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mmu_circSsx2ip_1071
Basic information of circular RNA
PanCircBase ID:
mmu_circSsx2ip_1071
mm39_Chr. Position ID:
chr3|146123361|146133922|+
Gene name:
Ssx2ip
Transcript:
ENSMUST00000106151.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,668,1528,5289,8716,10218,10380
Genomic length:
10561
Exon/intron sizes in nt:
184,170,213,111,136,76,181
Flanking exon/introns:
chr3:146110690-146123361|chr3:146133922-146136683
Splice length:
1071
Other database IDs:
circAtlas: mmu-Ssx2ip_0003
Human Ortholog IDs:
Mature spliced Sequence:
GAGATGCTCACGTAGGAGAGTGGCAGGAGCTGTCATAAGCATCGCAGCACTGAGCCGCCTCACGTAGGAGAGTGACAGGAGCTGTTGTAAGCGTCGCAGCACTGAGCCGCCTCCTCAGGTATCCTGGCTCTGGAACTTGCTATGGGAGATTGGATGACTGTGACAGATCCAGTTCTGTGTACAGAAAACAAAAATCTCTCTCAATATACCTCAGAAACAAAGATGTCTCCGTCCAGTTTGTACTCCCAGCAAGTTCTGTGCTCTTCAGTACCTTTATCCAAAAACGTGCATGGTGTTTTCGGTGTCTTCTGCACAGGAGAGAACATTGAACAAAGTATTTCCTATCTTGATCAGGAGCTGACCACCTTCGGGTTTCCTTCCTTGTATGAAGAATCCAAAAGTAAAGAGGCAAAGAGAGAATTAAATATAGTCGCTGTTCTGAACTGTATGAACGAGCTGCTCGTGCTTCAGCGGAAGAACCTGCTGGCCCAGGAGAGCGTGGAGACACAGAACTTGAAGCTGGGCAGTGACATGGACCACCTGCAGAGCTGCTACGCCAAACTTAAGGAGCAGTTGGAAACGTCCAGGCGGGAGATGATCGGGCTTCAAGAGAGAGACAGGCAGCTGCAGTGCAAGAACAGGAGTTTGCATCAGCTCCTGAAGAATGAGAAAGATGAGGTACAAAAATTACAAAATATCATAGCCAGCCGGGCTACTCAGTATAATCATGATGTGAAGAGGAAGGAGCGTGAATATAATAAGCTAAAGGAGCGCCTGCATCAGCTCGTTATGAACAAGAAGGATAAAAACATAGCCATGGATGTTTTAAATTATGTGGGTCGAGCTGATGGCAAACGAGGCTCATGGAGGACTGACAAAACAGAAGCCAGGAATGAAGATGAGATGTACAAAATTCTGTTGAATGATTATGAGTACCGCCAGAAGCAGATCCTGATGGAGAACGCGGAGCTGAAGAAGGTCCTCCAGCAGATGAAGAAGGAGATGATCTCTCTCCTGTCTCCTCAGAAGAAGAAGCCCAGGGAAAGAGCAGAGGACGGCACAGGCACTGTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAAGCCCAGGGAAAGAGC
59.96
CTGCGACGCTTACAACAGC
59.87
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAAGCCCAGGGAAAGAGC
59.96
GCTGCGACGCTTACAACAG
59.87
142
PCR template sequence:
GAAGAAGGTCCTCCAGCAGATGAAGAAGGAGATGATCTCTCTCCTGTCTCCTCAGAAGAAGAAGCCCAGGGAAAGAGCAGAGGACGGCACAGGCACTGTTGAGATGCTCACGTAGGAGAGTGGCAGGAGCTGTCATAAGCATCGCAGCACTGAGCCGCCTCACGTAGGAGAGTGACAGGAGCTGTTGTAAGCGTCGCAGC
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-33-5p(1), mmu-miR-184-3p(1), mmu-miR-185-5p(1), mmu-miR-381-3p(1), mmu-miR-24-3p(1), mmu-miR-434-5p(1), mmu-miR-483-5p(1), mmu-miR-324-3p(1), mmu-miR-335-3p(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CACAGGCACTGTTGAGATGCTCACGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSSX2IP_1071_ORF_1
1.1153
0.306224422
0.99225045
945
ORF sequence:
ATGGGAGATTGGATGACTGTGACAGATCCAGTTCTGTGTACAGAAAACAAAAATCTCTCTCAATATACCTCAGAAACAAAGATGTCTCCGTCCAGTTTGTACTCCCAGCAAGTTCTGTGCTCTTCAGTACCTTTATCCAAAAACGTGCATGGTGTTTTCGGTGTCTTCTGCACAGGAGAGAACATTGAACAAAGTATTTCCTATCTTGATCAGGAGCTGACCACCTTCGGGTTTCCTTCCTTGTATGAAGAATCCAAAAGTAAAGAGGCAAAGAGAGAATTAAATATAGTCGCTGTTCTGAACTGTATGAACGAGCTGCTCGTGCTTCAGCGGAAGAACCTGCTGGCCCAGGAGAGCGTGGAGACACAGAACTTGAAGCTGGGCAGTGACATGGACCACCTGCAGAGCTGCTACGCCAAACTTAAGGAGCAGTTGGAAACGTCCAGGCGGGAGATGATCGGGCTTCAAGAGAGAGACAGGCAGCTGCAGTGCAAGAACAGGAGTTTGCATCAGCTCCTGAAGAATGAGAAAGATGAGGTACAAAAATTACAAAATATCATAGCCAGCCGGGCTACTCAGTATAATCATGATGTGAAGAGGAAGGAGCGTGAATATAATAAGCTAAAGGAGCGCCTGCATCAGCTCGTTATGAACAAGAAGGATAAAAACATAGCCATGGATGTTTTAAATTATGTGGGTCGAGCTGATGGCAAACGAGGCTCATGGAGGACTGACAAAACAGAAGCCAGGAATGAAGATGAGATGTACAAAATTCTGTTGAATGATTATGAGTACCGCCAGAAGCAGATCCTGATGGAGAACGCGGAGCTGAAGAAGGTCCTCCAGCAGATGAAGAAGGAGATGATCTCTCTCCTGTCTCCTCAGAAGAAGAAGCCCAGGGAAAGAGCAGAGGACGGCACAGGCACTGTTGAGATGCTCACGTAG
Peptide sequence:
MGDWMTVTDPVLCTENKNLSQYTSETKMSPSSLYSQQVLCSSVPLSKNVHGVFGVFCTGENIEQSISYLDQELTTFGFPSLYEESKSKEAKRELNIVAVLNCMNELLVLQRKNLLAQESVETQNLKLGSDMDHLQSCYAKLKEQLETSRREMIGLQERDRQLQCKNRSLHQLLKNEKDEVQKLQNIIASRATQYNHDVKRKEREYNKLKERLHQLVMNKKDKNIAMDVLNYVGRADGKRGSWRTDKTEARNEDEMYKILLNDYEYRQKQILMENAELKKVLQQMKKEMISLLSPQKKKPRERAEDGTGTVEMLT
IRESfinder result
IRESfinder score
0.387137031
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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