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mmu_circDennd4c_1210
Basic information of circular RNA
PanCircBase ID:
mmu_circDennd4c_1210
mm39_Chr. Position ID:
chr4|86746204|86759339|+
Gene name:
Dennd4c
Transcript:
ENSMUST00000082026.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
24,25,26,27,28,29,30
Exon/intron offsets:
0,952,1523,8412,9413,11664,13017
Genomic length:
13135
Exon/intron sizes in nt:
181,110,176,183,196,246,118
Flanking exon/introns:
chr4:86744317-86746204|chr4:86759339-86763063
Splice length:
1210
Other database IDs:
circAtlas: mmu-Dennd4c_0025
circBase: hsa_circ_0086470, circAtlas: hsa-DENND4C_0043, CIRCpedia: HSA_CIRCpedia_111123
Human Ortholog IDs:
Mature spliced Sequence:
GAGGAAACTAATAAAGATTACAGTTTCCCAGCTGGCCTAGAAGACCATCATATAGTGGGAGAGACTCTGTCGCCTAACACAAGTGTCTCAGGGTTGGTTCCCAGTGAACTGACCCAGAGCAACACAAGCCTCGGCAGTAGTAGCAGCAGTGGAGACGTTGGAAAACTGCAGTGTCCAGCAGGTGAAGTTCCATTTTCAAGAAATATCAAAGGGCAGGACTTTGAAAAGTCAGACCATGGTTCTTCTCAGAATACCAGTATGTCTAGCATCTATCAAAATTGTGCGATGGAGGTTTTGATGTCGAGTTGCTCACAGTGCAGAGCTTGTGGCGCTCTGGTTTATGATGAGGAAATCATGGCTGGATGGACAGCAGATGACTCAAATTTGAATACAACCTGCCCGTTCTGTAAAAGCAACTTCTTGCCTCTTCTCAATGTAGAATTTAAAGACCTGCGAGGCTCTGCCAGCTTTTTCTTGAAACCAAGCACGTCTGGTGACAGTTTACAAAGCGGCAGCATTCCATCAGCCAGTGAGCCCTCTGAACACAAACCCACGTCCAGTTCAGCAGAACCTGACCTGATCAGCTTTATGGATTTCTCAAAACACAGTGAGACCATAACAGAAGAAGCAAGTTATACAGTCGAATCAAGTGATGAAATAAAGAAAACCAATGGTGATGTCCAGAGTGTGAAAATGTCATCTGTGCCTAACAGTTTATCTAAGCGAAACGTATCTTTGACTCGAAGTCACAGTGTTGGAGGCCCTCTGCAGAATATCGACTTCTCCCAGCGACCATTTCATGGCGTCTCAACAGTCAGTCTTCCAAGCAGTCTGCAGGAAGATGTGGACCATCTAGGCAAGCGACCCAGTCCTCCTCCTGTGTCTGTGCCCTATTTGAGTCCTCTAGTGCTTCGGAAGGAACTTGAATCTTTGCTAGAAAATGAAGGTGATCAGGTCATCCATACATCCTCATTCATCAATCAACACCCAATCATTTTCTGGAACCTGGTTTGGTATTTCAGACGTTTGGACCTTCCTAGCAACTTGCCAGGCCTTATTCTCACCTCTGAGCATTGTAATGGAGGTGTGCAGCTTCCTCTATCATCTTTGTCCCAGGACAGCAAACTGGTGTATATTCAACTGCTGTGGGATAATATCAACCTTCATCAGGAACCAGGAGAACCTCTGTATGTCTCTTGGAGGAACTTGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGAACCAGGAGAACCTCTGT
60.13
ACCAACCCTGAGACACTTGTG
60.13
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGGAACCAGGAGAACCTCT
59.85
CCAACCCTGAGACACTTGTGT
60.13
141
PCR template sequence:
