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mmu_circMsh3_1245
Basic information of circular RNA
PanCircBase ID:
mmu_circMsh3_1245
mm39_Chr. Position ID:
chr13|92372081|92436866|-
Gene name:
Msh3
Transcript:
ENSMUST00000185852.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
20,19,18,17,16,15,14,13,12,11
Exon/intron offsets:
0,14253,21121,28147,30353,38378,39156,50303,63579,64700
Genomic length:
64785
Exon/intron sizes in nt:
158,112,108,117,65,169,188,133,110,85
Flanking exon/introns:
chr13:92359804-92372081|chr13:92436866-92445952
Splice length:
1245
Other database IDs:
circBase: mmu_circ_0004876, CIRCpedia: MMU_CIRCpedia_34325, circAtlas: mmu-Msh3_0018
circAtlas: hsa-MSH3_0056
Human Ortholog IDs:
Mature spliced Sequence:
GAGTTTTAAACAGCTGTCAAGTGGAATGGAATTCATGAGAATTAATGGGACCACGCTAAGGAATCTGGAGATCCTTCAGAATCAGACTGATATGAAGACCAAAGGAAGCTTGCTTTGGGTTTTAGACCACACTAAAACTTCATTTGGGAGAAGGAAGTTAAAGAATTGGGTTACCCAGCCACTGCTTAAATTAAGGGAAATAAATGCCCGACTTGATGCAGTATCTGATGTTCTCCACTCAGAATCCAGTGTGTTTGAGCAGATAGAAAACCTTCTTCGTAAGTTACCGGATGTCGAGAGAGGACTATGTAGCATTTATCACAAGAAGTGCTCTACCCAAGAGTTCTTCTTGATCGTCAAAAGCCTATGTCAACTGAAGTCAGAGCTTCAAGCATTAATGCCTGCTGTTAATTCCCACGTTCAGTCCGACTTACTCCGAGCACTCATCGTGGAGGCTCCTGAGCTCCTCAGCCCAGTGGAACATTACTTAAAGGTTCTGAATGGGCCAGCTGCCAAAGTTGGCGATAAAACTGAATTATTCAAAGACCTCTCTGACTTCCCTTTAATAAAAAAGAGGAAAAATGAAATTCAGGAAGTCATTCACAGCATCCAAATGCGTTTACAGGAATTTCGGAAAATATTAAAACTTCCTTCTTTACAGTATGTGACTGTATCAGGACAAGAGTTTATGATTGAAATAAAGAACTCGGCTGTATCTTGCATCCCAGCTGATTGGGTGAAGGTTGGAAGCACAAAAGCTGTGAGCCGCTTTCACCCTCCCTTCATCGTGGAAAGCTACAGACGTCTGAATCAGCTCCGGGAGCAGCTAGTCCTTGACTGCAATGCTGAATGGCTTGGCTTCCTAGAGAATTTTGGTGAACATTATCACACTTTGTGTAAGGCTGTGGATCACCTAGCAACTGTTGACTGTATTTTCTCCCTGGCCAAGGTCGCTAAACAAGGAAATTACTGCAGGCCAACTCTACAAGAAGAAAAGAAGATCATCATAAAAAATGGAAGGCACCCTATGATTGATGTGTTGCTGGGTGAACAAGATCAGTTTGTGCCCAACAGTACGAGTTTATCACAGGACTCGGAGAGAGTAATGATAATCACCGGACCAAACATGGGTGGGAAAAGCTCCTACATAAAACAGGTTGCACTGGTTACCATCATGGCTCAGATTGGCTCCTACGTCCCTGCAGAGGAAGCCACAATTGGGATTGTGGATGGCATTTTCACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGGTTGCACTGGTTACCA
59.45
GATTCCTTAGCGTGGTCCCA
59.46
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCACTGGTTACCATCATGGC
59.26
GATTCCTTAGCGTGGTCCCA
59.46
151
PCR template sequence:
ACATAAAACAGGTTGCACTGGTTACCATCATGGCTCAGATTGGCTCCTACGTCCCTGCAGAGGAAGCCACAATTGGGATTGTGGATGGCATTTTCACAAGGAGTTTTAAACAGCTGTCAAGTGGAATGGAATTCATGAGAATTAATGGGACCACGCTAAGGAATCTGGAGATCCTTCAGAATCAGACTGATATGAAGACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-16-5p(1), mmu-miR-103-3p(1), mmu-miR-221-3p(1), mmu-miR-217-5p(1), mmu-miR-214-3p(1), mmu-miR-136-5p(1), mmu-miR-127-5p(1), mmu-miR-301b-3p(1), mmu-miR-218-5p(1), mmu-miR-107-3p(1), mmu-miR-301a-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCATTTTCACAAGGAGTTTTAAACAG
siRNA sets
CTGTTTAAAACTCCTTGTG, TTTAAAACTCCTTGTGAAA, TAAAACTCCTTGTGAAAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMSH3_1245_ORF_1
0.9804
0.111956134
0.999999609
2463
ORF sequence:
ATGGAATTCATGAGAATTAATGGGACCACGCTAAGGAATCTGGAGATCCTTCAGAATCAGACTGATATGAAGACCAAAGGAAGCTTGCTTTGGGTTTTAGACCACACTAAAACTTCATTTGGGAGAAGGAAGTTAAAGAATTGGGTTACCCAGCCACTGCTTAAATTAAGGGAAATAAATGCCCGACTTGATGCAGTATCTGATGTTCTCCACTCAGAATCCAGTGTGTTTGAGCAGATAGAAAACCTTCTTCGTAAGTTACCGGATGTCGAGAGAGGACTATGTAGCATTTATCACAAGAAGTGCTCTACCCAAGAGTTCTTCTTGATCGTCAAAAGCCTATGTCAACTGAAGTCAGAGCTTCAAGCATTAATGCCTGCTGTTAATTCCCACGTTCAGTCCGACTTACTCCGAGCACTCATCGTGGAGGCTCCTGAGCTCCTCAGCCCAGTGGAACATTACTTAAAGGTTCTGAATGGGCCAGCTGCCAAAGTTGGCGATAAAACTGAATTATTCAAAGACCTCTCTGACTTCCCTTTAATAAAAAAGAGGAAAAATGAAATTCAGGAAGTCATTCACAGCATCCAAATGCGTTTACAGGAATTTCGGAAAATATTAAAACTTCCTTCTTTACAGTATGTGACTGTATCAGGACAAGAGTTTATGATTGAAATAAAGAACTCGGCTGTATCTTGCATCCCAGCTGATTGGGTGAAGGTTGGAAGCACAAAAGCTGTGAGCCGCTTTCACCCTCCCTTCATCGTGGAAAGCTACAGACGTCTGAATCAGCTCCGGGAGCAGCTAGTCCTTGACTGCAATGCTGAATGGCTTGGCTTCCTAGAGAATTTTGGTGAACATTATCACACTTTGTGTAAGGCTGTGGATCACCTAGCAACTGTTGACTGTATTTTCTCCCTGGCCAAGGTCGCTAAACAAGGAAATTACTGCAGGCCAACTCTACAAGAAGAAAAGAAGATCATCATAAAAAATGGAAGGCACCCTATGATTGATGTGTTGCTGGGTGAACAAGATCAGTTTGTGCCCAACAGTACGAGTTTATCACAGGACTCGGAGAGAGTAATGATAATCACCGGACCAAACATGGGTGGGAAAAGCTCCTACATAAAACAGGTTGCACTGGTTACCATCATGGCTCAGATTGGCTCCTACGTCCCTGCAGAGGAAGCCACAATTGGGATTGTGGATGGCATTTTCACAAGGAGTTTTAAACAGCTGTCAAGTGGAATGGAATTCATGAGAATTAATGGGACCACGCTAAGGAATCTGGAGATCCTTCAGAATCAGACTGATATGAAGACCAAAGGAAGCTTGCTTTGGGTTTTAGACCACACTAAAACTTCATTTGGGAGAAGGAAGTTAAAGAATTGGGTTACCCAGCCACTGCTTAAATTAAGGGAAATAAATGCCCGACTTGATGCAGTATCTGATGTTCTCCACTCAGAATCCAGTGTGTTTGAGCAGATAGAAAACCTTCTTCGTAAGTTACCGGATGTCGAGAGAGGACTATGTAGCATTTATCACAAGAAGTGCTCTACCCAAGAGTTCTTCTTGATCGTCAAAAGCCTATGTCAACTGAAGTCAGAGCTTCAAGCATTAATGCCTGCTGTTAATTCCCACGTTCAGTCCGACTTACTCCGAGCACTCATCGTGGAGGCTCCTGAGCTCCTCAGCCCAGTGGAACATTACTTAAAGGTTCTGAATGGGCCAGCTGCCAAAGTTGGCGATAAAACTGAATTATTCAAAGACCTCTCTGACTTCCCTTTAATAAAAAAGAGGAAAAATGAAATTCAGGAAGTCATTCACAGCATCCAAATGCGTTTACAGGAATTTCGGAAAATATTAAAACTTCCTTCTTTACAGTATGTGACTGTATCAGGACAAGAGTTTATGATTGAAATAAAGAACTCGGCTGTATCTTGCATCCCAGCTGATTGGGTGAAGGTTGGAAGCACAAAAGCTGTGAGCCGCTTTCACCCTCCCTTCATCGTGGAAAGCTACAGACGTCTGAATCAGCTCCGGGAGCAGCTAGTCCTTGACTGCAATGCTGAATGGCTTGGCTTCCTAGAGAATTTTGGTGAACATTATCACACTTTGTGTAAGGCTGTGGATCACCTAGCAACTGTTGACTGTATTTTCTCCCTGGCCAAGGTCGCTAAACAAGGAAATTACTGCAGGCCAACTCTACAAGAAGAAAAGAAGATCATCATAAAAAATGGAAGGCACCCTATGATTGATGTGTTGCTGGGTGAACAAGATCAGTTTGTGCCCAACAGTACGAGTTTATCACAGGACTCGGAGAGAGTAATGATAATCACCGGACCAAACATGGGTGGGAAAAGCTCCTACATAAAACAGGTTGCACTGGTTACCATCATGGCTCAGATTGGCTCCTACGTCCCTGCAGAGGAAGCCACAATTGGGATTGTGGATGGCATTTTCACA
Peptide sequence:
MEFMRINGTTLRNLEILQNQTDMKTKGSLLWVLDHTKTSFGRRKLKNWVTQPLLKLREINARLDAVSDVLHSESSVFEQIENLLRKLPDVERGLCSIYHKKCSTQEFFLIVKSLCQLKSELQALMPAVNSHVQSDLLRALIVEAPELLSPVEHYLKVLNGPAAKVGDKTELFKDLSDFPLIKKRKNEIQEVIHSIQMRLQEFRKILKLPSLQYVTVSGQEFMIEIKNSAVSCIPADWVKVGSTKAVSRFHPPFIVESYRRLNQLREQLVLDCNAEWLGFLENFGEHYHTLCKAVDHLATVDCIFSLAKVAKQGNYCRPTLQEEKKIIIKNGRHPMIDVLLGEQDQFVPNSTSLSQDSERVMIITGPNMGGKSSYIKQVALVTIMAQIGSYVPAEEATIGIVDGIFTRSFKQLSSGMEFMRINGTTLRNLEILQNQTDMKTKGSLLWVLDHTKTSFGRRKLKNWVTQPLLKLREINARLDAVSDVLHSESSVFEQIENLLRKLPDVERGLCSIYHKKCSTQEFFLIVKSLCQLKSELQALMPAVNSHVQSDLLRALIVEAPELLSPVEHYLKVLNGPAAKVGDKTELFKDLSDFPLIKKRKNEIQEVIHSIQMRLQEFRKILKLPSLQYVTVSGQEFMIEIKNSAVSCIPADWVKVGSTKAVSRFHPPFIVESYRRLNQLREQLVLDCNAEWLGFLENFGEHYHTLCKAVDHLATVDCIFSLAKVAKQGNYCRPTLQEEKKIIIKNGRHPMIDVLLGEQDQFVPNSTSLSQDSERVMIITGPNMGGKSSYIKQVALVTIMAQIGSYVPAEEATIGIVDGIFT
IRESfinder result
IRESfinder score
0.650365558
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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