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mmu_circChd4_539
Basic information of circular RNA
PanCircBase ID:
mmu_circChd4_539
mm39_Chr. Position ID:
chr6|125090427|125091429|+
Gene name:
Chd4
Transcript:
ENSMUST00000112392.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
23,24,25
Exon/intron offsets:
0,435,826
Genomic length:
1002
Exon/intron sizes in nt:
12,52,38,176
Flanking exon/introns:
chr6:125087333-125090427|chr6:125091429-125097167
Splice length:
539
Other database IDs:
circAtlas: mmu-Chd4_0001
circBase: hsa_circ_0099056, circAtlas: hsa-CHD4_0001, CIRCpedia: HSA_CIRCpedia_9401
Human Ortholog IDs:
Mature spliced Sequence:
CACCGGGTGCTCAACAGTTCTGCTTCTTGCTTTCCACTCGAGCTGGGGGCCTTGGGATCAATCTGGCCACTGCGGACACAGTTATTATATATGACTCTGACTGGAACCCCCATAATGACATCCAGGCCTTTAGCAGAGCCCACCGTATTGGGCAAAATAAGAAGGTGATGATCTACCGGTTTGTGACCCGTGCATCAGTGGAGGAGCGCATCACGCAGGTGGCAAAGAAGAAGATGATGCTGACACATTTAGTGGTACGGCCTGGCCTGGGCTCCAAGACAGGCTCAATGTCTAAACAGGAGCTTGATGATATCCTCAAATTTGGCACTGAGGAGCTATTCAAGGATGAAGCCACGGATGGAGGAGGAGACAACAAGGAGGGAGAAGACAGCAGTGTTATCCACTATGACGATAAGGCCATTGAACGACTGCTGGATCGAAACCAGGATGAGACTGAAGACACAGAATTGCAGGGCATGAATGAATATTTGAGCTCATTCAAAGTGGCTCAGTATGTGGTACGGGAAGAAGAGATGGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGACACAGAATTGCAGGGCA
59.89
CAGTGGCCAGATTGATCCCA
59.74
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGACACAGAATTGCAGGGCA
59.89
TGGCCAGATTGATCCCAAGG
59.74
151
PCR template sequence:
AAACCAGGATGAGACTGAAGACACAGAATTGCAGGGCATGAATGAATATTTGAGCTCATTCAAAGTGGCTCAGTATGTGGTACGGGAAGAAGAGATGGGGCACCGGGTGCTCAACAGTTCTGCTTCTTGCTTTCCACTCGAGCTGGGGGCCTTGGGATCAATCTGGCCACTGCGGACACAGTTATTATATATGACTCTGA
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-29b-1-5p(1), mmu-miR-362-5p(1), mmu-miR-207(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAGAGATGGGGCACCGGGTGCTCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHD4_539_ORF_1
0.9147
0.338034028
0.847040875
540
ORF sequence:
ATGATCTACCGGTTTGTGACCCGTGCATCAGTGGAGGAGCGCATCACGCAGGTGGCAAAGAAGAAGATGATGCTGACACATTTAGTGGTACGGCCTGGCCTGGGCTCCAAGACAGGCTCAATGTCTAAACAGGAGCTTGATGATATCCTCAAATTTGGCACTGAGGAGCTATTCAAGGATGAAGCCACGGATGGAGGAGGAGACAACAAGGAGGGAGAAGACAGCAGTGTTATCCACTATGACGATAAGGCCATTGAACGACTGCTGGATCGAAACCAGGATGAGACTGAAGACACAGAATTGCAGGGCATGAATGAATATTTGAGCTCATTCAAAGTGGCTCAGTATGTGGTACGGGAAGAAGAGATGGGGCACCGGGTGCTCAACAGTTCTGCTTCTTGCTTTCCACTCGAGCTGGGGGCCTTGGGATCAATCTGGCCACTGCGGACACAGTTATTATATATGACTCTGACTGGAACCCCCATAATGACATCCAGGCCTTTAGCAGAGCCCACCGTATTGGGCAAAATAAGAAGGTGA
Peptide sequence:
MIYRFVTRASVEERITQVAKKKMMLTHLVVRPGLGSKTGSMSKQELDDILKFGTEELFKDEATDGGGDNKEGEDSSVIHYDDKAIERLLDRNQDETEDTELQGMNEYLSSFKVAQYVVREEEMGHRVLNSSASCFPLELGALGSIWPLRTQLLYMTLTGTPIMTSRPLAEPTVLGKIRR
IRESfinder result
IRESfinder score
0.278989187
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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