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mmu_circCdh4_474
Basic information of circular RNA
PanCircBase ID:
mmu_circCdh4_474
mm39_Chr. Position ID:
chr2|179484761|179502082|+
Gene name:
Cdh4
Transcript:
ENSMUST00000000314.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,6,7
Exon/intron offsets:
0,4251,17148
Genomic length:
17321
Exon/intron sizes in nt:
15,61,45,173
Flanking exon/introns:
chr2:179439421-179484761|chr2:179502082-179515864
Splice length:
474
Other database IDs:
CIRCpedia: MMU_CIRCpedia_12215, circAtlas: mmu-Cdh4_0004
circBase: hsa_circ_0061019, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_34881
Human Ortholog IDs:
Mature spliced Sequence:
ATCAGGTCGGACAAAGACAATGACATCCCCATCCGCTACAGCATCACGGGTGTGGGCGCCGACCAGCCCCCCATGGAGGTCTTCAACATCGACTCTATGTCTGGCCGGATGTATGTCACTCGGCCCATGGACCGGGAGGAAAGAGCCTCTTACCATCTCCGAGCCCACGCGGTGGATATGAACGGTAACAAGGTGGAGAATCCTATTGACCTGTACATCTACGTCATTGACATGAACGACAACCGTCCCGAGTTCATCAACCAGGTCTACAACGGCTCTGTGGATGAGGGCTCCAAGCCAGGTACATATGTGATGACCGTCACAGCCAACGATGCAGATGATAGCACCACAGCCAATGGCATGGTGAGGTACAGAATTGTCACCCAGACACCCCAGAGCCCATCCCAGAATATGTTCACCATCAACAGTGAAACAGGGGACATCGTGACCGTGGCAGCAGGCCTGGACAGAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGAGCCCATCCCAGAAT
61.36
GTTGAAGACCTCCATGGGGG
60.03
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGAGCCCATCCCAGAATA
58.56
GTTGAAGACCTCCATGGGGG
60.03
169
PCR template sequence:
AATTGTCACCCAGACACCCCAGAGCCCATCCCAGAATATGTTCACCATCAACAGTGAAACAGGGGACATCGTGACCGTGGCAGCAGGCCTGGACAGAGAGATCAGGTCGGACAAAGACAATGACATCCCCATCCGCTACAGCATCACGGGTGTGGGCGCCGACCAGCCCCCCATGGAGGTCTTCAACATCGACTCTATGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
CCTGGACAGAGAGATCAGGTCGGACA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDH4_474_ORF_1
1.3174
0.622612716
0.997651718
876
ORF sequence:
ATGGAGGTCTTCAACATCGACTCTATGTCTGGCCGGATGTATGTCACTCGGCCCATGGACCGGGAGGAAAGAGCCTCTTACCATCTCCGAGCCCACGCGGTGGATATGAACGGTAACAAGGTGGAGAATCCTATTGACCTGTACATCTACGTCATTGACATGAACGACAACCGTCCCGAGTTCATCAACCAGGTCTACAACGGCTCTGTGGATGAGGGCTCCAAGCCAGGTACATATGTGATGACCGTCACAGCCAACGATGCAGATGATAGCACCACAGCCAATGGCATGGTGAGGTACAGAATTGTCACCCAGACACCCCAGAGCCCATCCCAGAATATGTTCACCATCAACAGTGAAACAGGGGACATCGTGACCGTGGCAGCAGGCCTGGACAGAGAGATCAGGTCGGACAAAGACAATGACATCCCCATCCGCTACAGCATCACGGGTGTGGGCGCCGACCAGCCCCCCATGGAGGTCTTCAACATCGACTCTATGTCTGGCCGGATGTATGTCACTCGGCCCATGGACCGGGAGGAAAGAGCCTCTTACCATCTCCGAGCCCACGCGGTGGATATGAACGGTAACAAGGTGGAGAATCCTATTGACCTGTACATCTACGTCATTGACATGAACGACAACCGTCCCGAGTTCATCAACCAGGTCTACAACGGCTCTGTGGATGAGGGCTCCAAGCCAGGTACATATGTGATGACCGTCACAGCCAACGATGCAGATGATAGCACCACAGCCAATGGCATGGTGAGGTACAGAATTGTCACCCAGACACCCCAGAGCCCATCCCAGAATATGTTCACCATCAACAGTGAAACAGGGGACATCGTGACCGTGGCAGCAGGCCTGGACAGAGAG
Peptide sequence:
MEVFNIDSMSGRMYVTRPMDREERASYHLRAHAVDMNGNKVENPIDLYIYVIDMNDNRPEFINQVYNGSVDEGSKPGTYVMTVTANDADDSTTANGMVRYRIVTQTPQSPSQNMFTINSETGDIVTVAAGLDREIRSDKDNDIPIRYSITGVGADQPPMEVFNIDSMSGRMYVTRPMDREERASYHLRAHAVDMNGNKVENPIDLYIYVIDMNDNRPEFINQVYNGSVDEGSKPGTYVMTVTANDADDSTTANGMVRYRIVTQTPQSPSQNMFTINSETGDIVTVAAGLDRE
IRESfinder result
IRESfinder score
0.302423873
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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