top of page
mmu_circCdh2_960
Basic information of circular RNA
PanCircBase ID:
mmu_circCdh2_960
mm39_Chr. Position ID:
chr18|16773478|16907676|-
Gene name:
Cdh2
Transcript:
ENSMUST00000025166.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,6,5,4,3,2
Exon/intron offsets:
0,3508,6050,8065,9850,134086
Genomic length:
134198
Exon/intron sizes in nt:
173,145,156,147,227,112
Flanking exon/introns:
chr18:16766202-16773478|chr18:16907676-16941391
Splice length:
960
Other database IDs:
circAtlas: mmu-Cdh2_0008
circAtlas: hsa-CDH2_0005, CIRCpedia: HSA_CIRCpedia_181105
Human Ortholog IDs:
Mature spliced Sequence:
GCGTCTGTGGAGGCTTCTGGTGAAATTGCATTATGCAAGACTGGATTTCCTGAAGATGTTTACAGCGCAGTCTTACCGAAGGATGTGCACGAAGGACAGCCCCTTCTCAATGTGAAATTCAGCAACTGCAATAGAAAAAGGAAAGTTCAGTATGAAAGCAGCGAGCCAGCAGATTTCAAGGTGGACGAGGACGGCACGGTGTATGCTGTGAGAAGCTTCCCTCTCACTGCAGAGCAGGCAAAGTTCCTGATATATGCCCAAGACAAAGAAACCCAGGAAAAGTGGCAGGTAGCTGTAAACCTGAGCCGGGAGCCAACCCTGACTGAGGAGCCTATGAAGGAACCACATGAAATTGAAGAAATAGTATTCCCTAGACAACTTGCCAAGCACAGTGGAGCTCTACAAAGGCAGAAGAGAGACTGGGTCATCCCGCCAATCAACTTGCCAGAAAACTCCAGAGGACCCTTTCCTCAAGAGCTTGTCAGAATCAGGTCTGATAGAGATAAAAACCTTTCCCTGAGATACAGCGTCACTGGGCCAGGAGCTGACCAGCCTCCAACGGGCATCTTCATTATCAACCCCATCTCAGGACAGCTGTCAGTCACAAAGCCTCTGGATCGAGAGCTGATAGCCCGGTTTCACTTGAGAGCACATGCAGTGGACATCAATGGCAATCAAGTGGAGAACCCCATTGACATTGTCATCAATGTTATTGACATGAATGATAACAGACCTGAGTTTCTGCACCAGGTTTGGAATGGGTCTGTTCCAGAGGGATCAAAGCCTGGGACGTATGTGATGACGGTCACTGCCATTGATGCGGATGATCCAAATGCCCTGAATGGAATGCTGCGGTACAGGATCCTGTCCCAGGCGCCCAGCACACCTTCACCCAACATGTTTACAATCAACAATGAGACTGGGGACATCATCACTGTGGCAGCTGGTCTGGATCGAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACACCTTCACCCAACAT
59.81
CTGTCCTTCGTGCACATCCT
60.04
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCACACCTTCACCCAACATG
59.69
CTGTCCTTCGTGCACATCCT
60.04
179
PCR template sequence:
GATCCTGTCCCAGGCGCCCAGCACACCTTCACCCAACATGTTTACAATCAACAATGAGACTGGGGACATCATCACTGTGGCAGCTGGTCTGGATCGAGAGGCGTCTGTGGAGGCTTCTGGTGAAATTGCATTATGCAAGACTGGATTTCCTGAAGATGTTTACAGCGCAGTCTTACCGAAGGATGTGCACGAAGGACAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
22
Interacting miRNAs (#binding sites)
mmu-miR-30e-5p(2), mmu-miR-30a-5p(2), mmu-miR-23b-3p(1), mmu-miR-134-5p(1), mmu-miR-103-3p(1), mmu-miR-34c-5p(1), mmu-miR-205-5p(1), mmu-miR-30c-5p(1), mmu-miR-23a-3p(1), mmu-miR-139-5p(1), mmu-miR-30d-5p(1), mmu-miR-128-3p(1), mmu-miR-24-3p(1), mmu-miR-30b-5p(1), mmu-miR-149-5p(1), mmu-miR-431-5p(1), mmu-miR-22-3p(1), mmu-miR-382-5p(1), mmu-miR-107-3p(1), mmu-miR-499-5p(1), mmu-miR-452-3p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTGGATCGAGAGGCGTCTGTGGAGG
