTTGCTGATGAAATGGGCCTAGGAAAGACCATCCAGACCATATCGTTTCTCTCCTACCTGTTCCACCAGCACCAGCTCTATGGGCCTTTTCTTATAGTTGTTCCCTTGTCCACCCTTACCTCATGGCAGAGAGAGTTTGAGATCTGGGCACCAGAGATTAATGTCGTGGTTTACATAGGTGACCTGATGAGCAGAAATACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCACCCTTACCTCATGGCAG
60.11
TCTCGGAGCTCCAGACTCTC
60.11
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCACCCTTACCTCATGGC
60.11
TCTCGGAGCTCCAGACTCTC
60.11
174
PCR template sequence:
TCCCTTGTCCACCCTTACCTCATGGCAGAGAGAGTTTGAGATCTGGGCACCAGAGATTAATGTCGTGGTTTACATAGGTGACCTGATGAGCAGAAATACGGCTCTAAAGCAAAGGCCGAGATTTGTGGCTTTGAAGAAGCAGCCAGCTTATTTAGGAGGGGAGAGTCTGGAGCTCCGAGACTATCAGCTGGAGGGCCTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-138-5p(1), mmu-miR-185-5p(1), mmu-miR-484(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GAGCAGAAATACGGCTCTAAAGCAAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHD2_342_ORF_1
1.1366
0.146279949
0.783218767
531
ORF sequence:
ATGGGCCTAGGAAAGACCATCCAGACCATATCGTTTCTCTCCTACCTGTTCCACCAGCACCAGCTCTATGGGCCTTTTCTTATAGTTGTTCCCTTGTCCACCCTTACCTCATGGCAGAGAGAGTTTGAGATCTGGGCACCAGAGATTAATGTCGTGGTTTACATAGGTGACCTGATGAGCAGAAATACGGCTCTAAAGCAAAGGCCGAGATTTGTGGCTTTGAAGAAGCAGCCAGCTTATTTAGGAGGGGAGAGTCTGGAGCTCCGAGACTATCAGCTGGAGGGCCTCAACTGGCTGGCTCACTCCTGGTGCAAAAGTAACAGTGTAATCCTTGCTGATGAAATGGGCCTAGGAAAGACCATCCAGACCATATCGTTTCTCTCCTACCTGTTCCACCAGCACCAGCTCTATGGGCCTTTTCTTATAGTTGTTCCCTTGTCCACCCTTACCTCATGGCAGAGAGAGTTTGAGATCTGGGCACCAGAGATTAATGTCGTGGTTTACATAGGTGACCTGATGAGCAGAAATACG
Peptide sequence:
MGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVVYIGDLMSRNTALKQRPRFVALKKQPAYLGGESLELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVVYIGDLMSRNT
IRESfinder result
IRESfinder score
0.679359913
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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