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mmu_circSnx9_693
Basic information of circular RNA
PanCircBase ID:
mmu_circSnx9_693
mm39_Chr. Position ID:
chr17|5937271|5955248|+
Gene name:
Snx9
Transcript:
ENSMUST00000002436.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,3078,4777,12330,15367,17892
Genomic length:
17977
Exon/intron sizes in nt:
87,75,126,169,151,85
Flanking exon/introns:
chr17:5891821-5937271|chr17:5955248-5958628
Splice length:
693
Other database IDs:
CIRCpedia: MMU_CIRCpedia_24296, circAtlas: mmu-Snx9_0006
CIRCpedia: HSA_CIRCpedia_100448
Human Ortholog IDs:
Mature spliced Sequence:
GCTCGGGTCATGTACGACTTTGCTGCTGAGCCTGGAAACAATGAGCTGACCGTTACTGAAGGAGAAATCATCACAGTTACAAACCCGAATGTTGGTGGAGGATGGCTGGAAGGAAAGAACAACAAAGGAGAGCAGGGGCTTGTTCCTACTGACTACGTGGAAATTTTACCAAACGATGGAAAAGATCCGTTTTCTTGTGGGAATTCAGTAGCCGACCAAGCTTTCCTCGATTCCCTGACAGCTAGCACAGCTCAAACCAACTCATCTTCTGCCAACAGCAATAACCAGGTTGGTGGTGGCAATGACCCCTGGACAGCCTGGAATGCTCCCAAACCTGGGAACTGGGACAGCTCCGATGCCTGGGGCTCCAGGACAGACGGAACTAGCGCTCAGAGGAACAGCAGCGCCAACAACTGGGACACGGGCTTTGGCCACCCACAGGCCTACCAAGGACCAGCAACTGGTGATGATGACGAATGGGATGAAGACTGGGACGACCCCAAGTCCTCCTCACCTTACTTCAAGGATTCAGAACCAGCTGAAGCAGGGGGCATCCAGCGGGGAAACAGTCGTGCGGGTGCCTCCTCCATGAAGCTGCCCCTTAACAAATTTCCTGGATTTGCAAAACCTGGCATGGAGCAGTACTTGTTGGCCAAGCAGCTAGCAAAACCCAAAGAGAAAATCGCCATCATC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGCAGTACTTGTTGGCCA
60.25
CCACCAACATTCGGGTTTGT
58.96
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGCAGTACTTGTTGGCC
60.25
CCACCAACATTCGGGTTTGT
58.96
157
PCR template sequence:
GCTGCCCCTTAACAAATTTCCTGGATTTGCAAAACCTGGCATGGAGCAGTACTTGTTGGCCAAGCAGCTAGCAAAACCCAAAGAGAAAATCGCCATCATCGCTCGGGTCATGTACGACTTTGCTGCTGAGCCTGGAAACAATGAGCTGACCGTTACTGAAGGAGAAATCATCACAGTTACAAACCCGAATGTTGGTGGAG
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-24-3p(1), mmu-miR-362-5p(1), mmu-miR-484(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AATCGCCATCATCGCTCGGGTCATGT
siRNA sets
ATGACCCGAGCGATGATGG, TGACCCGAGCGATGATGGC, CATGACCCGAGCGATGATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSNX9_693_ORF_1
1.1192
0.328739594
0.999692512
1377
ORF sequence:
ATGTACGACTTTGCTGCTGAGCCTGGAAACAATGAGCTGACCGTTACTGAAGGAGAAATCATCACAGTTACAAACCCGAATGTTGGTGGAGGATGGCTGGAAGGAAAGAACAACAAAGGAGAGCAGGGGCTTGTTCCTACTGACTACGTGGAAATTTTACCAAACGATGGAAAAGATCCGTTTTCTTGTGGGAATTCAGTAGCCGACCAAGCTTTCCTCGATTCCCTGACAGCTAGCACAGCTCAAACCAACTCATCTTCTGCCAACAGCAATAACCAGGTTGGTGGTGGCAATGACCCCTGGACAGCCTGGAATGCTCCCAAACCTGGGAACTGGGACAGCTCCGATGCCTGGGGCTCCAGGACAGACGGAACTAGCGCTCAGAGGAACAGCAGCGCCAACAACTGGGACACGGGCTTTGGCCACCCACAGGCCTACCAAGGACCAGCAACTGGTGATGATGACGAATGGGATGAAGACTGGGACGACCCCAAGTCCTCCTCACCTTACTTCAAGGATTCAGAACCAGCTGAAGCAGGGGGCATCCAGCGGGGAAACAGTCGTGCGGGTGCCTCCTCCATGAAGCTGCCCCTTAACAAATTTCCTGGATTTGCAAAACCTGGCATGGAGCAGTACTTGTTGGCCAAGCAGCTAGCAAAACCCAAAGAGAAAATCGCCATCATCGCTCGGGTCATGTACGACTTTGCTGCTGAGCCTGGAAACAATGAGCTGACCGTTACTGAAGGAGAAATCATCACAGTTACAAACCCGAATGTTGGTGGAGGATGGCTGGAAGGAAAGAACAACAAAGGAGAGCAGGGGCTTGTTCCTACTGACTACGTGGAAATTTTACCAAACGATGGAAAAGATCCGTTTTCTTGTGGGAATTCAGTAGCCGACCAAGCTTTCCTCGATTCCCTGACAGCTAGCACAGCTCAAACCAACTCATCTTCTGCCAACAGCAATAACCAGGTTGGTGGTGGCAATGACCCCTGGACAGCCTGGAATGCTCCCAAACCTGGGAACTGGGACAGCTCCGATGCCTGGGGCTCCAGGACAGACGGAACTAGCGCTCAGAGGAACAGCAGCGCCAACAACTGGGACACGGGCTTTGGCCACCCACAGGCCTACCAAGGACCAGCAACTGGTGATGATGACGAATGGGATGAAGACTGGGACGACCCCAAGTCCTCCTCACCTTACTTCAAGGATTCAGAACCAGCTGAAGCAGGGGGCATCCAGCGGGGAAACAGTCGTGCGGGTGCCTCCTCCATGAAGCTGCCCCTTAACAAATTTCCTGGATTTGCAAAACCTGGCATGGAGCAGTACTTGTTGGCCAAGCAGCTAGCAAAACCCAAAGAGAAAATCGCCATCATC
Peptide sequence:
MYDFAAEPGNNELTVTEGEIITVTNPNVGGGWLEGKNNKGEQGLVPTDYVEILPNDGKDPFSCGNSVADQAFLDSLTASTAQTNSSSANSNNQVGGGNDPWTAWNAPKPGNWDSSDAWGSRTDGTSAQRNSSANNWDTGFGHPQAYQGPATGDDDEWDEDWDDPKSSSPYFKDSEPAEAGGIQRGNSRAGASSMKLPLNKFPGFAKPGMEQYLLAKQLAKPKEKIAIIARVMYDFAAEPGNNELTVTEGEIITVTNPNVGGGWLEGKNNKGEQGLVPTDYVEILPNDGKDPFSCGNSVADQAFLDSLTASTAQTNSSSANSNNQVGGGNDPWTAWNAPKPGNWDSSDAWGSRTDGTSAQRNSSANNWDTGFGHPQAYQGPATGDDDEWDEDWDDPKSSSPYFKDSEPAEAGGIQRGNSRAGASSMKLPLNKFPGFAKPGMEQYLLAKQLAKPKEKIAII
IRESfinder result
IRESfinder score
0.360481597
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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