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mmu_circSmarcb1_396
Basic information of circular RNA
PanCircBase ID:
mmu_circSmarcb1_396
mm39_Chr. Position ID:
chr10|75745987|75751027|-
Gene name:
Smarcb1
Transcript:
ENSMUST00000000925.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,1365,4910
Genomic length:
5040
Exon/intron sizes in nt:
12,81,38,130
Flanking exon/introns:
chr10:75742030-75745987|chr10:75751027-75752606
Splice length:
396
Other database IDs:
circAtlas: hsa-SMARCB1_0007, CIRCpedia: HSA_CIRCpedia_365119
Human Ortholog IDs:
Mature spliced Sequence:
ATCATGGATATACCACCCTGGCCACCAGCGTGACACTCCTGAAAGCCTCAGAGGTAGAAGAGATCCTGGATGGCAATGACGAGAAGTACAAGGCTGTGTCCATCAGCACAGAGCCCCCGACCTACCTCAGGGAGCAGAAGGCCAAGAGGAACAGCCAGTGGGTCCCCACCCTGCCCAACAGCTCCCACCACCTGGATGCTGTGCCCTGTTCCACCACCATCAACAGGAACCGCATGGGTCGGGACAAGAAGAGAACCTTCCCCTTGTGCTTTGATGACCACGACCCAGCTGTGATCCATGAGAATGCGTCACAGCCTGAGGTGCTGGTGCCCATCCGGCTCGACATGGAGATCGACGGGCAGAAGCTGCGAGACGCTTTTACCTGGAACATGAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCGACATGGAGATCGACGG
60.04
CTCGTCATTGCCATCCAGGA
59.82
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCGACATGGAGATCGACGG
60.04
TCTCGTCATTGCCATCCAGG
59.82
142
PCR template sequence:
CATGAGAATGCGTCACAGCCTGAGGTGCTGGTGCCCATCCGGCTCGACATGGAGATCGACGGGCAGAAGCTGCGAGACGCTTTTACCTGGAACATGAATGATCATGGATATACCACCCTGGCCACCAGCGTGACACTCCTGAAAGCCTCAGAGGTAGAAGAGATCCTGGATGGCAATGACGAGAAGTACAAGGCTGTGTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-122-5p(1), mmu-miR-705(1), mmu-miR-673-5p(1), mmu-miR-670-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TGGAACATGAATGATCATGGATATAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMARCB1_396_ORF_1
1.3113
0.59304934
0.974127392
558
ORF sequence:
ATGGGTCGGGACAAGAAGAGAACCTTCCCCTTGTGCTTTGATGACCACGACCCAGCTGTGATCCATGAGAATGCGTCACAGCCTGAGGTGCTGGTGCCCATCCGGCTCGACATGGAGATCGACGGGCAGAAGCTGCGAGACGCTTTTACCTGGAACATGAATGATCATGGATATACCACCCTGGCCACCAGCGTGACACTCCTGAAAGCCTCAGAGGTAGAAGAGATCCTGGATGGCAATGACGAGAAGTACAAGGCTGTGTCCATCAGCACAGAGCCCCCGACCTACCTCAGGGAGCAGAAGGCCAAGAGGAACAGCCAGTGGGTCCCCACCCTGCCCAACAGCTCCCACCACCTGGATGCTGTGCCCTGTTCCACCACCATCAACAGGAACCGCATGGGTCGGGACAAGAAGAGAACCTTCCCCTTGTGCTTTGATGACCACGACCCAGCTGTGATCCATGAGAATGCGTCACAGCCTGAGGTGCTGGTGCCCATCCGGCTCGACATGGAGATCGACGGGCAGAAGCTGCGAGACGCTTTTACCTGGAACATGAAT
Peptide sequence:
MGRDKKRTFPLCFDDHDPAVIHENASQPEVLVPIRLDMEIDGQKLRDAFTWNMNDHGYTTLATSVTLLKASEVEEILDGNDEKYKAVSISTEPPTYLREQKAKRNSQWVPTLPNSSHHLDAVPCSTTINRNRMGRDKKRTFPLCFDDHDPAVIHENASQPEVLVPIRLDMEIDGQKLRDAFTWNMN
IRESfinder result
IRESfinder score
0.272540827
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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