top of page
mmu_circCdh2_2342
Basic information of circular RNA
PanCircBase ID:
mmu_circCdh2_2342
mm39_Chr. Position ID:
chr18|16734678|16783555|-
Gene name:
Cdh2
Transcript:
ENSMUST00000025166.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
15,14,13,12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,20506,22529,23098,25946,27837,30582,31386,38800,42308,44850,46865,48650
Genomic length:
48877
Exon/intron sizes in nt:
16,51,40,23,42,34,14,30,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr18:16723410-16734678|chr18:16783555-16907564
Splice length:
2342
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11569, circAtlas: mmu-Cdh2_0003
circBase: hsa_circ_0108141, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_132130
Human Ortholog IDs:
Mature spliced Sequence:
TGAAATTCAGCAACTGCAATAGAAAAAGGAAAGTTCAGTATGAAAGCAGCGAGCCAGCAGATTTCAAGGTGGACGAGGACGGCACGGTGTATGCTGTGAGAAGCTTCCCTCTCACTGCAGAGCAGGCAAAGTTCCTGATATATGCCCAAGACAAAGAAACCCAGGAAAAGTGGCAGGTAGCTGTAAACCTGAGCCGGGAGCCAACCCTGACTGAGGAGCCTATGAAGGAACCACATGAAATTGAAGAAATAGTATTCCCTAGACAACTTGCCAAGCACAGTGGAGCTCTACAAAGGCAGAAGAGAGACTGGGTCATCCCGCCAATCAACTTGCCAGAAAACTCCAGAGGACCCTTTCCTCAAGAGCTTGTCAGAATCAGGTCTGATAGAGATAAAAACCTTTCCCTGAGATACAGCGTCACTGGGCCAGGAGCTGACCAGCCTCCAACGGGCATCTTCATTATCAACCCCATCTCAGGACAGCTGTCAGTCACAAAGCCTCTGGATCGAGAGCTGATAGCCCGGTTTCACTTGAGAGCACATGCAGTGGACATCAATGGCAATCAAGTGGAGAACCCCATTGACATTGTCATCAATGTTATTGACATGAATGATAACAGACCTGAGTTTCTGCACCAGGTTTGGAATGGGTCTGTTCCAGAGGGATCAAAGCCTGGGACGTATGTGATGACGGTCACTGCCATTGATGCGGATGATCCAAATGCCCTGAATGGAATGCTGCGGTACAGGATCCTGTCCCAGGCGCCCAGCACACCTTCACCCAACATGTTTACAATCAACAATGAGACTGGGGACATCATCACTGTGGCAGCTGGTCTGGATCGAGAGAAAGTGCAACAGTATACGTTAATAATTCAAGCCACAGACATGGAAGGCAATCCCACTTATGGCCTTTCAAACACAGCCACAGCCGTCATCACGGTGACAGATGTCAATGACAATCCTCCAGAGTTTACTGCCATGACTTTCTACGGAGAAGTCCCTGAGAACAGGGTGGACGTCATTGTAGCCAACCTAACTGTCACGGACAAAGATCAGCCCCACACGCCGGCCTGGAATGCGGCATACAGAATCAGTGGTGGAGACCCTACAGGAAGGTTTGCCATCCTGACAGACCCCAACAGCAATGATGGGCTAGTCACAGTGGTAAAACCAATTGACTTTGAAACGAATAGGATGTTTGTCCTTACTGTTGCTGCAGAAAACCAAGTGCCATTAGCTAAAGGCATTCAGCACCCACCTCAGTCGACAGCCACTGTGTCTGTGACAGTTATTGATGTCAATGAAAATCCTTATTTTGCCCCAAATCCTAAAATCATTCGCCAAGAGGAAGGCCTCCACGCAGGTACCATGCTGACCACGCTCACTGCTCAGGACCCCGATCGATATATGCAACAGAATATCAGATACACAAAATTGTCTGATCCTGCCAACTGGCTGAAAATAGACCCCGTGAATGGGCAGATCACTACTATTGCCGTTTTGGACAGAGAATCGCCAAATGTAAAAAACAACATCTATAATGCTACCTTCCTTGCTTCTGACAATGGAATCCCGCCTATGAGTGGGACAGGAACACTGCAAATCTATTTACTTGATATCAATGACAACGCCCCTCAGGTGTTACCTCAAGAGGCGGAGACCTGTGAAACTCCAGAACCCAACTCAATTAACATCACAGCACTTGATTATGACATAGACCCAAACGCCGGGCCGTTCGCGTTTGATCTTCCCTTATCTCCAGTGACTATTAAAAGAAACTGGACCATCAACCGGCTTAATGGTGATTTTGCTCAGCTCAATTTAAAGATAAAATTTTTGGAAGCTGGTATCTATGAAGTTCCCATCATTATCACAGATTCAGGGAATCCCCCCAAGTCCAACATTTCCATCCTGCGTGTGAAAGTTTGTCAGTGTGACTCCAATGGAGACTGCACGGACGTGGACAGGATCGTGGGTGCAGGGCTTGGCACGGGCGCCATCATCGCTATCCTTCTGTGTATCATCATCCTGCTGATCCTTGTTCTCATGTTTGTGGTATGGATGAAACGGCGGGATAAAGAGCGCCAAGCCAAGCAGCTTTTAATTGACCCAGAAGATGATGTAAGAGATAATATATTGAAATATGATGAAGAAGGTGGAGGAGAAGAAGACCAGGACTATGACTTGAGCCAGCTCCAGCAACCAGATACTGTGGAGCCTGATGCCATCAAGCCCGTGGGAATCAGACGGCTAGACGAGAGGCCTATCCATGCTGAGCCACAGTACCCAGTCCGATCCGCAGCCCCACACCCTGGGGATATTGGGGACTTCATTAATGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGAGAGGCCTATCCATGCTG
60.04
CGTCCTCGTCCACCTTGAAA
59.97
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACGAGAGGCCTATCCATGC
60.04
CGTCCTCGTCCACCTTGAAA
59.97
168
PCR template sequence:
AATCAGACGGCTAGACGAGAGGCCTATCCATGCTGAGCCACAGTACCCAGTCCGATCCGCAGCCCCACACCCTGGGGATATTGGGGACTTCATTAATGAGTGAAATTCAGCAACTGCAATAGAAAAAGGAAAGTTCAGTATGAAAGCAGCGAGCCAGCAGATTTCAAGGTGGACGAGGACGGCACGGTGTATGCTGTGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
24
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-103-3p(1), mmu-miR-34c-5p(1), mmu-miR-30e-5p(1), mmu-miR-205-5p(1), mmu-miR-30a-5p(1), mmu-miR-196a-5p(1), mmu-miR-25-3p(1), mmu-miR-139-5p(1), mmu-miR-128-3p(1), mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-26b-5p(1), mmu-miR-382-3p(1), mmu-miR-22-3p(1), mmu-miR-382-5p(1), mmu-miR-183-5p(1), mmu-miR-107-3p(1), mmu-miR-207(1), mmu-miR-532-5p(1), mmu-miR-452-3p(1), mmu-miR-670-5p(1), mmu-miR-697(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTCATTAATGAGTGAAATTCAGCAA
siRNA sets
GAATTTCACTCATTAATGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDH2_2342_ORF_1
1.0944
0.287476225
0.999998122
2124
ORF sequence:
ATGAAGGAACCACATGAAATTGAAGAAATAGTATTCCCTAGACAACTTGCCAAGCACAGTGGAGCTCTACAAAGGCAGAAGAGAGACTGGGTCATCCCGCCAATCAACTTGCCAGAAAACTCCAGAGGACCCTTTCCTCAAGAGCTTGTCAGAATCAGGTCTGATAGAGATAAAAACCTTTCCCTGAGATACAGCGTCACTGGGCCAGGAGCTGACCAGCCTCCAACGGGCATCTTCATTATCAACCCCATCTCAGGACAGCTGTCAGTCACAAAGCCTCTGGATCGAGAGCTGATAGCCCGGTTTCACTTGAGAGCACATGCAGTGGACATCAATGGCAATCAAGTGGAGAACCCCATTGACATTGTCATCAATGTTATTGACATGAATGATAACAGACCTGAGTTTCTGCACCAGGTTTGGAATGGGTCTGTTCCAGAGGGATCAAAGCCTGGGACGTATGTGATGACGGTCACTGCCATTGATGCGGATGATCCAAATGCCCTGAATGGAATGCTGCGGTACAGGATCCTGTCCCAGGCGCCCAGCACACCTTCACCCAACATGTTTACAATCAACAATGAGACTGGGGACATCATCACTGTGGCAGCTGGTCTGGATCGAGAGAAAGTGCAACAGTATACGTTAATAATTCAAGCCACAGACATGGAAGGCAATCCCACTTATGGCCTTTCAAACACAGCCACAGCCGTCATCACGGTGACAGATGTCAATGACAATCCTCCAGAGTTTACTGCCATGACTTTCTACGGAGAAGTCCCTGAGAACAGGGTGGACGTCATTGTAGCCAACCTAACTGTCACGGACAAAGATCAGCCCCACACGCCGGCCTGGAATGCGGCATACAGAATCAGTGGTGGAGACCCTACAGGAAGGTTTGCCATCCTGACAGACCCCAACAGCAATGATGGGCTAGTCACAGTGGTAAAACCAATTGACTTTGAAACGAATAGGATGTTTGTCCTTACTGTTGCTGCAGAAAACCAAGTGCCATTAGCTAAAGGCATTCAGCACCCACCTCAGTCGACAGCCACTGTGTCTGTGACAGTTATTGATGTCAATGAAAATCCTTATTTTGCCCCAAATCCTAAAATCATTCGCCAAGAGGAAGGCCTCCACGCAGGTACCATGCTGACCACGCTCACTGCTCAGGACCCCGATCGATATATGCAACAGAATATCAGATACACAAAATTGTCTGATCCTGCCAACTGGCTGAAAATAGACCCCGTGAATGGGCAGATCACTACTATTGCCGTTTTGGACAGAGAATCGCCAAATGTAAAAAACAACATCTATAATGCTACCTTCCTTGCTTCTGACAATGGAATCCCGCCTATGAGTGGGACAGGAACACTGCAAATCTATTTACTTGATATCAATGACAACGCCCCTCAGGTGTTACCTCAAGAGGCGGAGACCTGTGAAACTCCAGAACCCAACTCAATTAACATCACAGCACTTGATTATGACATAGACCCAAACGCCGGGCCGTTCGCGTTTGATCTTCCCTTATCTCCAGTGACTATTAAAAGAAACTGGACCATCAACCGGCTTAATGGTGATTTTGCTCAGCTCAATTTAAAGATAAAATTTTTGGAAGCTGGTATCTATGAAGTTCCCATCATTATCACAGATTCAGGGAATCCCCCCAAGTCCAACATTTCCATCCTGCGTGTGAAAGTTTGTCAGTGTGACTCCAATGGAGACTGCACGGACGTGGACAGGATCGTGGGTGCAGGGCTTGGCACGGGCGCCATCATCGCTATCCTTCTGTGTATCATCATCCTGCTGATCCTTGTTCTCATGTTTGTGGTATGGATGAAACGGCGGGATAAAGAGCGCCAAGCCAAGCAGCTTTTAATTGACCCAGAAGATGATGTAAGAGATAATATATTGAAATATGATGAAGAAGGTGGAGGAGAAGAAGACCAGGACTATGACTTGAGCCAGCTCCAGCAACCAGATACTGTGGAGCCTGATGCCATCAAGCCCGTGGGAATCAGACGGCTAGACGAGAGGCCTATCCATGCTGAGCCACAGTACCCAGTCCGATCCGCAGCCCCACACCCTGGGGATATTGGGGACTTCATTAATGAGTGA
Peptide sequence:
MKEPHEIEEIVFPRQLAKHSGALQRQKRDWVIPPINLPENSRGPFPQELVRIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRAHAVDINGNQVENPIDIVINVIDMNDNRPEFLHQVWNGSVPEGSKPGTYVMTVTAIDADDPNALNGMLRYRILSQAPSTPSPNMFTINNETGDIITVAAGLDREKVQQYTLIIQATDMEGNPTYGLSNTATAVITVTDVNDNPPEFTAMTFYGEVPENRVDVIVANLTVTDKDQPHTPAWNAAYRISGGDPTGRFAILTDPNSNDGLVTVVKPIDFETNRMFVLTVAAENQVPLAKGIQHPPQSTATVSVTVIDVNENPYFAPNPKIIRQEEGLHAGTMLTTLTAQDPDRYMQQNIRYTKLSDPANWLKIDPVNGQITTIAVLDRESPNVKNNIYNATFLASDNGIPPMSGTGTLQIYLLDINDNAPQVLPQEAETCETPEPNSINITALDYDIDPNAGPFAFDLPLSPVTIKRNWTINRLNGDFAQLNLKIKFLEAGIYEVPIIITDSGNPPKSNISILRVKVCQCDSNGDCTDVDRIVGAGLGTGAIIAILLCIIILLILVLMFVVWMKRRDKERQAKQLLIDPEDDVRDNILKYDEEGGGEEDQDYDLSQLQQPDTVEPDAIKPVGIRRLDERPIHAEPQYPVRSAAPHPGDIGDFINE
IRESfinder result
IRESfinder score
0.49373054
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page