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mmu_circMdm1_1469
Basic information of circular RNA
PanCircBase ID:
mmu_circMdm1_1469
mm39_Chr. Position ID:
chr10|117978754|117994509|+
Gene name:
Mdm1
Transcript:
ENSMUST00000020437.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
2,3,4,5,6,7,8,9
Exon/intron offsets:
0,3745,5131,7939,9152,9325,14345,15452
Genomic length:
15755
Exon/intron sizes in nt:
11,53,77,13,51,68,95,10,00,00,000
Flanking exon/introns:
chr10:117977867-117978754|chr10:117994509-117995351
Splice length:
1469
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGGCTGAGTGAATACCAGAGAAACTTCCTGTGGAAAAAGTCCTATTTGTCAGAGTCTTATAATCCCTCAGTGGGACAAAAGTACTCATGGGCAGGACTTAGATCGGATCAGTTGGGGATCACGAAAGAACCAGGTTTTATTTCAAAAAGAAGAGTTCCCTACCATGACCCTCAGATTTCAAAATACCTGGAGTGGAACGGAACCGTCAGAAAGAAGGATACGCTTGTCCCACCAGAACCCCAGGCCTTTGGAACGCCAAAGCCACAAGAGGCTGAGCAAGGAGAAGATGCCAATCAAGAAGCAGTTCTCTCACTAGAGGCCTCCAGGGTTCCCAAGAGAACTCGGTCTCATTCTGCGGACTCGAGAGCTGAAGGGGTTTCAGACACTGTGGAAAAGCACCAGGGTGTCACGAGAAGCCATGCGCCAGTTAGCGCGGATGTGGAGCTGAGACCTTCCAGCAAACAACCTCTCTCCCAGAGCATAGATCCCAGGTTGGATAGGCATCTTCGTAAGAAAGCTGGATTGGCCGTTGTTCCCACGAATAATGCCTTGAGAAATTCTGAATACCAAAGGCAGTTTGTTTGGAAGACTTCTAAAGAAAGCGCTCCAGTGTTTGCATCCAATCAGGTTTTCCGTAATAAAAGCCAAATTATTCCACAGTTCCAAGGCAATACATTCACCCACGAGACTGAATACAAGCGAAATTTCAAGGGTTTAACTCCAGTGAAGGAACCAAAGTCAAGAGAGTATTTGAAAGGAAACAGCAGTCTGGAGATGCTGACTCCAGTAAAGAAGGCAGATGAGCCTTTAGACTTAGAAGTAGACATGGCGTCGGAAGACTCAGACCAGTCTGTAAAGAAGCCTGCTTCATGGAGACACCAAAGGCTTGGAAAAGTGAATTCTGAATATAGAGCAAAGTTCCTGAGCCCAGCCCAGTATTTCTATAAAGCTGGAGCTTGGACCCGGGTGAAGGAGAACCTGTCAAACCAGGTTAAGGAGCTCCGAGAAAAGGCCGAATCTTACAGGAAGCGAGTTCAGGGGACACATTTTTCTCGGGACCATCTGAACCAGATTATGTCGGACAGCAACTGCTGTTGGGACGTCTCCTCAGTCACAAGCTCGGAAGGCACCGTCAGTAGCAACATCCGAGCACTGGATCTTGCTGGAGACCTTACAAACCACAGGACCCCCCAGAAACACCCTCCTACCAAACTAGAAGAAAGAAAAGTTGCCTCGGGAGAGCAGCCCCTGAAAAACTCCACCAGGAGACTGGAGATGCCAGAGCCTGCCGCCTCGGTCAGGAGGAAGCTGGCTTGGGATGCTGAGGAGAGCACGAAGGAAGACACCCAGGAGGAGCCCAGGGCGGAGGAGGACGGGAGAGAGGAGAGAGGACAGGACAAGCAGACCTGTGCGGTAGAGCTGGAGAAACCGGACACACAGACACCCAAGGCAGACAGACTGACAGAAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGACAGGACAAGCAGACC
60.04
AGTCCTGCCCATGAGTACTT
58.04
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGAAACCGGACACACAG
59.89
AGTCCTGCCCATGAGTACTT
58.04
147
PCR template sequence:
AGGACGGGAGAGAGGAGAGAGGACAGGACAAGCAGACCTGTGCGGTAGAGCTGGAGAAACCGGACACACAGACACCCAAGGCAGACAGACTGACAGAAGGGGGCTGAGTGAATACCAGAGAAACTTCCTGTGGAAAAAGTCCTATTTGTCAGAGTCTTATAATCCCTCAGTGGGACAAAAGTACTCATGGGCAGGACTTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(2), mmu-miR-207(2), mmu-miR-27a-3p(1), mmu-miR-146a-5p(1), mmu-miR-326-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-541-5p(1), mmu-miR-1198-5p(1), mmu-miR-484(1), mmu-miR-490-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACTGACAGAAGGGGGCTGAGTGAAT
siRNA sets
ATTCACTCAGCCCCCTTCT, TTCACTCAGCCCCCTTCTG, CACTCAGCCCCCTTCTGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMDM1_1469_ORF_1
0.7739
0.296355455
0.917201083
702
ORF sequence:
ATGCTGACTCCAGTAAAGAAGGCAGATGAGCCTTTAGACTTAGAAGTAGACATGGCGTCGGAAGACTCAGACCAGTCTGTAAAGAAGCCTGCTTCATGGAGACACCAAAGGCTTGGAAAAGTGAATTCTGAATATAGAGCAAAGTTCCTGAGCCCAGCCCAGTATTTCTATAAAGCTGGAGCTTGGACCCGGGTGAAGGAGAACCTGTCAAACCAGGTTAAGGAGCTCCGAGAAAAGGCCGAATCTTACAGGAAGCGAGTTCAGGGGACACATTTTTCTCGGGACCATCTGAACCAGATTATGTCGGACAGCAACTGCTGTTGGGACGTCTCCTCAGTCACAAGCTCGGAAGGCACCGTCAGTAGCAACATCCGAGCACTGGATCTTGCTGGAGACCTTACAAACCACAGGACCCCCCAGAAACACCCTCCTACCAAACTAGAAGAAAGAAAAGTTGCCTCGGGAGAGCAGCCCCTGAAAAACTCCACCAGGAGACTGGAGATGCCAGAGCCTGCCGCCTCGGTCAGGAGGAAGCTGGCTTGGGATGCTGAGGAGAGCACGAAGGAAGACACCCAGGAGGAGCCCAGGGCGGAGGAGGACGGGAGAGAGGAGAGAGGACAGGACAAGCAGACCTGTGCGGTAGAGCTGGAGAAACCGGACACACAGACACCCAAGGCAGACAGACTGACAGAAGGGGGCTGA
Peptide sequence:
MLTPVKKADEPLDLEVDMASEDSDQSVKKPASWRHQRLGKVNSEYRAKFLSPAQYFYKAGAWTRVKENLSNQVKELREKAESYRKRVQGTHFSRDHLNQIMSDSNCCWDVSSVTSSEGTVSSNIRALDLAGDLTNHRTPQKHPPTKLEERKVASGEQPLKNSTRRLEMPEPAASVRRKLAWDAEESTKEDTQEEPRAEEDGREERGQDKQTCAVELEKPDTQTPKADRLTEGG
IRESfinder result
IRESfinder score
0.424452163
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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