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mmu_circSnx4_645
Basic information of circular RNA
PanCircBase ID:
mmu_circSnx4_645
mm39_Chr. Position ID:
chr16|33088387|33110568|+
Gene name:
Snx4
Transcript:
ENSMUST00000231389.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
4,5,6,7,8,9,10
Exon/intron offsets:
0,1638,8924,12615,17926,19674,22081
Genomic length:
22181
Exon/intron sizes in nt:
15,04,85,69,21,09,90,100
Flanking exon/introns:
chr16:33087255-33088387|chr16:33110568-33112110
Splice length:
645
Other database IDs:
CIRCpedia: MMU_CIRCpedia_225490, circAtlas: mmu-Snx4_0018
Human Ortholog IDs:
Mature spliced Sequence:
GCAGAGTTCGTGTGGCATAAACTCTCTGCTGACAACATGGACCCAGACTTTGTGGAGAGACGACGCGTGGGCTTAGAAAACTTCCTCTTGAGGGTTGCTTCACATCCTGTCCTTTGTAGAGACAAAATCTTCTATTCATTTTTAACCCAGGAAGGTAACTGGAAGGAGACTGTGAATGAGACTGGATTTCAGCTGAAGGCAGACTCCAGGTTAAAAGCGCTTAATGCAACATTCAGAGTGAAAAACCCAGACAAGAGGTTTACTGAGCTGAGGCACTACAGTGATGAGCTGCAGTCTGTCATCTCGCATCTCCTTCGAGTCAGAGCTGTAAGTGATCTGGCACTCTAGCTAGTTCATGGTATTTTTGTTCTTTCTTTCTTTTCTTCTAGTGAATGGAGTGCCATCGAAAAAGAAATGGGGGATGGGCTGCAGAGTGCTGGGCATCACATGGACGTGTATGCATCTTCTATTGATGATATTTTGGAAGATGAAGAGCACTATGCAGATCAGCTGAAGGAGTATCTGTTTTATGCAGAAGCACTTCGGGCTGTGTGCAGGAAGCATGAGCTTATGCAGTATGACCTGGAGACAGCTGCTCAAGACCTGGCTGCCAAGAAGCAGCAGTGCGAGGAGCTGGCCACCGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGACAGCTGCTCAAGAC
59.68
GTTTTCTAAGCCCACGCGTC
59.83
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGACAGCTGCTCAAGACCTG
59.68
GTTTTCTAAGCCCACGCGTC
59.83
140
PCR template sequence:
GGCTGTGTGCAGGAAGCATGAGCTTATGCAGTATGACCTGGAGACAGCTGCTCAAGACCTGGCTGCCAAGAAGCAGCAGTGCGAGGAGCTGGCCACCGGGGCAGAGTTCGTGTGGCATAAACTCTCTGCTGACAACATGGACCCAGACTTTGTGGAGAGACGACGCGTGGGCTTAGAAAACTTCCTCTTGAGGGTTGCTT
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-136-5p(2), mmu-miR-143-3p(1), mmu-miR-452-3p(1), mmu-miR-3470b(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCTGGCCACCGGGGCAGAGTTCGTGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSNX4_645_ORF_1
1.1271
0.271889043
0.892125158
579
ORF sequence:
ATGGGGGATGGGCTGCAGAGTGCTGGGCATCACATGGACGTGTATGCATCTTCTATTGATGATATTTTGGAAGATGAAGAGCACTATGCAGATCAGCTGAAGGAGTATCTGTTTTATGCAGAAGCACTTCGGGCTGTGTGCAGGAAGCATGAGCTTATGCAGTATGACCTGGAGACAGCTGCTCAAGACCTGGCTGCCAAGAAGCAGCAGTGCGAGGAGCTGGCCACCGGGGCAGAGTTCGTGTGGCATAAACTCTCTGCTGACAACATGGACCCAGACTTTGTGGAGAGACGACGCGTGGGCTTAGAAAACTTCCTCTTGAGGGTTGCTTCACATCCTGTCCTTTGTAGAGACAAAATCTTCTATTCATTTTTAACCCAGGAAGGTAACTGGAAGGAGACTGTGAATGAGACTGGATTTCAGCTGAAGGCAGACTCCAGGTTAAAAGCGCTTAATGCAACATTCAGAGTGAAAAACCCAGACAAGAGGTTTACTGAGCTGAGGCACTACAGTGATGAGCTGCAGTCTGTCATCTCGCATCTCCTTCGAGTCAGAGCTGTAAGTGATCTGGCACTCTAG
Peptide sequence:
MGDGLQSAGHHMDVYASSIDDILEDEEHYADQLKEYLFYAEALRAVCRKHELMQYDLETAAQDLAAKKQQCEELATGAEFVWHKLSADNMDPDFVERRRVGLENFLLRVASHPVLCRDKIFYSFLTQEGNWKETVNETGFQLKADSRLKALNATFRVKNPDKRFTELRHYSDELQSVISHLLRVRAVSDLAL
IRESfinder result
IRESfinder score
0.682530794
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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