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mmu_circSepsecs_419
Basic information of circular RNA
PanCircBase ID:
mmu_circSepsecs_419
mm39_Chr. Position ID:
chr5|52804939|52818074|-
Gene name:
Sepsecs
Transcript:
ENSMUST00000031069.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
9,8,7,6
Exon/intron offsets:
0,8416,8628,13032
Genomic length:
13135
Exon/intron sizes in nt:
9,49,21,30,103
Flanking exon/introns:
chr5:52804548-52804939|chr5:52818074-52821509
Splice length:
419
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATTAGAAGAACTGGCTGTGATTTGTGCTAATTATGACATTCCACATGTAGTCAACAACGCTTATGGATTACAGTCTTCAAAGTGCATGCATCTCATTCAGCAGGGGGCTCGGGTTGGTAGAATTGATGCTTTCGTTCAGAGCTTGGACAAAAATTTTATGGTTCCAGTAGGTGGTGCTATAATTGCTGGCTTTAATGAGCCCTTCATTCAGGACATCAGCAAGATGTATCCAGGAAGAGCCTCAGCCTCGCCGTCCTTAGACGTCCTCATCACCTTGCTGTCACTGGGCTGCAGTGGCTACAGGAAGCTGTTGAAGGAGAGAAAGGAAATGTTTGTCTATTTATCCACCCAACTAAAGAAGTTGGCAGAGGCCCACAATGAAAGACTACTACAGACACCTCACAACCCTATATCCTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGAGGCCCACAATGAAAG
59.47
TGCATGCACTTTGAAGACTGT
58.7
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGAGGCCCACAATGAAAG
59.47
ATGCATGCACTTTGAAGACTGT
59.11
146
PCR template sequence:
AGAAAGGAAATGTTTGTCTATTTATCCACCCAACTAAAGAAGTTGGCAGAGGCCCACAATGAAAGACTACTACAGACACCTCACAACCCTATATCCTTAGATTAGAAGAACTGGCTGTGATTTGTGCTAATTATGACATTCCACATGTAGTCAACAACGCTTATGGATTACAGTCTTCAAAGTGCATGCATCTCATTCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-1a-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-138-5p(1), mmu-miR-673-5p(1), mmu-miR-296-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTATATCCTTAGATTAGAAGAACTG
siRNA sets
AGTTCTTCTAATCTAAGGA,CAGTTCTTCTAATCTAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEPSECS_419_ORF_1
0.9011
0.100415745
0.325174153
339
ORF sequence:
ATGCATCTCATTCAGCAGGGGGCTCGGGTTGGTAGAATTGATGCTTTCGTTCAGAGCTTGGACAAAAATTTTATGGTTCCAGTAGGTGGTGCTATAATTGCTGGCTTTAATGAGCCCTTCATTCAGGACATCAGCAAGATGTATCCAGGAAGAGCCTCAGCCTCGCCGTCCTTAGACGTCCTCATCACCTTGCTGTCACTGGGCTGCAGTGGCTACAGGAAGCTGTTGAAGGAGAGAAAGGAAATGTTTGTCTATTTATCCACCCAACTAAAGAAGTTGGCAGAGGCCCACAATGAAAGACTACTACAGACACCTCACAACCCTATATCCTTAGATTAG
Peptide sequence:
MHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNEPFIQDISKMYPGRASASPSLDVLITLLSLGCSGYRKLLKERKEMFVYLSTQLKKLAEAHNERLLQTPHNPISLD
IRESfinder result
IRESfinder score
0.674402061
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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