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mmu_circSphkap_451
Basic information of circular RNA
PanCircBase ID:
mmu_circSphkap_451
mm39_Chr. Position ID:
chr1|83258050|83268750|-
Gene name:
Sphkap
Transcript:
ENSMUST00000160953.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,5,4
Exon/intron offsets:
0,8432,10640
Genomic length:
10700
Exon/intron sizes in nt:
256,135,60
Flanking exon/introns:
chr1:83257056-83258050|chr1:83268750-83317255
Splice length:
451
Other database IDs:
circAtlas: mmu-Sphkap_0014
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTCTGCTTTGTGAACCTGGATGTCAACAAAGATGCCTGCATCACAGAGAACCTGCAGCAGAAACTGGTCAATGTTTCACCGGACCTTCCAAACCTCATCAGCTCCATGAATGTCCAACAGCCGAAAGAAAATGAAATTGTCCTCCTAAGTGGGTTAGCCTCTGGAAACCTCCAGGCAGATTTTGATGTTTCACAGTGCCCTTGGCTACCAGATATCTGCTTGGTCCAGTGTGCAAGAGGGAACAGACCAAACAGTACCAACTGCATCATCTTTGAGATCAACAAGTTCTTAATTGGTCTGGAAGTAGTGCAGGAGCGTCAGCTCCACCTGGAGACGAACGTGTTGAAGCTGGAGGATGATACAAACTGTTCTCTGTCTTCAATTGAAGAAGATTTTCTTACAGCCTCCGAGCATTTGGAGGAAGAAATCGAGGTGGACGACTGCAGAAGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TACAGCCTCCGAGCATTTGG
60.11
GGTTTGGAAGGTCCGGTGAA
60.18
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TACAGCCTCCGAGCATTTGG
60.11
ATGAGGTTTGGAAGGTCCGG
59.67
151
PCR template sequence:
GAGGATGATACAAACTGTTCTCTGTCTTCAATTGAAGAAGATTTTCTTACAGCCTCCGAGCATTTGGAGGAAGAAATCGAGGTGGACGACTGCAGAAGTGGTCTGCTTTGTGAACCTGGATGTCAACAAAGATGCCTGCATCACAGAGAACCTGCAGCAGAAACTGGTCAATGTTTCACCGGACCTTCCAAACCTCATCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(1), mmu-miR-181b-5p(1), mmu-miR-680(1), mmu-miR-350-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACTGCAGAAGTGGTCTGCTTTGTGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSPHKAP_451_ORF_1
1.2603
0.231343375
0.877127644
546
ORF sequence:
ATGATACAAACTGTTCTCTGTCTTCAATTGAAGAAGATTTTCTTACAGCCTCCGAGCATTTGGAGGAAGAAATCGAGGTGGACGACTGCAGAAGTGGTCTGCTTTGTGAACCTGGATGTCAACAAAGATGCCTGCATCACAGAGAACCTGCAGCAGAAACTGGTCAATGTTTCACCGGACCTTCCAAACCTCATCAGCTCCATGAATGTCCAACAGCCGAAAGAAAATGAAATTGTCCTCCTAAGTGGGTTAGCCTCTGGAAACCTCCAGGCAGATTTTGATGTTTCACAGTGCCCTTGGCTACCAGATATCTGCTTGGTCCAGTGTGCAAGAGGGAACAGACCAAACAGTACCAACTGCATCATCTTTGAGATCAACAAGTTCTTAATTGGTCTGGAAGTAGTGCAGGAGCGTCAGCTCCACCTGGAGACGAACGTGTTGAAGCTGGAGGATGATACAAACTGTTCTCTGTCTTCAATTGAAGAAGATTTTCTTACAGCCTCCGAGCATTTGGAGGAAGAAATCGAGGTGGACGACTGCAGAAGT
Peptide sequence:
MIQTVLCLQLKKIFLQPPSIWRKKSRWTTAEVVCFVNLDVNKDACITENLQQKLVNVSPDLPNLISSMNVQQPKENEIVLLSGLASGNLQADFDVSQCPWLPDICLVQCARGNRPNSTNCIIFEINKFLIGLEVVQERQLHLETNVLKLEDDTNCSLSSIEEDFLTASEHLEEEIEVDDCRS
IRESfinder result
IRESfinder score
0.654118882
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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