top of page
mmu_circArid5b_700
Basic information of circular RNA
PanCircBase ID:
mmu_circArid5b_700
mm39_Chr. Position ID:
chr10|67954080|68022086|-
Gene name:
Arid5b
Transcript:
ENSMUST00000219238.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,8448,10538,16743,67775
Genomic length:
68006
Exon/intron sizes in nt:
98,53,20,51,13,231
Flanking exon/introns:
chr10:67937923-67954080|chr10:68022086-68078833
Splice length:
700
Other database IDs:
circAtlas: mmu-Arid5b_0005
circAtlas: hsa-ARID5B_0008, CIRCpedia: HSA_CIRCpedia_129002
Human Ortholog IDs:
Mature spliced Sequence:
GGGAAGATGAGGAAGAAACCAACGTGATTGTGCTCAGTTACCCCCAGTACTGTCGGTACCGGTCCATGCTTAAACGGATCCAGGATAAGCCATCGTCCATCCTCACGGACCAGTTCGCATTAGCCCTGGGGGGCATCGCAGTGGTCAGCAGAAACCCCCAGATCCTGTACTGCCGGGATACCTTTGATCACCCCACTCTGATAGAAAACGAGAGTGTGTGTGATGAGTTCGCGCCAAATCTTAAAGGCAGACCACGCAAAAAGAAAACATGTCCCCAGAGAAGAGATTCCTTCAGTGGCTCAAAGGACCCCAACAATAACTGTGACGGTAAAGTTATCAGCAAGGTGAAAGGAGAGGCCAGGTCAGCCTTGACCAAGCCGAAGAATAACCACAATAACTGTAAAAAAACCTCAAATGAAGAAAAGCCAAAGCTGTCTATTGGCGAAGAATGCAGGGCAGATGAACAAGCCTTCTTAGTGGCCCTGTATAAATACATGAAAGAAAGAAAAACGCCCATCGAGCGAATTCCCTACTTGGGTTTCAAACAGATTAACCTTTGGACTATGTTTCAAGCTGCTCAAAAACTGGGAGGATATGAAACAATAACAGCCCGCCGTCAGTGGAAACATATTTATGACGAGTTAGGTGGTAATCCTGGGAGCACCAGTGCGGCCACCTGTACTCGCAGACACTACGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGTAATCCTGGGAGCACC
60.11
TGGACGATGGCTTATCCTGG
59.24
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGGTAATCCTGGGAGCAC
60.11
TGGACGATGGCTTATCCTGG
59.24
155
PCR template sequence:
CAATAACAGCCCGCCGTCAGTGGAAACATATTTATGACGAGTTAGGTGGTAATCCTGGGAGCACCAGTGCGGCCACCTGTACTCGCAGACACTACGAAAGGGGAAGATGAGGAAGAAACCAACGTGATTGTGCTCAGTTACCCCCAGTACTGTCGGTACCGGTCCATGCTTAAACGGATCCAGGATAAGCCATCGTCCAT
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-101a-3p(1), mmu-miR-127-3p(1), mmu-miR-377-3p(1), mmu-miR-129-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GACACTACGAAAGGGGAAGATGAGGA
siRNA sets
ATCTTCCCCTTTCGTAGTG, CATCTTCCCCTTTCGTAGT, CTTCCCCTTTCGTAGTGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARID5B_700_ORF_1
0.6267
0.212736189
0.804377968
645
ORF sequence:
ATGCTTAAACGGATCCAGGATAAGCCATCGTCCATCCTCACGGACCAGTTCGCATTAGCCCTGGGGGGCATCGCAGTGGTCAGCAGAAACCCCCAGATCCTGTACTGCCGGGATACCTTTGATCACCCCACTCTGATAGAAAACGAGAGTGTGTGTGATGAGTTCGCGCCAAATCTTAAAGGCAGACCACGCAAAAAGAAAACATGTCCCCAGAGAAGAGATTCCTTCAGTGGCTCAAAGGACCCCAACAATAACTGTGACGGTAAAGTTATCAGCAAGGTGAAAGGAGAGGCCAGGTCAGCCTTGACCAAGCCGAAGAATAACCACAATAACTGTAAAAAAACCTCAAATGAAGAAAAGCCAAAGCTGTCTATTGGCGAAGAATGCAGGGCAGATGAACAAGCCTTCTTAGTGGCCCTGTATAAATACATGAAAGAAAGAAAAACGCCCATCGAGCGAATTCCCTACTTGGGTTTCAAACAGATTAACCTTTGGACTATGTTTCAAGCTGCTCAAAAACTGGGAGGATATGAAACAATAACAGCCCGCCGTCAGTGGAAACATATTTATGACGAGTTAGGTGGTAATCCTGGGAGCACCAGTGCGGCCACCTGTACTCGCAGACACTACGAAAGGGGAAGATGA
Peptide sequence:
MLKRIQDKPSSILTDQFALALGGIAVVSRNPQILYCRDTFDHPTLIENESVCDEFAPNLKGRPRKKKTCPQRRDSFSGSKDPNNNCDGKVISKVKGEARSALTKPKNNHNNCKKTSNEEKPKLSIGEECRADEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERGR
IRESfinder result
IRESfinder score
0.474581988
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page