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mmu_circSpag9_393
Basic information of circular RNA
PanCircBase ID:
mmu_circSpag9_393
mm39_Chr. Position ID:
chr11|93973585|93980481|+
Gene name:
Spag9
Transcript:
ENSMUST00000041956.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,11,12,13
Exon/intron offsets:
0,1188,3487,6839
Genomic length:
6896
Exon/intron sizes in nt:
153,52,131,57
Flanking exon/introns:
chr11:93972223-93973585|chr11:93980481-93981383
Splice length:
393
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AAACGCTCTGAATGTAGTGAAGAATGACTTAATAGCCAAAGTGGATGAGCTGACCTGTGAGAAGGACGTGCTGCAGGGGGAGCTGGAGGCTGTGAAGCAAGCCAAGCTGAAGCTGGAGGACAAGAACAGAGAGCTGGAGGAGGAGCTCAGGAAAGCTCGTGCAGAAGCTGAAGATGCAAGGCAAAAAGCAAAAGACGATGATGATAGTGACATTCCCACAGCCCAGAGGAAGAGGTTTACCAGAGTAGAAATGGCCCGAGTTCTCATGGAGAGAAACCAGTACAAAGAGAGGCTGATGGAGCTTCAAGAAGCTGTTCGATGGACGGAGATGATCCGGGCCTCACGAGAGAACCCAGCTATGCAAGAAAAGAAAAGGTCAAGCATCTGGCAATT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTTCGATGGACGGAGAT
59.9
CGTCCTTCTCACAGGTCAGC
60.39
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCTGTTCGATGGACGGAG
60.11
CGTCCTTCTCACAGGTCAGC
60.39
153
PCR template sequence:
TGATGGAGCTTCAAGAAGCTGTTCGATGGACGGAGATGATCCGGGCCTCACGAGAGAACCCAGCTATGCAAGAAAAGAAAAGGTCAAGCATCTGGCAATTAAACGCTCTGAATGTAGTGAAGAATGACTTAATAGCCAAAGTGGATGAGCTGACCTGTGAGAAGGACGTGCTGCAGGGGGAGCTGGAGGCTGTGAAGCAA
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-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCATCTGGCAATTAAACGCTCTGAAT
siRNA sets
ATTCAGAGCGTTTAATTGC, TTCAGAGCGTTTAATTGCC, AGAGCGTTTAATTGCCAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSPAG9_393_ORF_1
1.0453
0.454049324
0.916239293
534
ORF sequence:
ATGGCCCGAGTTCTCATGGAGAGAAACCAGTACAAAGAGAGGCTGATGGAGCTTCAAGAAGCTGTTCGATGGACGGAGATGATCCGGGCCTCACGAGAGAACCCAGCTATGCAAGAAAAGAAAAGGTCAAGCATCTGGCAATTAAACGCTCTGAATGTAGTGAAGAATGACTTAATAGCCAAAGTGGATGAGCTGACCTGTGAGAAGGACGTGCTGCAGGGGGAGCTGGAGGCTGTGAAGCAAGCCAAGCTGAAGCTGGAGGACAAGAACAGAGAGCTGGAGGAGGAGCTCAGGAAAGCTCGTGCAGAAGCTGAAGATGCAAGGCAAAAAGCAAAAGACGATGATGATAGTGACATTCCCACAGCCCAGAGGAAGAGGTTTACCAGAGTAGAAATGGCCCGAGTTCTCATGGAGAGAAACCAGTACAAAGAGAGGCTGATGGAGCTTCAAGAAGCTGTTCGATGGACGGAGATGATCCGGGCCTCACGAGAGAACCCAGCTATGCAAGAAAAGAAAAGGTCAAGCATCTGGCAA
Peptide sequence:
MARVLMERNQYKERLMELQEAVRWTEMIRASRENPAMQEKKRSSIWQLNALNVVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEDKNRELEEELRKARAEAEDARQKAKDDDDSDIPTAQRKRFTRVEMARVLMERNQYKERLMELQEAVRWTEMIRASRENPAMQEKKRSSIWQ
IRESfinder result
IRESfinder score
0.134000495
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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