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mmu_circScaper_376
Basic information of circular RNA
PanCircBase ID:
mmu_circScaper_376
mm39_Chr. Position ID:
chr9|55791130|55802666|-
Gene name:
Scaper
Transcript:
ENSMUST00000214747.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,8,7
Exon/intron offsets:
0,8325,11435
Genomic length:
11536
Exon/intron sizes in nt:
15,81,17,101
Flanking exon/introns:
chr9:55782188-55791130|chr9:55802666-55819323
Splice length:
376
Other database IDs:
CIRCpedia: MMU_CIRCpedia_23356, circAtlas: mmu-Scaper_0014
circAtlas: hsa-SCAPER_0012, CIRCpedia: HSA_CIRCpedia_15765
Human Ortholog IDs:
Mature spliced Sequence:
GAGGTGTTAATGATGCTGGATTACTATGTGAGAGATTTCAAAGCATTGATTGACTGGATTCAACTTCAGGAAAAGTTAGAGAAGACAGATGCTCAAAGCAGACCAACCTCACTGGCGTGGGAAGTAAAGAAGATGTCTCCAGGACGTCATGTGATTCAAAGCCCATCAACAGATAGAATGAATGTAACATCAACTGCAAGAAGAAGCTTAAACTTTGGGAGTTTACCTGGTGCAGTAACTGCCCCATGTCTGGCTCCCACAGGTGTCAGTTGGGCTGACAAGGTAAAGGCTCATCATACTGGTTCTGCTCCTCCTGAGGCCACACCTGCTCAATCCTGTGCACCAATGACAGTGCAAAAGACGTCCCGGAAAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCACACCTGCTCAATCCTGT
59.96
GCTTTGAGCATCTGTCTTCTCT
58.4
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGGTTCTGCTCCTCCTGA
60.18
GCTTTGAGCATCTGTCTTCTCT
58.4
178
PCR template sequence:
GACAAGGTAAAGGCTCATCATACTGGTTCTGCTCCTCCTGAGGCCACACCTGCTCAATCCTGTGCACCAATGACAGTGCAAAAGACGTCCCGGAAAAATGGAGGTGTTAATGATGCTGGATTACTATGTGAGAGATTTCAAAGCATTGATTGACTGGATTCAACTTCAGGAAAAGTTAGAGAAGACAGATGCTCAAAGCA
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-181a-5p(1), mmu-miR-217-5p(1), mmu-miR-181b-5p(1), mmu-miR-705(1), mmu-miR-338-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCCGGAAAAATGGAGGTGTTAATGA
siRNA sets
TTAACACCTCCATTTTTCC, TAACACCTCCATTTTTCCG, AACACCTCCATTTTTCCGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCAPER_376_ORF_1
1.017
-0.019403752
0.397018967
420
ORF sequence:
ATGATGCTGGATTACTATGTGAGAGATTTCAAAGCATTGATTGACTGGATTCAACTTCAGGAAAAGTTAGAGAAGACAGATGCTCAAAGCAGACCAACCTCACTGGCGTGGGAAGTAAAGAAGATGTCTCCAGGACGTCATGTGATTCAAAGCCCATCAACAGATAGAATGAATGTAACATCAACTGCAAGAAGAAGCTTAAACTTTGGGAGTTTACCTGGTGCAGTAACTGCCCCATGTCTGGCTCCCACAGGTGTCAGTTGGGCTGACAAGGTAAAGGCTCATCATACTGGTTCTGCTCCTCCTGAGGCCACACCTGCTCAATCCTGTGCACCAATGACAGTGCAAAAGACGTCCCGGAAAAATGGAGGTGTTAATGATGCTGGATTACTATGTGAGAGATTTCAAAGCATTGATTGA
Peptide sequence:
MMLDYYVRDFKALIDWIQLQEKLEKTDAQSRPTSLAWEVKKMSPGRHVIQSPSTDRMNVTSTARRSLNFGSLPGAVTAPCLAPTGVSWADKVKAHHTGSAPPEATPAQSCAPMTVQKTSRKNGGVNDAGLLCERFQSID
IRESfinder result
IRESfinder score
0.48187329
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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