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mmu_circScaper_1459
Basic information of circular RNA
PanCircBase ID:
mmu_circScaper_1459
mm39_Chr. Position ID:
chr9|55593163|55765809|-
Gene name:
Scaper
Transcript:
ENSMUST00000214747.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
25,24,23,22,21,20,19,18,17,16,15,14
Exon/intron offsets:
0,57663,72113,76348,121133,121726,123222,129481,130774,152240,172201,172528
Genomic length:
172646
Exon/intron sizes in nt:
1,16,12,76,61,37,10,81,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr9:55563312-55593163|chr9:55765809-55766282
Splice length:
1459
Other database IDs:
CIRCpedia: MMU_CIRCpedia_222777, circAtlas: mmu-Scaper_0145
Human Ortholog IDs:
Mature spliced Sequence:
CTCGTGAATCATGGCGTCAAAATACATCCTGGGGAGATATTGTAGAAGAGGAGCCTGCCAGACTTCCAGGGCATGGAATTCACATGCATGAAAAACTTTCATCACCTTCTCGTAAAAGGACAATCGCAGAATCTAAAAAGAAATATGAAGAAAAACACATGAAAGCTCAACAGTTAAGGGAAAAGCTACGCGAAGAGAAGACACTAAAGCTTCAAAAGTTGTTAGAAAGGGAGAAAGATGTCCGAAAGTGGAAGGAAGAATTACTAGATCAACGACGTAGGATGATGGAAGAGAAATTACTTCATGCAGAATTTAAACGAGAGGTACAGCTACAAGCTATTGTGAAGAAAGCTCAAGAGGAAGAAGCTAAGGTTAATGAGATTGCCTTCATAAATACCCTTGAAGCTCAGAATAAACGTCACGATGTTTTATCAAAACTGAAGGAATATGAGCAGAGGCTTAATGAATTGCAGGAAGAACGTCAGAGAAGACAAGAAGAAAAGCAAGCTCGTGATGAGGCTGTGCAGGAACGTAAGAGAGCCTTGGAGGCAGAAAGGCAGGCCCGTGTAGAGGAATTATTGATGAAGAGGAAAGAGCAAGAAGCCCGAATTGAGCAACAGAGGCAAGAGAAGGAGAAAGCTCGTGAAGATGCAGCCCGGGAAAGAGCAAGAGACAGGGAAGAACGGTTGGCAGCGCTCACAGCAGCTCAGCAAGAAGCTATGGAAGAGCTGCAGAAAAAAATTCAGCTCAAGCATGATGAAAGCATTCGAAGGCACATGGAACAGATTGAGCAAAGGAAAGAAAAAGCTGCTGAATTAAGCAGTGGGCGGCATGCAAGCACCGATTACGCCCCTAAACTGACCCCTTATGAAAGAAAGAAGCAGTGTTCTCTCTGCAATGTCCTGATCGCTTCTGAAGTATATCTCTTTAGCCACATTAAAGGGAAAAAACATCAGCAGGCTGTGAGAGAGAATAGCAGTATCCAGGGCCGTGAACTTTCTGATGAGGAAGTGGAACATCTGTCTTTGAAGAAGTATGTTGTTGACATTGTGATTGAAAGTGCAGCTCCACCAGAGCCTGTAAAAGATGGAGAAGAACGGCAAAAGAATAAGAAAAAAGCTAAAAAGATAAAAGCACGGATGAACATCAGGGCGAAAGAATATGAGAATTTAGTGGAAACCAAAAATTCTGGCTCCGAGTCACCTTATAAAGCAAAGCTTCAGAGATTAACCAAAGATCTTGTAAAACAACTTCAAGTACAAGACAGTGGCTCTTGGGTAAATAATAAGGCTTCAGCTTTGGATCGGACCCTTGGTGAGATTGCTAGAATATTGGAGAAAGAGAATGTGCCAGATCAGATTTCGTTTCAAGTTGCTGGTGGATTAACAGCCCTTGAAAACATCCTTCAAGTAGTGACTCCAGCCACAAACATGAACACGGTTTCACGAATTCCTCCTAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTTTCAAGTTGCTGGTGGA
58.98
TGGCAGGCTCCTCTTCTACA
60.25
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTTTCAAGTTGCTGGTGG
58.98
TGGCAGGCTCCTCTTCTACA
60.25
158
PCR template sequence:
