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mmu_circShq1_461
Basic information of circular RNA
PanCircBase ID:
mmu_circShq1_461
mm39_Chr. Position ID:
chr6|100607843|100625252|-
Gene name:
Shq1
Transcript:
ENSMUST00000170667.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
9,8,7,6
Exon/intron offsets:
0,1356,6085,17281
Genomic length:
17409
Exon/intron sizes in nt:
12,45,41,55,128
Flanking exon/introns:
chr6:100588817-100607843|chr6:100625252-100632219
Splice length:
461
Other database IDs:
CIRCpedia: MMU_CIRCpedia_231, circAtlas: mmu-Shq1_0012
Human Ortholog IDs:
Mature spliced Sequence:
AGCTGACTTCTTTGAAGACGAGGCAGTTGAGCAGATTTTGAAGTACAGTCCTTGGTGGAATGATGCACATGCAGAAATGGTGGCCTCTTTGGGAAAGAACCAAGAGCAAGGGGACTCTGCTGCATTAGTGTCTTTTTCAGAAGAGGAAAAATATCAGCTACGAAAATTTGTGAATAAGTCTTACCTGCTAGACAAGACGGCTCACCGTCAAGTGTACTATGGTTTGGTTGACATCCTGCTGGCCTATTGCTATGAAGTACGTGTCACTGAAGGAGAGCACAGCGTTGAATCTGCGTGGACCATCAGAAAGCTGAGTCCAACACTCTGCTGGTTTGAGACCTGGACAGACGTTCATGAAATCCTGGTGTCCTTTGGAAGGAGAGTTTTGTGCTATCCACTTTATCGTCATTTCAAGCTGGTGCTGAAAGCCTACCGAGACACTATAAAGATACTGCAACTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTCATTTCAAGCTGGTGC
59.13
GGCCACCATTTCTGCATGTG
60.11
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTCATTTCAAGCTGGTGC
59.13
TCTTTCCCAAAGAGGCCACC
59.89
157
PCR template sequence:
CTGGTGTCCTTTGGAAGGAGAGTTTTGTGCTATCCACTTTATCGTCATTTCAAGCTGGTGCTGAAAGCCTACCGAGACACTATAAAGATACTGCAACTAGAGCTGACTTCTTTGAAGACGAGGCAGTTGAGCAGATTTTGAAGTACAGTCCTTGGTGGAATGATGCACATGCAGAAATGGTGGCCTCTTTGGGAAAGAAC
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-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-433-5p(1), mmu-miR-499-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATACTGCAACTAGAGCTGACTTCTTT
siRNA sets
AAGTCAGCTCTAGTTGCAG, AGAAGTCAGCTCTAGTTGC, AAAGAAGTCAGCTCTAGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSHQ1_461_ORF_1
0.7217
0.137458438
0.428879955
426
ORF sequence:
ATGGTGGCCTCTTTGGGAAAGAACCAAGAGCAAGGGGACTCTGCTGCATTAGTGTCTTTTTCAGAAGAGGAAAAATATCAGCTACGAAAATTTGTGAATAAGTCTTACCTGCTAGACAAGACGGCTCACCGTCAAGTGTACTATGGTTTGGTTGACATCCTGCTGGCCTATTGCTATGAAGTACGTGTCACTGAAGGAGAGCACAGCGTTGAATCTGCGTGGACCATCAGAAAGCTGAGTCCAACACTCTGCTGGTTTGAGACCTGGACAGACGTTCATGAAATCCTGGTGTCCTTTGGAAGGAGAGTTTTGTGCTATCCACTTTATCGTCATTTCAAGCTGGTGCTGAAAGCCTACCGAGACACTATAAAGATACTGCAACTAGAGCTGACTTCTTTGAAGACGAGGCAGTTGAGCAGATTTTGA
Peptide sequence:
MVASLGKNQEQGDSAALVSFSEEEKYQLRKFVNKSYLLDKTAHRQVYYGLVDILLAYCYEVRVTEGEHSVESAWTIRKLSPTLCWFETWTDVHEILVSFGRRVLCYPLYRHFKLVLKAYRDTIKILQLELTSLKTRQLSRF
IRESfinder result
IRESfinder score
0.653345097
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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