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mmu_circScn9a_2307
Basic information of circular RNA
PanCircBase ID:
mmu_circScn9a_2307
mm39_Chr. Position ID:
chr2|66338863|66373663|-
Gene name:
Scn9a
Transcript:
ENSMUST00000100064.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
19,18,17,16,15,14,13,12,11
Exon/intron offsets:
0,6795,18088,24542,25594,27578,28750,31744,34515
Genomic length:
34800
Exon/intron sizes in nt:
15,51,18,47,73,57,17,40,00,00,00,00,000
Flanking exon/introns:
chr2:66335366-66338863|chr2:66373663-66377366
Splice length:
2307
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCGATCGCTGCAGCCGCTGCTGAGTACACGAGTTTAGGGCGGAGCAGGATTATGGGACTCTCTGAGAGCTCTTCAGAAACCTCCAGGCTGAGCTCAAAGAGTGCCAAGGAGAGAAGAAACCGAAGAAAGAAAAAAAAACAGAAGCTGTCCAGTGGCGAGGAAAAGGGTGATGATGAGAAGCTGTCCAAGTCAGGGTCAGAGGAAAGCATCCGAAAGAAAAGCTTCCATCTCGGCGTGGAAGGGCACCACCGGGCCAGGGAAAAGAGGCTGTCCACCCCCAACCAGTCACCACTCAGCATTCGTGGGTCCTTGTTTTCTGCCAGGCGCAGCAGCAGAACAAGTCTCTTCAGTTTTAAGGGGCGAGGAAGAGATCTGGGATCTGAAACGGAATTTGCTGATGATGAGCATAGCATTTTTGGAGACAACGAGAGCAGAAGGGGTTCACTATTTGTACCCCATAGACCCCGGGAGCGGCGCAGCAGTAACATCAGCCAGGCCAGTAGGTCCCCACCAGTGCTGCCGGTGAACGGGAAGATGCACAGTGCAGTGGACTGCAATGGCGTGGTGTCGCTTGTTGATGGACCCTCAGCCCTCATGCTCCCCAATGGACAGCTTCTTCCAGAGGTGATAATAGATAAGGCAACTTCCGACGACAGCGGCACAACTAATCAGATGCGTAAAAAAAGGCTCTCTAGTTCTTACTTTTTGTCTGAGGACATGCTGAATGACCCACATCTCAGGCAAAGGGCCATGAGCAGAGCAAGCATTCTAACCAACACAGTAGAAGAACTTGAAGAATCTAGACAAAAATGTCCACCATGGTGGTACAGATTTGCTCACACATTTTTAATCTGGAATTGTTCTCCATATTGGATAAAATTCAAAAAGTTCATCTATTTTATTGTAATGGATCCTTTTGTAGATCTTGCAATTACCATTTGCATAGTTTTAAACACCTTGTTTATGGCTATGGAGCACCATCCAATGACGGATGAATTCAAAAATGTACTTGCAGTCGGGAACCTGGTCTTCACAGGGATCTTCGCAGCTGAAATGGTACTGAAGTTAATAGCCATGGATCCCTATGAATATTTCCAAGTAGGGTGGAATATTTTTGACAGCCTGATTGTGACGTTGAGTTTGGTGGAGCTTTTCCTAGCAGATGTGGAAGGATTATCAGTCCTGCGGTCCTTTAGATTGCTGCGAGTCTTCAAGTTGGCAAAATCCTGGCCCACACTGAATATGCTCATTAAGATCATCGGCAACTCGGTGGGCGCACTGGGCAACCTGACCCTGGTGCTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTTTGCAAGATCAACGAGAACTGCAAGCTCCCACGCTGGCACATGAACGACTTCTTCCACTCCTTCCTGATCGTGTTCCGTGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTTGCGGGCCAGACCATGTGCCTTATTGTTTACATGATGGTCATGGTGATTGGGAACCTTGTGGTCCTGAACCTGTTTCTGGCTTTATTACTGAGTTCCTTTAGTTCTGACAATCTTACAGCAATTGAAGAAGACACCGACGCAAACAACCTCCAGATTGCAGTGGCCAGAATTAAAAGAGGGATCAATTATGTGAAACAGACCCTGCGTGAATTCATTCTAAAGTCATTTTCCAAAAAGCCAAAGGGCTCCAAGGACACAAAACGAACAGCGGATCCCAACAACAAAAGAGAAAACTATATCTCAAACCGTACCCTTGCGGAGATAAGCAAAGATCACAATTTCCTCAAAGAAAAGGATAAGATCAGTGGTTTTAGCAGCAGTCTAGACAAAAGCTTTATGGATGAAAACGATTACCAGTCCTTTATTCATAATCCCAGCCTCACAGTGACAGTGCCCATTGCACCTGGGGAGTCTGATTTGGAGAATATGAACACAGAAGAGCTTAGCAGTGACTCAGATAGTGACTACAGCAAAGAGAGACGGAACCGATCAAGTTCTTCAGAGTGCAGCACAGTTGATAACCCTCTGCCAGGAGAAGAGGAGGCAGAAGCTGAGCCTATCAATGCAGATGAGCCCGAAGCCTGTTTTACAGATGGCTGTGTGAGGAGATTTCCATGCTGCCAAGTTAACATAGACTCCGGGAAAGGGAAAGTTTGGTGGACCATCCGGAAGACCTGCTACAGGATAGTGGAGCACAGCTGGTTTGAAAGCTTCATTGTTCTCATGATCCTGCTCAGCAGTGGAGCTCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTGGTGGACCATCCGGAAG
59.96
AATCCTGCTCCGCCCTAAAC
60.11
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCATCCGGAAGACCTGCTAC
59.89
AATCCTGCTCCGCCCTAAAC
60.11
140
PCR template sequence:
AGTTTGGTGGACCATCCGGAAGACCTGCTACAGGATAGTGGAGCACAGCTGGTTTGAAAGCTTCATTGTTCTCATGATCCTGCTCAGCAGTGGAGCTCTGGCGATCGCTGCAGCCGCTGCTGAGTACACGAGTTTAGGGCGGAGCAGGATTATGGGACTCTCTGAGAGCTCTTCAGAAACCTCCAGGCTGAGCTCAAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
23
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-134-5p(1), mmu-miR-204-5p(1), mmu-miR-33-5p(1), mmu-miR-24-3p(1), mmu-miR-503-5p(1), mmu-miR-127-5p(1), mmu-miR-301b-3p(1), mmu-miR-382-5p(1), mmu-miR-301a-3p(1), mmu-miR-27a-5p(1), mmu-miR-499-5p(1), mmu-miR-342-3p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-207(1), mmu-miR-5101(1), mmu-miR-335-3p(1), mmu-miR-188-3p(1), mmu-miR-3470b(1), mmu-miR-1199-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CAGTGGAGCTCTGGCGATCGCTGCAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCN9A_2307_ORF_1
0.8908
0.200167799
1
4563
ORF sequence:
