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mmu_circSmarca2_1281
Basic information of circular RNA
PanCircBase ID:
mmu_circSmarca2_1281
mm39_Chr. Position ID:
chr19|26659270|26698347|+
Gene name:
Smarca2
Transcript:
ENSMUST00000176769.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
18,19,20,21,22,23,24,25,26,27
Exon/intron offsets:
0,1938,9474,10310,14305,16475,24197,28587,34244,38858
Genomic length:
39077
Exon/intron sizes in nt:
6,91,14,10,88,74,71,67,00,00,00,00,000
Flanking exon/introns:
chr19:26656584-26659270|chr19:26698347-26729223
Splice length:
1281
Other database IDs:
circAtlas: mmu-Smarca2_0031
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATTCGGTGGAAGTACATGATCGTGGACGAAGGCCACCGGATGAAGAATCACCACTGCAAGCTAACCCAGGTGGACCTGAACGAAGAAGAAACGATTTTGATCATCAGGCGTCTACACAAGGTGCTGAGACCCTTTTTACTGAGGAGGCTGAAGAAAGAGGTTGAGTCTCAGCTTCCGGAAAAGGTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGAATCCTTTGCTGAACACCTGGGCTATTCGAATGGGGTCATCAATGGGGCTGAGCTGTATCGGGCCTCGGGAAAGTTTGAGCTGCTTGATCGTATTCTGCCCAAATTGAGAGCGACTAACCACCGCGTGCTGCTTTTCTGCCAGATGACGTCACTCATGACCATTATGGAGGATTACTTTGCTTTTCGGAACTTCCTGTACCTGCGCCTTGACGGCACCACCAAGTCTGAAGATCGTGCTGCTTTGCTAAAGAAATTCAATGAACCTGGGTCCCAGTATTTCATTTTCTTGCTGAGCACAAGAGCAGGGGGCCTGGGCTTAAATCTTCAGGCGGCAGACACGGTGGTCATATTTGACAGCGACTGGAATCCTCACCAGGATCTGCAGGCCCAAGACCGAGCTCACCGCATTGGCCAACAAAACGAGGTCCGGGTGCTGAGGCTTTGCACCGTCAACAGTGTGGAGGAAAAGATTCTCGCGGCTGCCAAGTACAAGCTGAACGTGGATCAGAAGGTTATCCAAGCAGGCATGTTTGACCAGAAGTCATCCAGCCACGAGCGGAGGGCCTTCCTGCAGGCCATTCTGGAGCACGAGGAGGAGAATGAGGAAGAAGATGAGGTACCAGACGACGAGACCCTGAACCAGATGATTGCTCGCCGGGAGGAAGAATTTGATCTTTTTATGCGCATGGACATGGACCGGCGGAGGGAGGATGCCCGGAACCCGAAGCGCAAACCCCGCTTGATGGAGGAAGATGAGCTGCCCTCCTGGATTATCAAGGATGACGCCGAAGTGGAAAGGCTCACCTGTGAAGAAGAGGAGGAGAAGATATTTGGGAGGGGCTCTCGCCAGCGCCGGGATGTGGACTACAGTGATGCCCTCACCGAGAAGCAATGGCTCAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GATATTTGGGAGGGGCTCTCG
60
GGGTTAGCTTGCAGTGGTGA
60.25
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATATTTGGGAGGGGCTCTCG
60
CTGGGTTAGCTTGCAGTGGT
60.25
145
PCR template sequence:
CACCTGTGAAGAAGAGGAGGAGAAGATATTTGGGAGGGGCTCTCGCCAGCGCCGGGATGTGGACTACAGTGATGCCCTCACCGAGAAGCAATGGCTCAGGATTCGGTGGAAGTACATGATCGTGGACGAAGGCCACCGGATGAAGAATCACCACTGCAAGCTAACCCAGGTGGACCTGAACGAAGAAGAAACGATTTTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(2), mmu-miR-15a-5p(2), mmu-miR-15b-5p(2), mmu-miR-19b-3p(1), mmu-miR-322-5p(1), mmu-miR-19a-3p(1), mmu-miR-494-3p(1), mmu-miR-362-5p(1), mmu-miR-207(1), mmu-miR-452-3p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
GCAATGGCTCAGGATTCGGTGGAAGT
siRNA sets
CTTCCACCGAATCCTGAGC, TTCCACCGAATCCTGAGCC, ACTTCCACCGAATCCTGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMARCA2_1281_ORF_1
1.2679
0.461502783
0.99999997
2547
ORF sequence:
