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mmu_circSpag9_787
Basic information of circular RNA
PanCircBase ID:
mmu_circSpag9_787
mm39_Chr. Position ID:
chr11|93973585|93983253|+
Gene name:
Spag9
Transcript:
ENSMUST00000041956.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
10,11,12,13,14,15,16
Exon/intron offsets:
0,1188,3487,6839,7798,9004,9578
Genomic length:
9668
Exon/intron sizes in nt:
153,52,131,57,174,130,90
Flanking exon/introns:
chr11:93972223-93973585|chr11:93983253-93983640
Splice length:
787
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AAACGCTCTGAATGTAGTGAAGAATGACTTAATAGCCAAAGTGGATGAGCTGACCTGTGAGAAGGACGTGCTGCAGGGGGAGCTGGAGGCTGTGAAGCAAGCCAAGCTGAAGCTGGAGGACAAGAACAGAGAGCTGGAGGAGGAGCTCAGGAAAGCTCGTGCAGAAGCTGAAGATGCAAGGCAAAAAGCAAAAGACGATGATGATAGTGACATTCCCACAGCCCAGAGGAAGAGGTTTACCAGAGTAGAAATGGCCCGAGTTCTCATGGAGAGAAACCAGTACAAAGAGAGGCTGATGGAGCTTCAAGAAGCTGTTCGATGGACGGAGATGATCCGGGCCTCACGAGAGAACCCAGCTATGCAAGAAAAGAAAAGGTCAAGCATCTGGCAATTTTTCAGCCGACTTTTTAGCTCTTCAAGTAATGCAACAAAGAAGCCTGAACCCCCTGTTAACCTGAAGTACAACGCCCCCACCTCTCACGTGACTCCCTCCGTGAAGAAAAGGAGCAGCACTTTATCTCAGCTCCCTGGGGACAAGTCCAAGGCATTTGATTTCCTCAGTGAGGAAACTGAGGCTAGTTTAGCCTCCCGCAGAGAGCAAAAGAGAGAGCAGTATCGGCAGGTGAAGGCTCACGTTCAGAAGGAAGATGGCCGAGTGCAAGCTTTCGGCTGGAGTCTGCCTCAGAAGTACAAACAGGTAGCCAATGGTCAAGGGGAAACTAAGATGAAAAATTTACCTGTGCCTGTCTATCTCAGACCACTAGACGAAAAAGATGCGTCTATGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTAGCCAATGGTCAAGGGG
60.4
CGTCCTTCTCACAGGTCAGC
60.39
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCAATGGTCAAGGGGAAA
59.51
CGTCCTTCTCACAGGTCAGC
60.39
156
PCR template sequence:
GTACAAACAGGTAGCCAATGGTCAAGGGGAAACTAAGATGAAAAATTTACCTGTGCCTGTCTATCTCAGACCACTAGACGAAAAAGATGCGTCTATGAAGAAACGCTCTGAATGTAGTGAAGAATGACTTAATAGCCAAAGTGGATGAGCTGACCTGTGAGAAGGACGTGCTGCAGGGGGAGCTGGAGGCTGTGAAGCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-93-5p(1), mmu-miR-106b-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-705(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1), mmu-miR-5101(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCGTCTATGAAGAAACGCTCTGAAT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSPAG9_787_ORF_1
0.7998
0.265654224
0.796339689
564
ORF sequence:
ATGGCCCGAGTTCTCATGGAGAGAAACCAGTACAAAGAGAGGCTGATGGAGCTTCAAGAAGCTGTTCGATGGACGGAGATGATCCGGGCCTCACGAGAGAACCCAGCTATGCAAGAAAAGAAAAGGTCAAGCATCTGGCAATTTTTCAGCCGACTTTTTAGCTCTTCAAGTAATGCAACAAAGAAGCCTGAACCCCCTGTTAACCTGAAGTACAACGCCCCCACCTCTCACGTGACTCCCTCCGTGAAGAAAAGGAGCAGCACTTTATCTCAGCTCCCTGGGGACAAGTCCAAGGCATTTGATTTCCTCAGTGAGGAAACTGAGGCTAGTTTAGCCTCCCGCAGAGAGCAAAAGAGAGAGCAGTATCGGCAGGTGAAGGCTCACGTTCAGAAGGAAGATGGCCGAGTGCAAGCTTTCGGCTGGAGTCTGCCTCAGAAGTACAAACAGGTAGCCAATGGTCAAGGGGAAACTAAGATGAAAAATTTACCTGTGCCTGTCTATCTCAGACCACTAGACGAAAAAGATGCGTCTATGAAGAAACGCTCTGAATGTAGTGAAGAATGA
Peptide sequence:
MARVLMERNQYKERLMELQEAVRWTEMIRASRENPAMQEKKRSSIWQFFSRLFSSSSNATKKPEPPVNLKYNAPTSHVTPSVKKRSSTLSQLPGDKSKAFDFLSEETEASLASRREQKREQYRQVKAHVQKEDGRVQAFGWSLPQKYKQVANGQGETKMKNLPVPVYLRPLDEKDASMKKRSECSEE
IRESfinder result
IRESfinder score
0.318226377
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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