top of page
mmu_ciSmarca2_1836
Basic information of circular RNA
PanCircBase ID:
mmu_ciSmarca2_1836
mm39_Chr. Position ID:
chr19|26624547|26626383|+
Gene name:
Smarca2
Transcript:
ENSMUST00000176769.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
6
Exon/intron offsets:
0
Genomic length:
1836
Exon/intron sizes in nt:
1836
Flanking exon/introns:
chr19:26624547-26626383
Splice length:
1836
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAATACCTTTTTCCCCCGTGATGTAGGAAATCAATGTGATTGTTGCTAAGGTGTGACCTGGGAGCTTCCTCAAGTCTACCTGATCTTGTTATAAAGCTTAGTGAGATAGTGCGTCTTCAGACTGACAGCTCACGGCTGAGAGTGAGGAGTATGAACCGCTCGTTATTCTTTTCCCCTTCTGTATGCATTGAAATGTACACAATCAGTTCTCGAACTCTGGTACCCTGGAGGAAAACCATGACAACGGATTGTGAAGATCTGTGTCTCATCTTCGTGAATCCAAGGAAAACCACAGAGGTGGTAGATTGTGTTCCTGGTAAACCCAAATACACAAAGGTAGCCATGACTCCAGAAACAGAAAATATGGTAGTCAGTCTTGCTCCTAATCACTAGCCCAGTTTTATAGAAACAAACAAAGAAAAAAAAAAAACCCCAATGTCTTTACCTTAATTATTCAACAAAACTTAACTTGGGGTCACTGAGCCACATCAGAGTCACAGGTTGACTGATAAGGAGTCACTGTCTCCTAGAACTATTACTATTGAGATCTGGCATAGTGATCTATTTTCTGATTTCTAAATTAGTAGGTGTGCAATGGAATGAAGTAGAGCAAATTTTCCCTTGGCTGAGTTCTGTCAAAGTGTGCAGGCCCCTTGTCCACAGATTGCCTGTCTGAGTCCAGGGGGACAAGGAGCCCCTCTTCTGTCGGATGGGTTGTCCTAAAGTATGGGACATACAGAATGAACTGTTATTTTGTAAGCACAGTGTGGAGGCATTGAATTCTGTCTGCTGGAGGATCTGACTGAAATCACAAAGTCACCTCTTTGGCTGACCATCTCTGAACTGGAGTTCACATTTGAATTCCTGGATGTCATATGATGGAGGGGGGCATCTGTTGTCTAGGGGCTACCTGGCTAGGGTTTTGAGAGAGCAGAAATCAGGTTTCATTTAAAAGGGAGGAGGAAAAGAAAAAAGCCTCCAGGTTCCATTGCATCTTAATTAGAGGAAAGTTTTTTATAGAAGCAAATAAAATTTTGGACACAGGTTTAGGAAATGAGACATGAGTCTCTCTCCTCAAATCCTGCTGGTCCTTGTCTTTTGTTTGATATTATCTATTATCTACAAAGTTTTCTGGAAAATCTGTTATCTACAAAGTTTCCTGGATAGATGTGACTGATACTAATTTCAGGTTCAATGTAAGGTAGACCCCCAAGTGCCCACTGCCTACCAGCATATAATATGTAATACTGTCACATTGTTATATGACTATAATCTAAAACAAGTCCACAGCACAATATAAAATTTCAATACTAAAGAATATCACTTTTGGAGAGGAAGAAAACCCAGACGGGTATTTTTATGATTTCTTTGAAGCTGTGAATTTACATTGTTGGAGTTACTGTTGTTACTTGGAACATGAATGGACAGCAACTCTCTTGTTCTTCTTGTAGATCAGCAACAGAATGATAATATGACAGTTAAAAAAAATTAAAAGGTTTATTGACTAAGCAATGCCATTACAATAATTAAACAGAGTGAATAACTTTATTTCAAACCTAGCATAGCATCCTCTTATCTTTTTTTACTGTTACAATTGTATAATTGTTTTTTATGTGAATTATGTGAAAGAAGATGTATACAGTCCTTGAAATTACCATGTAAAATGGCTCCAATTTCCATTTCTTGCTTTTTGTAATTGACCAACTGCAATTGGATTGAGAATCTTGCGTCAGAATCCTCTTTCTGTTCCATTGAGTTGAAACTCCAGGAGCTCGGGGCTCAGGGTCTGGCATGTGTTTGGGGGGATTCTCTAACCACTATTCTCTTCCTGATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAACTCCAGGAGCTCGG
59.68
CTTGAGGAAGCTCCCAGGTC
59.75
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAACTCCAGGAGCTCGG
59.68
GACTTGAGGAAGCTCCCAGG
59.75
156
PCR template sequence:
TCCTCTTTCTGTTCCATTGAGTTGAAACTCCAGGAGCTCGGGGCTCAGGGTCTGGCATGTGTTTGGGGGGATTCTCTAACCACTATTCTCTTCCTGATAGGTAATACCTTTTTCCCCCGTGATGTAGGAAATCAATGTGATTGTTGCTAAGGTGTGACCTGGGAGCTTCCTCAAGTCTACCTGATCTTGTTATAAAGCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-32-5p(1), mmu-miR-146a-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-125b-5p(1), mmu-miR-185-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-541-5p(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-5101(1), mmu-miR-490-3p(1), mmu-miR-1904(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCTTCCTGATAGGTAATACCTTTTT
siRNA sets
TATTACCTATCAGGAAGAG, GTATTACCTATCAGGAAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.831227062
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page