TTTCGTTTCAAGTTGCTGGTGGATTAACAGCCCTTGAAAACATCCTTCAAGTAGTGACTCCAGCCACAAACATGAACACGGTTTCACGAATTCCTCCTAACTCGTGAATCATGGCGTCAAAATACATCCTGGGGAGATATTGTAGAAGAGGAGCCTGCCAGACTTCCAGGGCATGGAATTCACATGCATGAAAAACTTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-298-5p(1), mmu-miR-382-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAATTCCTCCTAACTCGTGAATCATG
siRNA sets
ATGATTCACGAGTTAGGAG,CATGATTCACGAGTTAGGA,ATTCACGAGTTAGGAGGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCAPER_1459_ORF_1
1.1961
0.21129982
0.9995725
1383
ORF sequence:
ATGCATGAAAAACTTTCATCACCTTCTCGTAAAAGGACAATCGCAGAATCTAAAAAGAAATATGAAGAAAAACACATGAAAGCTCAACAGTTAAGGGAAAAGCTACGCGAAGAGAAGACACTAAAGCTTCAAAAGTTGTTAGAAAGGGAGAAAGATGTCCGAAAGTGGAAGGAAGAATTACTAGATCAACGACGTAGGATGATGGAAGAGAAATTACTTCATGCAGAATTTAAACGAGAGGTACAGCTACAAGCTATTGTGAAGAAAGCTCAAGAGGAAGAAGCTAAGGTTAATGAGATTGCCTTCATAAATACCCTTGAAGCTCAGAATAAACGTCACGATGTTTTATCAAAACTGAAGGAATATGAGCAGAGGCTTAATGAATTGCAGGAAGAACGTCAGAGAAGACAAGAAGAAAAGCAAGCTCGTGATGAGGCTGTGCAGGAACGTAAGAGAGCCTTGGAGGCAGAAAGGCAGGCCCGTGTAGAGGAATTATTGATGAAGAGGAAAGAGCAAGAAGCCCGAATTGAGCAACAGAGGCAAGAGAAGGAGAAAGCTCGTGAAGATGCAGCCCGGGAAAGAGCAAGAGACAGGGAAGAACGGTTGGCAGCGCTCACAGCAGCTCAGCAAGAAGCTATGGAAGAGCTGCAGAAAAAAATTCAGCTCAAGCATGATGAAAGCATTCGAAGGCACATGGAACAGATTGAGCAAAGGAAAGAAAAAGCTGCTGAATTAAGCAGTGGGCGGCATGCAAGCACCGATTACGCCCCTAAACTGACCCCTTATGAAAGAAAGAAGCAGTGTTCTCTCTGCAATGTCCTGATCGCTTCTGAAGTATATCTCTTTAGCCACATTAAAGGGAAAAAACATCAGCAGGCTGTGAGAGAGAATAGCAGTATCCAGGGCCGTGAACTTTCTGATGAGGAAGTGGAACATCTGTCTTTGAAGAAGTATGTTGTTGACATTGTGATTGAAAGTGCAGCTCCACCAGAGCCTGTAAAAGATGGAGAAGAACGGCAAAAGAATAAGAAAAAAGCTAAAAAGATAAAAGCACGGATGAACATCAGGGCGAAAGAATATGAGAATTTAGTGGAAACCAAAAATTCTGGCTCCGAGTCACCTTATAAAGCAAAGCTTCAGAGATTAACCAAAGATCTTGTAAAACAACTTCAAGTACAAGACAGTGGCTCTTGGGTAAATAATAAGGCTTCAGCTTTGGATCGGACCCTTGGTGAGATTGCTAGAATATTGGAGAAAGAGAATGTGCCAGATCAGATTTCGTTTCAAGTTGCTGGTGGATTAACAGCCCTTGAAAACATCCTTCAAGTAGTGACTCCAGCCACAAACATGAACACGGTTTCACGAATTCCTCCTAACTCGTGA
Peptide sequence:
MHEKLSSPSRKRTIAESKKKYEEKHMKAQQLREKLREEKTLKLQKLLEREKDVRKWKEELLDQRRRMMEEKLLHAEFKREVQLQAIVKKAQEEEAKVNEIAFINTLEAQNKRHDVLSKLKEYEQRLNELQEERQRRQEEKQARDEAVQERKRALEAERQARVEELLMKRKEQEARIEQQRQEKEKAREDAARERARDREERLAALTAAQQEAMEELQKKIQLKHDESIRRHMEQIEQRKEKAAELSSGRHASTDYAPKLTPYERKKQCSLCNVLIASEVYLFSHIKGKKHQQAVRENSSIQGRELSDEEVEHLSLKKYVVDIVIESAAPPEPVKDGEERQKNKKKAKKIKARMNIRAKEYENLVETKNSGSESPYKAKLQRLTKDLVKQLQVQDSGSWVNNKASALDRTLGEIARILEKENVPDQISFQVAGGLTALENILQVVTPATNMNTVSRIPPNS
IRESfinder result
IRESfinder score
0.445881619
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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