ATGGGACTCTCTGAGAGCTCTTCAGAAACCTCCAGGCTGAGCTCAAAGAGTGCCAAGGAGAGAAGAAACCGAAGAAAGAAAAAAAAACAGAAGCTGTCCAGTGGCGAGGAAAAGGGTGATGATGAGAAGCTGTCCAAGTCAGGGTCAGAGGAAAGCATCCGAAAGAAAAGCTTCCATCTCGGCGTGGAAGGGCACCACCGGGCCAGGGAAAAGAGGCTGTCCACCCCCAACCAGTCACCACTCAGCATTCGTGGGTCCTTGTTTTCTGCCAGGCGCAGCAGCAGAACAAGTCTCTTCAGTTTTAAGGGGCGAGGAAGAGATCTGGGATCTGAAACGGAATTTGCTGATGATGAGCATAGCATTTTTGGAGACAACGAGAGCAGAAGGGGTTCACTATTTGTACCCCATAGACCCCGGGAGCGGCGCAGCAGTAACATCAGCCAGGCCAGTAGGTCCCCACCAGTGCTGCCGGTGAACGGGAAGATGCACAGTGCAGTGGACTGCAATGGCGTGGTGTCGCTTGTTGATGGACCCTCAGCCCTCATGCTCCCCAATGGACAGCTTCTTCCAGAGGTGATAATAGATAAGGCAACTTCCGACGACAGCGGCACAACTAATCAGATGCGTAAAAAAAGGCTCTCTAGTTCTTACTTTTTGTCTGAGGACATGCTGAATGACCCACATCTCAGGCAAAGGGCCATGAGCAGAGCAAGCATTCTAACCAACACAGTAGAAGAACTTGAAGAATCTAGACAAAAATGTCCACCATGGTGGTACAGATTTGCTCACACATTTTTAATCTGGAATTGTTCTCCATATTGGATAAAATTCAAAAAGTTCATCTATTTTATTGTAATGGATCCTTTTGTAGATCTTGCAATTACCATTTGCATAGTTTTAAACACCTTGTTTATGGCTATGGAGCACCATCCAATGACGGATGAATTCAAAAATGTACTTGCAGTCGGGAACCTGGTCTTCACAGGGATCTTCGCAGCTGAAATGGTACTGAAGTTAATAGCCATGGATCCCTATGAATATTTCCAAGTAGGGTGGAATATTTTTGACAGCCTGATTGTGACGTTGAGTTTGGTGGAGCTTTTCCTAGCAGATGTGGAAGGATTATCAGTCCTGCGGTCCTTTAGATTGCTGCGAGTCTTCAAGTTGGCAAAATCCTGGCCCACACTGAATATGCTCATTAAGATCATCGGCAACTCGGTGGGCGCACTGGGCAACCTGACCCTGGTGCTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTTTGCAAGATCAACGAGAACTGCAAGCTCCCACGCTGGCACATGAACGACTTCTTCCACTCCTTCCTGATCGTGTTCCGTGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTTGCGGGCCAGACCATGTGCCTTATTGTTTACATGATGGTCATGGTGATTGGGAACCTTGTGGTCCTGAACCTGTTTCTGGCTTTATTACTGAGTTCCTTTAGTTCTGACAATCTTACAGCAATTGAAGAAGACACCGACGCAAACAACCTCCAGATTGCAGTGGCCAGAATTAAAAGAGGGATCAATTATGTGAAACAGACCCTGCGTGAATTCATTCTAAAGTCATTTTCCAAAAAGCCAAAGGGCTCCAAGGACACAAAACGAACAGCGGATCCCAACAACAAAAGAGAAAACTATATCTCAAACCGTACCCTTGCGGAGATAAGCAAAGATCACAATTTCCTCAAAGAAAAGGATAAGATCAGTGGTTTTAGCAGCAGTCTAGACAAAAGCTTTATGGATGAAAACGATTACCAGTCCTTTATTCATAATCCCAGCCTCACAGTGACAGTGCCCATTGCACCTGGGGAGTCTGATTTGGAGAATATGAACACAGAAGAGCTTAGCAGTGACTCAGATAGTGACTACAGCAAAGAGAGACGGAACCGATCAAGTTCTTCAGAGTGCAGCACAGTTGATAACCCTCTGCCAGGAGAAGAGGAGGCAGAAGCTGAGCCTATCAATGCAGATGAGCCCGAAGCCTGTTTTACAGATGGCTGTGTGAGGAGATTTCCATGCTGCCAAGTTAACATAGACTCCGGGAAAGGGAAAGTTTGGTGGACCATCCGGAAGACCTGCTACAGGATAGTGGAGCACAGCTGGTTTGAAAGCTTCATTGTTCTCATGATCCTGCTCAGCAGTGGAGCTCTGGCGATCGCTGCAGCCGCTGCTGAGTACACGAGTTTAGGGCGGAGCAGGATTATGGGACTCTCTGAGAGCTCTTCAGAAACCTCCAGGCTGAGCTCAAAGAGTGCCAAGGAGAGAAGAAACCGAAGAAAGAAAAAAAAACAGAAGCTGTCCAGTGGCGAGGAAAAGGGTGATGATGAGAAGCTGTCCAAGTCAGGGTCAGAGGAAAGCATCCGAAAGAAAAGCTTCCATCTCGGCGTGGAAGGGCACCACCGGGCCAGGGAAAAGAGGCTGTCCACCCCCAACCAGTCACCACTCAGCATTCGTGGGTCCTTGTTTTCTGCCAGGCGCAGCAGCAGAACAAGTCTCTTCAGTTTTAAGGGGCGAGGAAGAGATCTGGGATCTGAAACGGAATTTGCTGATGATGAGCATAGCATTTTTGGAGACAACGAGAGCAGAAGGGGTTCACTATTTGTACCCCATAGACCCCGGGAGCGGCGCAGCAGTAACATCAGCCAGGCCAGTAGGTCCCCACCAGTGCTGCCGGTGAACGGGAAGATGCACAGTGCAGTGGACTGCAATGGCGTGGTGTCGCTTGTTGATGGACCCTCAGCCCTCATGCTCCCCAATGGACAGCTTCTTCCAGAGGTGATAATAGATAAGGCAACTTCCGACGACAGCGGCACAACTAATCAGATGCGTAAAAAAAGGCTCTCTAGTTCTTACTTTTTGTCTGAGGACATGCTGAATGACCCACATCTCAGGCAAAGGGCCATGAGCAGAGCAAGCATTCTAACCAACACAGTAGAAGAACTTGAAGAATCTAGACAAAAATGTCCACCATGGTGGTACAGATTTGCTCACACATTTTTAATCTGGAATTGTTCTCCATATTGGATAAAATTCAAAAAGTTCATCTATTTTATTGTAATGGATCCTTTTGTAGATCTTGCAATTACCATTTGCATAGTTTTAAACACCTTGTTTATGGCTATGGAGCACCATCCAATGACGGATGAATTCAAAAATGTACTTGCAGTCGGGAACCTGGTCTTCACAGGGATCTTCGCAGCTGAAATGGTACTGAAGTTAATAGCCATGGATCCCTATGAATATTTCCAAGTAGGGTGGAATATTTTTGACAGCCTGATTGTGACGTTGAGTTTGGTGGAGCTTTTCCTAGCAGATGTGGAAGGATTATCAGTCCTGCGGTCCTTTAGATTGCTGCGAGTCTTCAAGTTGGCAAAATCCTGGCCCACACTGAATATGCTCATTAAGATCATCGGCAACTCGGTGGGCGCACTGGGCAACCTGACCCTGGTGCTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTTTGCAAGATCAACGAGAACTGCAAGCTCCCACGCTGGCACATGAACGACTTCTTCCACTCCTTCCTGATCGTGTTCCGTGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTTGCGGGCCAGACCATGTGCCTTATTGTTTACATGATGGTCATGGTGATTGGGAACCTTGTGGTCCTGAACCTGTTTCTGGCTTTATTACTGAGTTCCTTTAGTTCTGACAATCTTACAGCAATTGAAGAAGACACCGACGCAAACAACCTCCAGATTGCAGTGGCCAGAATTAAAAGAGGGATCAATTATGTGAAACAGACCCTGCGTGAATTCATTCTAAAGTCATTTTCCAAAAAGCCAAAGGGCTCCAAGGACACAAAACGAACAGCGGATCCCAACAACAAAAGAGAAAACTATATCTCAAACCGTACCCTTGCGGAGATAAGCAAAGATCACAATTTCCTCAAAGAAAAGGATAAGATCAGTGGTTTTAGCAGCAGTCTAGACAAAAGCTTTATGGATGAAAACGATTACCAGTCCTTTATTCATAATCCCAGCCTCACAGTGACAGTGCCCATTGCACCTGGGGAGTCTGATTTGGAGAATATGAACACAGAAGAGCTTAGCAGTGACTCAGATAGTGACTACAGCAAAGAGAGACGGAACCGATCAAGTTCTTCAGAGTGCAGCACAGTTGATAACCCTCTGCCAGGAGAAGAGGAGGCAGAAGCTGAGCCTATCAATGCAGATGAGCCCGAAGCCTGTTTTACAGATGGCTGTGTGAGGAGATTTCCATGCTGCCAAGTTAACATAGACTCCGGGAAAGGGAAAGTTTGGTGGACCATCCGGAAGACCTGCTACAGGATAGTGGAGCACAGCTGGTTTGAAAGCTTCATTGTTCTCATGATCCTGCTCAGCAGTGGAGCTCTG
Peptide sequence:
MGLSESSSETSRLSSKSAKERRNRRKKKKQKLSSGEEKGDDEKLSKSGSEESIRKKSFHLGVEGHHRAREKRLSTPNQSPLSIRGSLFSARRSSRTSLFSFKGRGRDLGSETEFADDEHSIFGDNESRRGSLFVPHRPRERRSSNISQASRSPPVLPVNGKMHSAVDCNGVVSLVDGPSALMLPNGQLLPEVIIDKATSDDSGTTNQMRKKRLSSSYFLSEDMLNDPHLRQRAMSRASILTNTVEELEESRQKCPPWWYRFAHTFLIWNCSPYWIKFKKFIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTDEFKNVLAVGNLVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINENCKLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQTMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIEEDTDANNLQIAVARIKRGINYVKQTLREFILKSFSKKPKGSKDTKRTADPNNKRENYISNRTLAEISKDHNFLKEKDKISGFSSSLDKSFMDENDYQSFIHNPSLTVTVPIAPGESDLENMNTEELSSDSDSDYSKERRNRSSSSECSTVDNPLPGEEEAEAEPINADEPEACFTDGCVRRFPCCQVNIDSGKGKVWWTIRKTCYRIVEHSWFESFIVLMILLSSGALAIAAAAAEYTSLGRSRIMGLSESSSETSRLSSKSAKERRNRRKKKKQKLSSGEEKGDDEKLSKSGSEESIRKKSFHLGVEGHHRAREKRLSTPNQSPLSIRGSLFSARRSSRTSLFSFKGRGRDLGSETEFADDEHSIFGDNESRRGSLFVPHRPRERRSSNISQASRSPPVLPVNGKMHSAVDCNGVVSLVDGPSALMLPNGQLLPEVIIDKATSDDSGTTNQMRKKRLSSSYFLSEDMLNDPHLRQRAMSRASILTNTVEELEESRQKCPPWWYRFAHTFLIWNCSPYWIKFKKFIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTDEFKNVLAVGNLVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINENCKLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQTMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIEEDTDANNLQIAVARIKRGINYVKQTLREFILKSFSKKPKGSKDTKRTADPNNKRENYISNRTLAEISKDHNFLKEKDKISGFSSSLDKSFMDENDYQSFIHNPSLTVTVPIAPGESDLENMNTEELSSDSDSDYSKERRNRSSSSECSTVDNPLPGEEEAEAEPINADEPEACFTDGCVRRFPCCQVNIDSGKGKVWWTIRKTCYRIVEHSWFESFIVLMILLSSGAL
IRESfinder result
IRESfinder score
0.569971291
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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