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mmu_circSf3a1_718
Basic information of circular RNA
PanCircBase ID:
mmu_circSf3a1_718
mm39_Chr. Position ID:
chr11|4121061|4125580|+
Gene name:
Sf3a1
Transcript:
ENSMUST00000002198.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
5,6,7,8,9
Exon/intron offsets:
0,2018,2970,3974,4333
Genomic length:
4519
Exon/intron sizes in nt:
7,51,51,18,81,18,186
Flanking exon/introns:
chr11:4117890-4121061|chr11:4125580-4126269
Splice length:
718
Other database IDs:
circAtlas: mmu-Sf3a1_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATCTTGATTCCACCCAAAGGCTTATTTTCAAAGCTCAAGAAAGAGGCTGAAAATCCTCGAGAAGTTTTGGACCAGGTTTGTTACCGAGTAGAATGGGCCAAATTTCAGGAACGTGAGAGGAAGAAGGAAGAAGAGGAGAAAGAGAAGGAGCGAGTAGCTTATGCTCAGATTGACTGGCATGATTTTGTGGTGGTGGAGACAGTGGATTTTCAACCCAATGAGCAAGGAAACTTTCCACCCCCAACAACACCAGAGGAACTGGGAGCTCGGATCCTCATTCAGGAGCGCTACGAGAAGTTTGGGGAGAGCGAGGAAGTGGAGATGGAGGTTGAGTCAGATGAGGAAGATCAGGAGAAGGCCGAGGAGACTCCTTCCCAGCTGGACCAGGATACTCAAGTACAGGACATGGATGAGGGTTCAGATGATGAAGAAGAAGGGCAGAAAGTGCCTCCACCCCCAGAGACACCCATGCCTCCACCTCTGCCCCCAACACCAGACCAAGTCATTGTGCGGAAGGACTATGATCCCAAAGCTTCCAAGCCCCTCCCTCCAGCCCCTGCTCCCGATGAGTATCTTGTATCCCCCATCACTGGGGAGAAGATTCCTGCCAGCAAAATGCAGGAGCACATGCGCATTGGGCTTCTTGACCCCCGCTGGCTGGAGCAGCGGGACCGCTCCATCCGAGAGAAGCAGAGTGATGATGAGGTTTATGCACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCCATCCGAGAGAAGCAG
60.25
GGCCCATTCTACTCGGTAACA
59.52
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCCATCCGAGAGAAGCAG
60.25
TGGCCCATTCTACTCGGTAAC
59.52
145
PCR template sequence:
CAGGAGCACATGCGCATTGGGCTTCTTGACCCCCGCTGGCTGGAGCAGCGGGACCGCTCCATCCGAGAGAAGCAGAGTGATGATGAGGTTTATGCACCAGATCTTGATTCCACCCAAAGGCTTATTTTCAAAGCTCAAGAAAGAGGCTGAAAATCCTCGAGAAGTTTTGGACCAGGTTTGTTACCGAGTAGAATGGGCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-495-3p(1), mmu-miR-207(1), mmu-miR-490-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GTTTATGCACCAGATCTTGATTCCAC
siRNA sets
TGGAATCAAGATCTGGTGC, AATCAAGATCTGGTGCATA, GTGGAATCAAGATCTGGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSF3A1_718_ORF_1
0.9602
0.231039133
0.998713297
1275
ORF sequence:
ATGCTCAGATTGACTGGCATGATTTTGTGGTGGTGGAGACAGTGGATTTTCAACCCAATGAGCAAGGAAACTTTCCACCCCCAACAACACCAGAGGAACTGGGAGCTCGGATCCTCATTCAGGAGCGCTACGAGAAGTTTGGGGAGAGCGAGGAAGTGGAGATGGAGGTTGAGTCAGATGAGGAAGATCAGGAGAAGGCCGAGGAGACTCCTTCCCAGCTGGACCAGGATACTCAAGTACAGGACATGGATGAGGGTTCAGATGATGAAGAAGAAGGGCAGAAAGTGCCTCCACCCCCAGAGACACCCATGCCTCCACCTCTGCCCCCAACACCAGACCAAGTCATTGTGCGGAAGGACTATGATCCCAAAGCTTCCAAGCCCCTCCCTCCAGCCCCTGCTCCCGATGAGTATCTTGTATCCCCCATCACTGGGGAGAAGATTCCTGCCAGCAAAATGCAGGAGCACATGCGCATTGGGCTTCTTGACCCCCGCTGGCTGGAGCAGCGGGACCGCTCCATCCGAGAGAAGCAGAGTGATGATGAGGTTTATGCACCAGATCTTGATTCCACCCAAAGGCTTATTTTCAAAGCTCAAGAAAGAGGCTGAAAATCCTCGAGAAGTTTTGGACCAGGTTTGTTACCGAGTAGAATGGGCCAAATTTCAGGAACGTGAGAGGAAGAAGGAAGAAGAGGAGAAAGAGAAGGAGCGAGTAGCTTATGCTCAGATTGACTGGCATGATTTTGTGGTGGTGGAGACAGTGGATTTTCAACCCAATGAGCAAGGAAACTTTCCACCCCCAACAACACCAGAGGAACTGGGAGCTCGGATCCTCATTCAGGAGCGCTACGAGAAGTTTGGGGAGAGCGAGGAAGTGGAGATGGAGGTTGAGTCAGATGAGGAAGATCAGGAGAAGGCCGAGGAGACTCCTTCCCAGCTGGACCAGGATACTCAAGTACAGGACATGGATGAGGGTTCAGATGATGAAGAAGAAGGGCAGAAAGTGCCTCCACCCCCAGAGACACCCATGCCTCCACCTCTGCCCCCAACACCAGACCAAGTCATTGTGCGGAAGGACTATGATCCCAAAGCTTCCAAGCCCCTCCCTCCAGCCCCTGCTCCCGATGAGTATCTTGTATCCCCCATCACTGGGGAGAAGATTCCTGCCAGCAAAATGCAGGAGCACATGCGCATTGGGCTTCTTGACCCCCGCTGGCTGGAGCAGCGGGACCGCTCCATCCGAGAGAAGCAGAGTGATGATGAGGTTTATGCACCA
Peptide sequence:
MLRLTGMILWWWRQWIFNPMSKETFHPQQHQRNWELGSSFRSATRSLGRARKWRWRLSQMRKIRRRPRRLLPSWTRILKYRTWMRVQMMKKKGRKCLHPQRHPCLHLCPQHQTKSLCGRTMIPKLPSPSLQPLLPMSILYPPSLGRRFLPAKCRSTCALGFLTPAGWSSGTAPSERSRVMMRFMHQILIPPKGLFSKLKKEAENPREVLDQVCYRVEWAKFQERERKKEEEEKEKERVAYAQIDWHDFVVVETVDFQPNEQGNFPPPTTPEELGARILIQERYEKFGESEEVEMEVESDEEDQEKAEETPSQLDQDTQVQDMDEGSDDEEEGQKVPPPPETPMPPPLPPTPDQVIVRKDYDPKASKPLPPAPAPDEYLVSPITGEKIPASKMQEHMRIGLLDPRWLEQRDRSIREKQSDDEVYAP
IRESfinder result
IRESfinder score
0.451087426
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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