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mmu_circShc4_290
Basic information of circular RNA
PanCircBase ID:
mmu_circShc4_290
mm39_Chr. Position ID:
chr2|125508192|125522070|-
Gene name:
Shc4
Transcript:
ENSMUST00000042246.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,3994,12415,13814
Genomic length:
13878
Exon/intron sizes in nt:
52,54,120,64
Flanking exon/introns:
chr2:125499529-125508192|chr2:125522070-125536745
Splice length:
290
Other database IDs:
circAtlas: mmu-Shc4_0004
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GGAAGCAATAAGTCGCCTGTGTGAAGCTGTCCCCGGGGCCCATGGAGCCATTAAAAAACGAAAGGCTCCCGTTAAGTTCCTGACAACGGTTCTTGGCAAAAGCAATCTTCAGTTTTCAGGAATGAATATAAAACTGACTGTTTCAACAAGCAGCCTCACACTGATGAACCTTGACAACCAACAGATTATTGCAAATCACCAAATGCAATCGATTTCATTTGCCTCTGGAGGGGACCCTGATACCACAGACTATGTTGCCTATGTAGCTAAAGATCCAGTCAACCAACGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACCCTGATACCACAGAC
59.17
GCCAAGAACCGTTGTCAGGA
60.53
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACCCTGATACCACAGAC
59.17
TCAGGAACTTAACGGGAGCC
59.39
143
PCR template sequence:
GCAAATCACCAAATGCAATCGATTTCATTTGCCTCTGGAGGGGACCCTGATACCACAGACTATGTTGCCTATGTAGCTAAAGATCCAGTCAACCAACGAGGGAAGCAATAAGTCGCCTGTGTGAAGCTGTCCCCGGGGCCCATGGAGCCATTAAAAAACGAAAGGCTCCCGTTAAGTTCCTGACAACGGTTCTTGGCAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-221-3p(1), mmu-miR-222-3p(1), mmu-miR-377-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCAACCAACGAGGGAAGCAATAAGT
siRNA sets
TTATTGCTTCCCTCGTTGG, TATTGCTTCCCTCGTTGGT, ATTGCTTCCCTCGTTGGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSHC4_290_ORF_1
0.934
0.02434023
0.107042551
180
ORF sequence:
ATGAATATAAAACTGACTGTTTCAACAAGCAGCCTCACACTGATGAACCTTGACAACCAACAGATTATTGCAAATCACCAAATGCAATCGATTTCATTTGCCTCTGGAGGGGACCCTGATACCACAGACTATGTTGCCTATGTAGCTAAAGATCCAGTCAACCAACGAGGGAAGCAATAA
Peptide sequence:
MNIKLTVSTSSLTLMNLDNQQIIANHQMQSISFASGGDPDTTDYVAYVAKDPVNQRGKQ
IRESfinder result
IRESfinder score
0.72460993
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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