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mmu_circSnx2_522
Basic information of circular RNA
PanCircBase ID:
mmu_circSnx2_522
mm39_Chr. Position ID:
chr18|53330926|53343515|+
Gene name:
Snx2
Transcript:
ENSMUST00000037850.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
4,5,6,7,8,9
Exon/intron offsets:
0,331,1902,5186,11733,12475
Genomic length:
12589
Exon/intron sizes in nt:
6,74,41,42,79,76,114
Flanking exon/introns:
chr18:53327665-53330926|chr18:53343515-53343770
Splice length:
522
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATTGAAGAAGAAGCAAATGGAGATATTTTTGATATAGAAATTGGTGTGTCAGATCCGGAAAAAGTTGGTGATGGCATGAATGCTTACATGGCATATAGAGTAACAACAAAGACTTCTCTTTCCATGTTCAGTAAGAGTGAATTTTCAGTCAAAAGAAGATTCAGTGACTTTCTTGGTTTGCATAGCAAATTAGCAAGCAAATATTTACATGTTGGTTACATCGTGCCACCCGCTCCAGAAAAGAGTATAGTAGGTATGACCAAGGTCAAAGTAGGTAAAGAAGATTCATCATCCACTGAGTTTGTAGAAAAACGAAGAGCGGCACTGGAGAGGTATCTTCAGAGAACAGTAAAGCATCCGACATTGCTTCAGGATCCTGACTTAAGGCAGTTTTTGGAAAGCTCAGAGCTGCCGAGAGCAGTTAATACGCAGGCTCTGAGTGGAGCAGGAATATTGAGGATGGTGAACAAGGCTGCCGACGCTGTCAACAAAATGACAATCAAGATGAATGAATCGGATGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATACGCAGGCTCTGAGTGG
59.82
TTCCGGATCTGACACACCAA
58.95
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AATACGCAGGCTCTGAGTGG
59.82
TTTCCGGATCTGACACACCA
58.95
160
PCR template sequence:
TAATACGCAGGCTCTGAGTGGAGCAGGAATATTGAGGATGGTGAACAAGGCTGCCGACGCTGTCAACAAAATGACAATCAAGATGAATGAATCGGATGCAATTGAAGAAGAAGCAAATGGAGATATTTTTGATATAGAAATTGGTGTGTCAGATCCGGAAAAAGTTGGTGATGGCATGAATGCTTACATGGCATATAGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-136-5p(1), mmu-miR-224-5p(1), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAATCGGATGCAATTGAAGAAGAAG
siRNA sets
TTCTTCTTCAATTGCATCC, TCTTCTTCAATTGCATCCG, CTTCTTCTTCAATTGCATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSNX2_522_ORF_1
0.9735
0.059888018
0.977693719
969
ORF sequence:
ATGAATGCTTACATGGCATATAGAGTAACAACAAAGACTTCTCTTTCCATGTTCAGTAAGAGTGAATTTTCAGTCAAAAGAAGATTCAGTGACTTTCTTGGTTTGCATAGCAAATTAGCAAGCAAATATTTACATGTTGGTTACATCGTGCCACCCGCTCCAGAAAAGAGTATAGTAGGTATGACCAAGGTCAAAGTAGGTAAAGAAGATTCATCATCCACTGAGTTTGTAGAAAAACGAAGAGCGGCACTGGAGAGGTATCTTCAGAGAACAGTAAAGCATCCGACATTGCTTCAGGATCCTGACTTAAGGCAGTTTTTGGAAAGCTCAGAGCTGCCGAGAGCAGTTAATACGCAGGCTCTGAGTGGAGCAGGAATATTGAGGATGGTGAACAAGGCTGCCGACGCTGTCAACAAAATGACAATCAAGATGAATGAATCGGATGCAATTGAAGAAGAAGCAAATGGAGATATTTTTGATATAGAAATTGGTGTGTCAGATCCGGAAAAAGTTGGTGATGGCATGAATGCTTACATGGCATATAGAGTAACAACAAAGACTTCTCTTTCCATGTTCAGTAAGAGTGAATTTTCAGTCAAAAGAAGATTCAGTGACTTTCTTGGTTTGCATAGCAAATTAGCAAGCAAATATTTACATGTTGGTTACATCGTGCCACCCGCTCCAGAAAAGAGTATAGTAGGTATGACCAAGGTCAAAGTAGGTAAAGAAGATTCATCATCCACTGAGTTTGTAGAAAAACGAAGAGCGGCACTGGAGAGGTATCTTCAGAGAACAGTAAAGCATCCGACATTGCTTCAGGATCCTGACTTAAGGCAGTTTTTGGAAAGCTCAGAGCTGCCGAGAGCAGTTAATACGCAGGCTCTGAGTGGAGCAGGAATATTGAGGATGGTGAACAAGGCTGCCGACGCTGTCAACAAAATGACAATCAAGATGAATGAATCGGATGCA
Peptide sequence:
MNAYMAYRVTTKTSLSMFSKSEFSVKRRFSDFLGLHSKLASKYLHVGYIVPPAPEKSIVGMTKVKVGKEDSSSTEFVEKRRAALERYLQRTVKHPTLLQDPDLRQFLESSELPRAVNTQALSGAGILRMVNKAADAVNKMTIKMNESDAIEEEANGDIFDIEIGVSDPEKVGDGMNAYMAYRVTTKTSLSMFSKSEFSVKRRFSDFLGLHSKLASKYLHVGYIVPPAPEKSIVGMTKVKVGKEDSSSTEFVEKRRAALERYLQRTVKHPTLLQDPDLRQFLESSELPRAVNTQALSGAGILRMVNKAADAVNKMTIKMNESDA
IRESfinder result
IRESfinder score
0.493790478
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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