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mmu_circRubcn_327
Basic information of circular RNA
PanCircBase ID:
mmu_circRubcn_327
mm39_Chr. Position ID:
chr16|32656779|32658723|-
Gene name:
Rubcn
Transcript:
ENSMUST00000115105.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
10,9
Exon/intron offsets:
0,1828
Genomic length:
1944
Exon/intron sizes in nt:
2,11,116
Flanking exon/introns:
chr16:32656385-32656779|chr16:32658723-32663367
Splice length:
327
Other database IDs:
circAtlas: mmu-1700021K19Rik_0008
Human Ortholog IDs:
Mature spliced Sequence:
AGGGTGGTCAGTACCTCTGCTCAGGAGAAGGCATGTTTAGAAGACCATCAGAAGGACAGTCCCTCATCAGTTACCTCTCTGAGCAAGACTTTGGCAGCTGTGCAGACCTGGAAAAGGAAAACGCCCACTTCAGCATCTCCGAGTCCTTGATTGCCGCCATTGAGCTGATGAAGTGCAACATGATGAGCCAGTGTCTAGAAGAGGAGGAAGTAGAGGAGGAAGATAGTGACCGAGAGATCCAGGAACTGAAGCAGAAGATCCGCCTTCGGCGCCAGCAGATCCGCACCAAAAACCTGCTCCCTGCGTACCGGGAGACTGAGAATGGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAACCTGCTCCCTGCGTA
59.89
CAGCTGCCAAAGTCTTGCTC
59.76
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAAGCAGAAGATCCGCCT
59.82
GCTGCCAAAGTCTTGCTCAG
59.76
180
PCR template sequence:
GACCGAGAGATCCAGGAACTGAAGCAGAAGATCCGCCTTCGGCGCCAGCAGATCCGCACCAAAAACCTGCTCCCTGCGTACCGGGAGACTGAGAATGGAAAGGGTGGTCAGTACCTCTGCTCAGGAGAAGGCATGTTTAGAAGACCATCAGAAGGACAGTCCCTCATCAGTTACCTCTCTGAGCAAGACTTTGGCAGCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(1), mmu-miR-149-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGAGAATGGAAAGGGTGGTCAGTA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRUBCN_327_ORF_1
1.0889
0.546636422
0.970195728
621
ORF sequence:
ATGTTTAGAAGACCATCAGAAGGACAGTCCCTCATCAGTTACCTCTCTGAGCAAGACTTTGGCAGCTGTGCAGACCTGGAAAAGGAAAACGCCCACTTCAGCATCTCCGAGTCCTTGATTGCCGCCATTGAGCTGATGAAGTGCAACATGATGAGCCAGTGTCTAGAAGAGGAGGAAGTAGAGGAGGAAGATAGTGACCGAGAGATCCAGGAACTGAAGCAGAAGATCCGCCTTCGGCGCCAGCAGATCCGCACCAAAAACCTGCTCCCTGCGTACCGGGAGACTGAGAATGGAAAGGGTGGTCAGTACCTCTGCTCAGGAGAAGGCATGTTTAGAAGACCATCAGAAGGACAGTCCCTCATCAGTTACCTCTCTGAGCAAGACTTTGGCAGCTGTGCAGACCTGGAAAAGGAAAACGCCCACTTCAGCATCTCCGAGTCCTTGATTGCCGCCATTGAGCTGATGAAGTGCAACATGATGAGCCAGTGTCTAGAAGAGGAGGAAGTAGAGGAGGAAGATAGTGACCGAGAGATCCAGGAACTGAAGCAGAAGATCCGCCTTCGGCGCCAGCAGATCCGCACCAAAAACCTGCTCCCTGCGTACCGGGAGACTGAGAATGGA
Peptide sequence:
MFRRPSEGQSLISYLSEQDFGSCADLEKENAHFSISESLIAAIELMKCNMMSQCLEEEEVEEEDSDREIQELKQKIRLRRQQIRTKNLLPAYRETENGKGGQYLCSGEGMFRRPSEGQSLISYLSEQDFGSCADLEKENAHFSISESLIAAIELMKCNMMSQCLEEEEVEEEDSDREIQELKQKIRLRRQQIRTKNLLPAYRETENG
IRESfinder result
IRESfinder score
0.47300691
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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