ATGATCGTGGACGAAGGCCACCGGATGAAGAATCACCACTGCAAGCTAACCCAGGTGGACCTGAACGAAGAAGAAACGATTTTGATCATCAGGCGTCTACACAAGGTGCTGAGACCCTTTTTACTGAGGAGGCTGAAGAAAGAGGTTGAGTCTCAGCTTCCGGAAAAGGTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGAATCCTTTGCTGAACACCTGGGCTATTCGAATGGGGTCATCAATGGGGCTGAGCTGTATCGGGCCTCGGGAAAGTTTGAGCTGCTTGATCGTATTCTGCCCAAATTGAGAGCGACTAACCACCGCGTGCTGCTTTTCTGCCAGATGACGTCACTCATGACCATTATGGAGGATTACTTTGCTTTTCGGAACTTCCTGTACCTGCGCCTTGACGGCACCACCAAGTCTGAAGATCGTGCTGCTTTGCTAAAGAAATTCAATGAACCTGGGTCCCAGTATTTCATTTTCTTGCTGAGCACAAGAGCAGGGGGCCTGGGCTTAAATCTTCAGGCGGCAGACACGGTGGTCATATTTGACAGCGACTGGAATCCTCACCAGGATCTGCAGGCCCAAGACCGAGCTCACCGCATTGGCCAACAAAACGAGGTCCGGGTGCTGAGGCTTTGCACCGTCAACAGTGTGGAGGAAAAGATTCTCGCGGCTGCCAAGTACAAGCTGAACGTGGATCAGAAGGTTATCCAAGCAGGCATGTTTGACCAGAAGTCATCCAGCCACGAGCGGAGGGCCTTCCTGCAGGCCATTCTGGAGCACGAGGAGGAGAATGAGGAAGAAGATGAGGTACCAGACGACGAGACCCTGAACCAGATGATTGCTCGCCGGGAGGAAGAATTTGATCTTTTTATGCGCATGGACATGGACCGGCGGAGGGAGGATGCCCGGAACCCGAAGCGCAAACCCCGCTTGATGGAGGAAGATGAGCTGCCCTCCTGGATTATCAAGGATGACGCCGAAGTGGAAAGGCTCACCTGTGAAGAAGAGGAGGAGAAGATATTTGGGAGGGGCTCTCGCCAGCGCCGGGATGTGGACTACAGTGATGCCCTCACCGAGAAGCAATGGCTCAGGATTCGGTGGAAGTACATGATCGTGGACGAAGGCCACCGGATGAAGAATCACCACTGCAAGCTAACCCAGGTGGACCTGAACGAAGAAGAAACGATTTTGATCATCAGGCGTCTACACAAGGTGCTGAGACCCTTTTTACTGAGGAGGCTGAAGAAAGAGGTTGAGTCTCAGCTTCCGGAAAAGGTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGAATCCTTTGCTGAACACCTGGGCTATTCGAATGGGGTCATCAATGGGGCTGAGCTGTATCGGGCCTCGGGAAAGTTTGAGCTGCTTGATCGTATTCTGCCCAAATTGAGAGCGACTAACCACCGCGTGCTGCTTTTCTGCCAGATGACGTCACTCATGACCATTATGGAGGATTACTTTGCTTTTCGGAACTTCCTGTACCTGCGCCTTGACGGCACCACCAAGTCTGAAGATCGTGCTGCTTTGCTAAAGAAATTCAATGAACCTGGGTCCCAGTATTTCATTTTCTTGCTGAGCACAAGAGCAGGGGGCCTGGGCTTAAATCTTCAGGCGGCAGACACGGTGGTCATATTTGACAGCGACTGGAATCCTCACCAGGATCTGCAGGCCCAAGACCGAGCTCACCGCATTGGCCAACAAAACGAGGTCCGGGTGCTGAGGCTTTGCACCGTCAACAGTGTGGAGGAAAAGATTCTCGCGGCTGCCAAGTACAAGCTGAACGTGGATCAGAAGGTTATCCAAGCAGGCATGTTTGACCAGAAGTCATCCAGCCACGAGCGGAGGGCCTTCCTGCAGGCCATTCTGGAGCACGAGGAGGAGAATGAGGAAGAAGATGAGGTACCAGACGACGAGACCCTGAACCAGATGATTGCTCGCCGGGAGGAAGAATTTGATCTTTTTATGCGCATGGACATGGACCGGCGGAGGGAGGATGCCCGGAACCCGAAGCGCAAACCCCGCTTGATGGAGGAAGATGAGCTGCCCTCCTGGATTATCAAGGATGACGCCGAAGTGGAAAGGCTCACCTGTGAAGAAGAGGAGGAGAAGATATTTGGGAGGGGCTCTCGCCAGCGCCGGGATGTGGACTACAGTGATGCCCTCACCGAGAAGCAATGGCTCAGG
Peptide sequence:
MIVDEGHRMKNHHCKLTQVDLNEEETILIIRRLHKVLRPFLLRRLKKEVESQLPEKVEYVIKCDMSALQKILYRHMQAKGILLTDGSEKDKKGKGGAKTLMNTIMQLRKICNHPYMFQHIEESFAEHLGYSNGVINGAELYRASGKFELLDRILPKLRATNHRVLLFCQMTSLMTIMEDYFAFRNFLYLRLDGTTKSEDRAALLKKFNEPGSQYFIFLLSTRAGGLGLNLQAADTVVIFDSDWNPHQDLQAQDRAHRIGQQNEVRVLRLCTVNSVEEKILAAAKYKLNVDQKVIQAGMFDQKSSSHERRAFLQAILEHEEENEEEDEVPDDETLNQMIARREEEFDLFMRMDMDRRREDARNPKRKPRLMEEDELPSWIIKDDAEVERLTCEEEEEKIFGRGSRQRRDVDYSDALTEKQWLRIRWKYMIVDEGHRMKNHHCKLTQVDLNEEETILIIRRLHKVLRPFLLRRLKKEVESQLPEKVEYVIKCDMSALQKILYRHMQAKGILLTDGSEKDKKGKGGAKTLMNTIMQLRKICNHPYMFQHIEESFAEHLGYSNGVINGAELYRASGKFELLDRILPKLRATNHRVLLFCQMTSLMTIMEDYFAFRNFLYLRLDGTTKSEDRAALLKKFNEPGSQYFIFLLSTRAGGLGLNLQAADTVVIFDSDWNPHQDLQAQDRAHRIGQQNEVRVLRLCTVNSVEEKILAAAKYKLNVDQKVIQAGMFDQKSSSHERRAFLQAILEHEEENEEEDEVPDDETLNQMIARREEEFDLFMRMDMDRRREDARNPKRKPRLMEEDELPSWIIKDDAEVERLTCEEEEEKIFGRGSRQRRDVDYSDALTEKQWLR
IRESfinder result
IRESfinder score
0.270355801
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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