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mmu_circSmarca2_573
Basic information of circular RNA
PanCircBase ID:
mmu_circSmarca2_573
mm39_Chr. Position ID:
chr19|26668744|26683631|+
Gene name:
Smarca2
Transcript:
ENSMUST00000176769.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
20,21,22,23,24
Exon/intron offsets:
0,836,4831,7001,14723
Genomic length:
14887
Exon/intron sizes in nt:
10,88,74,71,67,164
Flanking exon/introns:
chr19:26661322-26668744|chr19:26683631-26687857
Splice length:
573
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_111008
Human Ortholog IDs:
Mature spliced Sequence:
GTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGAATCCTTTGCTGAACACCTGGGCTATTCGAATGGGGTCATCAATGGGGCTGAGCTGTATCGGGCCTCGGGAAAGTTTGAGCTGCTTGATCGTATTCTGCCCAAATTGAGAGCGACTAACCACCGCGTGCTGCTTTTCTGCCAGATGACGTCACTCATGACCATTATGGAGGATTACTTTGCTTTTCGGAACTTCCTGTACCTGCGCCTTGACGGCACCACCAAGTCTGAAGATCGTGCTGCTTTGCTAAAGAAATTCAATGAACCTGGGTCCCAGTATTTCATTTTCTTGCTGAGCACAAGAGCAGGGGGCCTGGGCTTAAATCTTCAGGCGGCAGACACGGTGGTCATATTTGACAGCGACTGGAATCCTCACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTGCTGAGCACAAGAGCA
59.89
TTGGCTTGCATGTGACGGTA
60.25
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGGCCTGGGCTTAAATCTT
60.03
CTTTCTCAGACCCGTCCGTG
60.39
171
PCR template sequence:
TTTCATTTTCTTGCTGAGCACAAGAGCAGGGGGCCTGGGCTTAAATCTTCAGGCGGCAGACACGGTGGTCATATTTGACAGCGACTGGAATCCTCACCAGGTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAG
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-16-5p(2), mmu-miR-15a-5p(2), mmu-miR-15b-5p(2), mmu-miR-322-5p(1), mmu-miR-494-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAATCCTCACCAGGTTGAGTATGTGA
siRNA sets
TCACATACTCAACCTGGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMARCA2_573_ORF_1
1.2501
0.336279985
0.998537986
1122
ORF sequence:
ATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGAATCCTTTGCTGAACACCTGGGCTATTCGAATGGGGTCATCAATGGGGCTGAGCTGTATCGGGCCTCGGGAAAGTTTGAGCTGCTTGATCGTATTCTGCCCAAATTGAGAGCGACTAACCACCGCGTGCTGCTTTTCTGCCAGATGACGTCACTCATGACCATTATGGAGGATTACTTTGCTTTTCGGAACTTCCTGTACCTGCGCCTTGACGGCACCACCAAGTCTGAAGATCGTGCTGCTTTGCTAAAGAAATTCAATGAACCTGGGTCCCAGTATTTCATTTTCTTGCTGAGCACAAGAGCAGGGGGCCTGGGCTTAAATCTTCAGGCGGCAGACACGGTGGTCATATTTGACAGCGACTGGAATCCTCACCAGGTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGAATCCTTTGCTGAACACCTGGGCTATTCGAATGGGGTCATCAATGGGGCTGAGCTGTATCGGGCCTCGGGAAAGTTTGAGCTGCTTGATCGTATTCTGCCCAAATTGAGAGCGACTAACCACCGCGTGCTGCTTTTCTGCCAGATGACGTCACTCATGACCATTATGGAGGATTACTTTGCTTTTCGGAACTTCCTGTACCTGCGCCTTGACGGCACCACCAAGTCTGAAGATCGTGCTGCTTTGCTAAAGAAATTCAATGAACCTGGGTCCCAGTATTTCATTTTCTTGCTGAGCACAAGAGCAGGGGGCCTGGGCTTAAATCTTCAGGCGGCAGACACGGTGGTCATATTTGACAGCGACTGGAATCCTCACCAG
Peptide sequence:
MSALQKILYRHMQAKGILLTDGSEKDKKGKGGAKTLMNTIMQLRKICNHPYMFQHIEESFAEHLGYSNGVINGAELYRASGKFELLDRILPKLRATNHRVLLFCQMTSLMTIMEDYFAFRNFLYLRLDGTTKSEDRAALLKKFNEPGSQYFIFLLSTRAGGLGLNLQAADTVVIFDSDWNPHQVEYVIKCDMSALQKILYRHMQAKGILLTDGSEKDKKGKGGAKTLMNTIMQLRKICNHPYMFQHIEESFAEHLGYSNGVINGAELYRASGKFELLDRILPKLRATNHRVLLFCQMTSLMTIMEDYFAFRNFLYLRLDGTTKSEDRAALLKKFNEPGSQYFIFLLSTRAGGLGLNLQAADTVVIFDSDWNPHQ
IRESfinder result
IRESfinder score
0.511955653
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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