top of page
mmu_circScly_400
Basic information of circular RNA
PanCircBase ID:
mmu_circScly_400
mm39_Chr. Position ID:
chr1|91236035|91237625|+
Gene name:
Scly
Transcript:
ENSMUST00000027532.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,6,7
Exon/intron offsets:
0,337,1483
Genomic length:
1590
Exon/intron sizes in nt:
12,81,65,107
Flanking exon/introns:
chr1:91233176-91236035|chr1:91237625-91243210
Splice length:
400
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGGTCACTTTTGTCCCAGTGTCGAAGGTGAATGGGCAGGCAGAGGTCGAGGATATCCTGGCGGCTGTCCGTCCCACCACATGCCTTGTGACCATCATGCTGGCCAATAATGAGACCGGCGTCATCATGCCTGTCTCCGAGATCAGTCGGCGAATTAAAGCCCTGAACCAGATCCGGGCTGCCTCGGGGCTGCCCCGAGTCCTGGTGCACACAGACGCTGCTCAGGCACTGGGGAAGAGGCGAGTGGATGTCGAAGACCTGGGCGTGGACTTCCTGACCATCGTGGGACATAAGTTCTACGGCCCCAGGATCGGTGCTCTGTATGTACGAGGGGTCGGTAAACTTACCCCCCTGTACCCCATGCTGTTTGGAGGTGGACAAGAGTGGAATTTCAGGCCAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTGTACCCCATGCTGTTT
59.96
AGCATGATGGTCACAAGGCA
59.96
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCATGCTGTTTGGAGGTGGA
60.25
AGCATGATGGTCACAAGGCA
59.96
143
PCR template sequence:
GCCCCAGGATCGGTGCTCTGTATGTACGAGGGGTCGGTAAACTTACCCCCCTGTACCCCATGCTGTTTGGAGGTGGACAAGAGTGGAATTTCAGGCCAGGAGGTCACTTTTGTCCCAGTGTCGAAGGTGAATGGGCAGGCAGAGGTCGAGGATATCCTGGCGGCTGTCCGTCCCACCACATGCCTTGTGACCATCATGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-184-3p(1), mmu-miR-382-3p(1), mmu-miR-466b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTTCAGGCCAGGAGGTCACTTTTGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCLY_400_ORF_1
1.1794
0.39141929
0.878038214
477
ORF sequence:
ATGTACGAGGGGTCGGTAAACTTACCCCCCTGTACCCCATGCTGTTTGGAGGTGGACAAGAGTGGAATTTCAGGCCAGGAGGTCACTTTTGTCCCAGTGTCGAAGGTGAATGGGCAGGCAGAGGTCGAGGATATCCTGGCGGCTGTCCGTCCCACCACATGCCTTGTGACCATCATGCTGGCCAATAATGAGACCGGCGTCATCATGCCTGTCTCCGAGATCAGTCGGCGAATTAAAGCCCTGAACCAGATCCGGGCTGCCTCGGGGCTGCCCCGAGTCCTGGTGCACACAGACGCTGCTCAGGCACTGGGGAAGAGGCGAGTGGATGTCGAAGACCTGGGCGTGGACTTCCTGACCATCGTGGGACATAAGTTCTACGGCCCCAGGATCGGTGCTCTGTATGTACGAGGGGTCGGTAAACTTACCCCCCTGTACCCCATGCTGTTTGGAGGTGGACAAGAGTGGAATTTCAGGCCA
Peptide sequence:
MYEGSVNLPPCTPCCLEVDKSGISGQEVTFVPVSKVNGQAEVEDILAAVRPTTCLVTIMLANNETGVIMPVSEISRRIKALNQIRAASGLPRVLVHTDAAQALGKRRVDVEDLGVDFLTIVGHKFYGPRIGALYVRGVGKLTPLYPMLFGGGQEWNFRP
IRESfinder result
IRESfinder score
0.214790518
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page