siRNA sets
CACAGACGCCTCTCGATCC, ACAGACGCCTCTCGATCCA, CTCCACAGACGCCTCTCGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDH2_960_ORF_1
1.1235
0.301174338
0.999924024
1587
ORF sequence:
ATGAAGGAACCACATGAAATTGAAGAAATAGTATTCCCTAGACAACTTGCCAAGCACAGTGGAGCTCTACAAAGGCAGAAGAGAGACTGGGTCATCCCGCCAATCAACTTGCCAGAAAACTCCAGAGGACCCTTTCCTCAAGAGCTTGTCAGAATCAGGTCTGATAGAGATAAAAACCTTTCCCTGAGATACAGCGTCACTGGGCCAGGAGCTGACCAGCCTCCAACGGGCATCTTCATTATCAACCCCATCTCAGGACAGCTGTCAGTCACAAAGCCTCTGGATCGAGAGCTGATAGCCCGGTTTCACTTGAGAGCACATGCAGTGGACATCAATGGCAATCAAGTGGAGAACCCCATTGACATTGTCATCAATGTTATTGACATGAATGATAACAGACCTGAGTTTCTGCACCAGGTTTGGAATGGGTCTGTTCCAGAGGGATCAAAGCCTGGGACGTATGTGATGACGGTCACTGCCATTGATGCGGATGATCCAAATGCCCTGAATGGAATGCTGCGGTACAGGATCCTGTCCCAGGCGCCCAGCACACCTTCACCCAACATGTTTACAATCAACAATGAGACTGGGGACATCATCACTGTGGCAGCTGGTCTGGATCGAGAGGCGTCTGTGGAGGCTTCTGGTGAAATTGCATTATGCAAGACTGGATTTCCTGAAGATGTTTACAGCGCAGTCTTACCGAAGGATGTGCACGAAGGACAGCCCCTTCTCAATGTGAAATTCAGCAACTGCAATAGAAAAAGGAAAGTTCAGTATGAAAGCAGCGAGCCAGCAGATTTCAAGGTGGACGAGGACGGCACGGTGTATGCTGTGAGAAGCTTCCCTCTCACTGCAGAGCAGGCAAAGTTCCTGATATATGCCCAAGACAAAGAAACCCAGGAAAAGTGGCAGGTAGCTGTAAACCTGAGCCGGGAGCCAACCCTGACTGAGGAGCCTATGAAGGAACCACATGAAATTGAAGAAATAGTATTCCCTAGACAACTTGCCAAGCACAGTGGAGCTCTACAAAGGCAGAAGAGAGACTGGGTCATCCCGCCAATCAACTTGCCAGAAAACTCCAGAGGACCCTTTCCTCAAGAGCTTGTCAGAATCAGGTCTGATAGAGATAAAAACCTTTCCCTGAGATACAGCGTCACTGGGCCAGGAGCTGACCAGCCTCCAACGGGCATCTTCATTATCAACCCCATCTCAGGACAGCTGTCAGTCACAAAGCCTCTGGATCGAGAGCTGATAGCCCGGTTTCACTTGAGAGCACATGCAGTGGACATCAATGGCAATCAAGTGGAGAACCCCATTGACATTGTCATCAATGTTATTGACATGAATGATAACAGACCTGAGTTTCTGCACCAGGTTTGGAATGGGTCTGTTCCAGAGGGATCAAAGCCTGGGACGTATGTGATGACGGTCACTGCCATTGATGCGGATGATCCAAATGCCCTGAATGGAATGCTGCGGTACAGGATCCTGTCCCAGGCGCCCAGCACACCTTCACCCAACATGTTTACAATCAACAATGAGACTGGGGACATCATCACTGTGGCAGCTGGTCTGGATCGAGAG
Peptide sequence:
MKEPHEIEEIVFPRQLAKHSGALQRQKRDWVIPPINLPENSRGPFPQELVRIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRAHAVDINGNQVENPIDIVINVIDMNDNRPEFLHQVWNGSVPEGSKPGTYVMTVTAIDADDPNALNGMLRYRILSQAPSTPSPNMFTINNETGDIITVAAGLDREASVEASGEIALCKTGFPEDVYSAVLPKDVHEGQPLLNVKFSNCNRKRKVQYESSEPADFKVDEDGTVYAVRSFPLTAEQAKFLIYAQDKETQEKWQVAVNLSREPTLTEEPMKEPHEIEEIVFPRQLAKHSGALQRQKRDWVIPPINLPENSRGPFPQELVRIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRAHAVDINGNQVENPIDIVINVIDMNDNRPEFLHQVWNGSVPEGSKPGTYVMTVTAIDADDPNALNGMLRYRILSQAPSTPSPNMFTINNETGDIITVAAGLDRE
IRESfinder result
IRESfinder score
0.499639205
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page