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mmu_circSmarca2_1610
Basic information of circular RNA
PanCircBase ID:
mmu_circSmarca2_1610
mm39_Chr. Position ID:
chr19|26656473|26729441|+
Gene name:
Smarca2
Transcript:
ENSMUST00000176769.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
17,18,19,20,21,22,23,24,25,26,27,28
Exon/intron offsets:
0,2797,4735,12271,13107,17102,19272,26994,31384,37041,41655,72750
Genomic length:
72968
Exon/intron sizes in nt:
1,11,69,11,41,08,87,47,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr19:26655782-26656473|chr19:26729441-26748337
Splice length:
1610
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_358557
Human Ortholog IDs:
Mature spliced Sequence:
GGTACCCCTGCCATGCGACGCTCCCTCGTTCCCCAGCTACGGAGTGGCAAATTCAATGTCCTCCTGACTACTTACGAGTACATTATAAAAGACAAGCACATTCTTGCAAAGATTCGGTGGAAGTACATGATCGTGGACGAAGGCCACCGGATGAAGAATCACCACTGCAAGCTAACCCAGGTGGACCTGAACGAAGAAGAAACGATTTTGATCATCAGGCGTCTACACAAGGTGCTGAGACCCTTTTTACTGAGGAGGCTGAAGAAAGAGGTTGAGTCTCAGCTTCCGGAAAAGGTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGAATCCTTTGCTGAACACCTGGGCTATTCGAATGGGGTCATCAATGGGGCTGAGCTGTATCGGGCCTCGGGAAAGTTTGAGCTGCTTGATCGTATTCTGCCCAAATTGAGAGCGACTAACCACCGCGTGCTGCTTTTCTGCCAGATGACGTCACTCATGACCATTATGGAGGATTACTTTGCTTTTCGGAACTTCCTGTACCTGCGCCTTGACGGCACCACCAAGTCTGAAGATCGTGCTGCTTTGCTAAAGAAATTCAATGAACCTGGGTCCCAGTATTTCATTTTCTTGCTGAGCACAAGAGCAGGGGGCCTGGGCTTAAATCTTCAGGCGGCAGACACGGTGGTCATATTTGACAGCGACTGGAATCCTCACCAGGATCTGCAGGCCCAAGACCGAGCTCACCGCATTGGCCAACAAAACGAGGTCCGGGTGCTGAGGCTTTGCACCGTCAACAGTGTGGAGGAAAAGATTCTCGCGGCTGCCAAGTACAAGCTGAACGTGGATCAGAAGGTTATCCAAGCAGGCATGTTTGACCAGAAGTCATCCAGCCACGAGCGGAGGGCCTTCCTGCAGGCCATTCTGGAGCACGAGGAGGAGAATGAGGAAGAAGATGAGGTACCAGACGACGAGACCCTGAACCAGATGATTGCTCGCCGGGAGGAAGAATTTGATCTTTTTATGCGCATGGACATGGACCGGCGGAGGGAGGATGCCCGGAACCCGAAGCGCAAACCCCGCTTGATGGAGGAAGATGAGCTGCCCTCCTGGATTATCAAGGATGACGCCGAAGTGGAAAGGCTCACCTGTGAAGAAGAGGAGGAGAAGATATTTGGGAGGGGCTCTCGCCAGCGCCGGGATGTGGACTACAGTGATGCCCTCACCGAGAAGCAATGGCTCAGGGCCATCGAAGACGGCAATTTGGAAGAAATGGAAGAGGAGGTACGGCTTAAGAAGAGAAAAAGACGAAGAAATGTGGATAAAGACCCCGTGAAGGAAGATGTGGAAAAAGCGAAGAAAAGAAGAGGCCGCCCTCCGGCTGAGAAGTTGTCACCAAATCCCCCAAAACTAACGAAGCAGATGAACGCCATCATTGATACTGTGATAAACTACAAAGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCCGGCTGAGAAGTTGTCA
59.68
ATTTGCCACTCCGTAGCTGG
60.39
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCCGGCTGAGAAGTTGTC
60.39
ATTTGCCACTCCGTAGCTGG
60.39
141
PCR template sequence:
GAAGAGGCCGCCCTCCGGCTGAGAAGTTGTCACCAAATCCCCCAAAACTAACGAAGCAGATGAACGCCATCATTGATACTGTGATAAACTACAAAGACAGGGTACCCCTGCCATGCGACGCTCCCTCGTTCCCCAGCTACGGAGTGGCAAATTCAATGTCCTCCTGACTACTTACGAGTACATTATAAAAGACAAGCACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