TCCCAGGACAGCAAACTGGTGTATATTCAACTGCTGTGGGATAATATCAACCTTCATCAGGAACCAGGAGAACCTCTGTATGTCTCTTGGAGGAACTTGAGAGGAAACTAATAAAGATTACAGTTTCCCAGCTGGCCTAGAAGACCATCATATAGTGGGAGAGACTCTGTCGCCTAACACAAGTGTCTCAGGGTTGGTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-141-3p(1), mmu-miR-7b-5p(1), mmu-miR-31-5p(1), mmu-miR-205-5p(1), mmu-miR-7a-5p(1), mmu-miR-125b-5p(1), mmu-miR-125a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-188-3p(1), mmu-miR-3470b(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TGGAGGAACTTGAGAGGAAACTAATA
siRNA sets
TATTAGTTTCCTCTCAAGT, TTAGTTTCCTCTCAAGTTC, TAGTTTCCTCTCAAGTTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDENND4C_1210_ORF_1
0.6064
0.084675315
0.957852376
963
ORF sequence:
ATGTCTAGCATCTATCAAAATTGTGCGATGGAGGTTTTGATGTCGAGTTGCTCACAGTGCAGAGCTTGTGGCGCTCTGGTTTATGATGAGGAAATCATGGCTGGATGGACAGCAGATGACTCAAATTTGAATACAACCTGCCCGTTCTGTAAAAGCAACTTCTTGCCTCTTCTCAATGTAGAATTTAAAGACCTGCGAGGCTCTGCCAGCTTTTTCTTGAAACCAAGCACGTCTGGTGACAGTTTACAAAGCGGCAGCATTCCATCAGCCAGTGAGCCCTCTGAACACAAACCCACGTCCAGTTCAGCAGAACCTGACCTGATCAGCTTTATGGATTTCTCAAAACACAGTGAGACCATAACAGAAGAAGCAAGTTATACAGTCGAATCAAGTGATGAAATAAAGAAAACCAATGGTGATGTCCAGAGTGTGAAAATGTCATCTGTGCCTAACAGTTTATCTAAGCGAAACGTATCTTTGACTCGAAGTCACAGTGTTGGAGGCCCTCTGCAGAATATCGACTTCTCCCAGCGACCATTTCATGGCGTCTCAACAGTCAGTCTTCCAAGCAGTCTGCAGGAAGATGTGGACCATCTAGGCAAGCGACCCAGTCCTCCTCCTGTGTCTGTGCCCTATTTGAGTCCTCTAGTGCTTCGGAAGGAACTTGAATCTTTGCTAGAAAATGAAGGTGATCAGGTCATCCATACATCCTCATTCATCAATCAACACCCAATCATTTTCTGGAACCTGGTTTGGTATTTCAGACGTTTGGACCTTCCTAGCAACTTGCCAGGCCTTATTCTCACCTCTGAGCATTGTAATGGAGGTGTGCAGCTTCCTCTATCATCTTTGTCCCAGGACAGCAAACTGGTGTATATTCAACTGCTGTGGGATAATATCAACCTTCATCAGGAACCAGGAGAACCTCTGTATGTCTCTTGGAGGAACTTGAGAGGAAACTAA
Peptide sequence:
MSSIYQNCAMEVLMSSCSQCRACGALVYDEEIMAGWTADDSNLNTTCPFCKSNFLPLLNVEFKDLRGSASFFLKPSTSGDSLQSGSIPSASEPSEHKPTSSSAEPDLISFMDFSKHSETITEEASYTVESSDEIKKTNGDVQSVKMSSVPNSLSKRNVSLTRSHSVGGPLQNIDFSQRPFHGVSTVSLPSSLQEDVDHLGKRPSPPPVSVPYLSPLVLRKELESLLENEGDQVIHTSSFINQHPIIFWNLVWYFRRLDLPSNLPGLILTSEHCNGGVQLPLSSLSQDSKLVYIQLLWDNINLHQEPGEPLYVSWRNLRGN
IRESfinder result
IRESfinder score
0.663181743
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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