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mmu_ciSec31a_828
Basic information of circular RNA
PanCircBase ID:
mmu_ciSec31a_828
mm39_Chr. Position ID:
chr5|100535564|100536392|-
Gene name:
Sec31a
Transcript:
ENSMUST00000094578.11
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
14
Exon/intron offsets:
0
Genomic length:
828
Exon/intron sizes in nt:
828
Flanking exon/introns:
chr5:100534062-100536392
Splice length:
828
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACTGATTTTTTATATTCTTTTGGACAACTGTGTGATAATTGTGTATCTCACCTGAAACTTTGGACATTGTTGACTAATTGTTGCCAACTGTGTTTGAATGTATTGTTTCCTTAGGTATGTTTAGGTAAGATTCTGTTCACCTCACTTAACAGAAGTATCTCTGTGCTCTTAGTTCCTTGGCCCAGCTTCTGGATTGTATGGCTTAAAATTAGCAGCAGATGTGAGATATCCTTAATTGGCTCAGAGGCTGCCAGATGCTAAACCAAAGAGAGATTTTATTTGAAAATGCAGTTGCCTTGCATGTCAACTTAATGCTGTTTTCTTGGCACATTAATTTGTATAGCTCACTGTCAGTGATAGAGGCTTCAAAATTAGTCCTGCACCTGGAATGCCAGTAAAGAGTATTTTATAAAACTAAACCAACTGTGATGATTTACTACGTGTCCTTAGCTGTGCTTGGTAATTCCTGAAGCTAATTGAGAAGAGACCTTGAATACAAACTTGTATCATTAATTGGTTTCCTTTTGATTCTCTTTCTTTCTCCTCCAACTAACAACTAACTCTAGAATTTACTGGTTTTGCTTTTTAATTTTATTTAATCTTGGAAAATTAATCAGGTTCTTATTTCATATCTAATCTTTGACTTTTTCATTGCCTTTTATGATAGGGGAATATCTTGACTATGAAATGCTTACAAACATAATTCATGAATGTTTTGGGCTACTACAAACTGATTATAAAATATGTTTTCTATTGAAATCAAGTCTTAGAATTTATGAAGGAAATAAGGAGCTTTGTAAAGTCTTCCTCAACCTTTGAACTAGTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTATGAAGGAAATAAGGAGCTTTGT
56.74
GGCAACAATTAGTCAACAATGTCC
59.08
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTATGAAGGAAATAAGGAGCTTTGT
57.35
GGCAACAATTAGTCAACAATGTCC
59.08
141
PCR template sequence:
CAAACTGATTATAAAATATGTTTTCTATTGAAATCAAGTCTTAGAATTTATGAAGGAAATAAGGAGCTTTGTAAAGTCTTCCTCAACCTTTGAACTAGTTGTACTGATTTTTTATATTCTTTTGGACAACTGTGTGATAATTGTGTATCTCACCTGAAACTTTGGACATTGTTGACTAATTGTTGCCAACTGTGTTTGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-7b-5p(1), mmu-miR-181a-5p(1), mmu-miR-181b-5p(1), mmu-miR-381-3p(1), mmu-miR-182-5p(1), mmu-miR-499-5p(1), mmu-miR-300-3p(1), mmu-miR-296-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTTGAACTAGTTGTACTGATTTTTT
siRNA sets
AAAAAATCAGTACAACTAG,AAATCAGTACAACTAGTTC,AAAAATCAGTACAACTAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CISEC31A_828_ORF_5
0.8973
-0.268299367
0.019251241
108
ORF sequence:
ATGAAGGAAATAAGGAGCTTTGTAAAGTCTTCCTCAACCTTTGAACTAGTTGTACTGATTTTTTATATTCTTTTGGACAACTGTGTGATAATTGTGTATCTCACCTGA
Peptide sequence:
MKEIRSFVKSSSTFELVVLIFYILLDNCVIIVYLT
IRESfinder result
IRESfinder score
0.948924187
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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