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-125b-5p(1), mmu-miR-494-3p(1), mmu-miR-218-5p(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
ACTACAAAGACAGGGTACCCCTGCCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMARCA2_1610_ORF_1
1.2934
0.428772233
0.999980696
1665
ORF sequence:
ATGCGACGCTCCCTCGTTCCCCAGCTACGGAGTGGCAAATTCAATGTCCTCCTGACTACTTACGAGTACATTATAAAAGACAAGCACATTCTTGCAAAGATTCGGTGGAAGTACATGATCGTGGACGAAGGCCACCGGATGAAGAATCACCACTGCAAGCTAACCCAGGTGGACCTGAACGAAGAAGAAACGATTTTGATCATCAGGCGTCTACACAAGGTGCTGAGACCCTTTTTACTGAGGAGGCTGAAGAAAGAGGTTGAGTCTCAGCTTCCGGAAAAGGTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGAATCCTTTGCTGAACACCTGGGCTATTCGAATGGGGTCATCAATGGGGCTGAGCTGTATCGGGCCTCGGGAAAGTTTGAGCTGCTTGATCGTATTCTGCCCAAATTGAGAGCGACTAACCACCGCGTGCTGCTTTTCTGCCAGATGACGTCACTCATGACCATTATGGAGGATTACTTTGCTTTTCGGAACTTCCTGTACCTGCGCCTTGACGGCACCACCAAGTCTGAAGATCGTGCTGCTTTGCTAAAGAAATTCAATGAACCTGGGTCCCAGTATTTCATTTTCTTGCTGAGCACAAGAGCAGGGGGCCTGGGCTTAAATCTTCAGGCGGCAGACACGGTGGTCATATTTGACAGCGACTGGAATCCTCACCAGGATCTGCAGGCCCAAGACCGAGCTCACCGCATTGGCCAACAAAACGAGGTCCGGGTGCTGAGGCTTTGCACCGTCAACAGTGTGGAGGAAAAGATTCTCGCGGCTGCCAAGTACAAGCTGAACGTGGATCAGAAGGTTATCCAAGCAGGCATGTTTGACCAGAAGTCATCCAGCCACGAGCGGAGGGCCTTCCTGCAGGCCATTCTGGAGCACGAGGAGGAGAATGAGGAAGAAGATGAGGTACCAGACGACGAGACCCTGAACCAGATGATTGCTCGCCGGGAGGAAGAATTTGATCTTTTTATGCGCATGGACATGGACCGGCGGAGGGAGGATGCCCGGAACCCGAAGCGCAAACCCCGCTTGATGGAGGAAGATGAGCTGCCCTCCTGGATTATCAAGGATGACGCCGAAGTGGAAAGGCTCACCTGTGAAGAAGAGGAGGAGAAGATATTTGGGAGGGGCTCTCGCCAGCGCCGGGATGTGGACTACAGTGATGCCCTCACCGAGAAGCAATGGCTCAGGGCCATCGAAGACGGCAATTTGGAAGAAATGGAAGAGGAGGTACGGCTTAAGAAGAGAAAAAGACGAAGAAATGTGGATAAAGACCCCGTGAAGGAAGATGTGGAAAAAGCGAAGAAAAGAAGAGGCCGCCCTCCGGCTGAGAAGTTGTCACCAAATCCCCCAAAACTAACGAAGCAGATGAACGCCATCATTGATACTGTGATAAACTACAAAGACAGGGTACCCCTGCCATGCGACGCTCCCTCGTTCCCCAGCTACGGAGTGGCAAATTCAATGTCCTCCTGA
Peptide sequence:
MRRSLVPQLRSGKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHHCKLTQVDLNEEETILIIRRLHKVLRPFLLRRLKKEVESQLPEKVEYVIKCDMSALQKILYRHMQAKGILLTDGSEKDKKGKGGAKTLMNTIMQLRKICNHPYMFQHIEESFAEHLGYSNGVINGAELYRASGKFELLDRILPKLRATNHRVLLFCQMTSLMTIMEDYFAFRNFLYLRLDGTTKSEDRAALLKKFNEPGSQYFIFLLSTRAGGLGLNLQAADTVVIFDSDWNPHQDLQAQDRAHRIGQQNEVRVLRLCTVNSVEEKILAAAKYKLNVDQKVIQAGMFDQKSSSHERRAFLQAILEHEEENEEEDEVPDDETLNQMIARREEEFDLFMRMDMDRRREDARNPKRKPRLMEEDELPSWIIKDDAEVERLTCEEEEEKIFGRGSRQRRDVDYSDALTEKQWLRAIEDGNLEEMEEEVRLKKRKRRRNVDKDPVKEDVEKAKKRRGRPPAEKLSPNPPKLTKQMNAIIDTVINYKDRVPLPCDAPSFPSYGVANSMSS
IRESfinder result
IRESfinder score
0.253110502
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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