top of page
mmu_circSmurf2_544_1
Basic information of circular RNA
PanCircBase ID:
mmu_circSmurf2_544_1
mm39_Chr. Position ID:
chr11|106730013|106740658|-
Gene name:
Smurf2
Transcript:
ENSMUST00000103067.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,10,9,8
Exon/intron offsets:
0,2412,6795,10560
Genomic length:
10645
Exon/intron sizes in nt:
104,196,159,85
Flanking exon/introns:
chr11:106727010-106730013|chr11:106740658-106743272
Splice length:
544
Other database IDs:
CIRCpedia: MMU_CIRCpedia_38392
circBase: hsa_circ_0107459, circAtlas: hsa-SMURF2_0007, CIRCpedia: HSA_CIRCpedia_156124
Human Ortholog IDs:
Mature spliced Sequence:
AACAAAGGACAACGCAGCAGGGTCAGGTATATTTCTTACATACTCAGACTGGTGTGAGCACATGGCATGATCCACGAGTGCCTAGGGATCTTAGCAACATCAATTGTGAAGAGCTCGGTCCTTTGCCTCCTGGATGGGAGATCCGCAATACCGCAACAGGAAGAGTTTATTTCGTTGACCATAACAACAGAACAACACAATTTACAGATCCCCGGCTCTCTGCTAACTTGCATTTAGTTTTAAATCGTCAGAACCAGTTGAAAGACCAACAGCAACAGCAAGTGGTGCCATTGTGTCCCGATGACACTGAGTGTCTGACAGTGCCAAGATACAAGCGAGATTTGGTTCAAAAACTAAAAATCTTGCGGCAAGAACTTTCCCAACAGCAGCCTCAAGCTGGCCACTGCCGTATTGAGGTGTCTAGGGAAGAGATTTTTGAGGAATCATATAGACAGGTCATGAAAATGAGGCCAAAAGATCTATGGAAGCGATTAATGATAAAATTTCGTGGAGAAGAAGGTCTTGACTATGGAGGAGTTGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGGTCATGAAAATGAGGCCA
60.23
CCATGTGCTCACACCAGTCT
59.96
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCAAAAGATCTATGGAAGCG
59.71
CCATGTGCTCACACCAGTCT
59.96
141
PCR template sequence:
CATATAGACAGGTCATGAAAATGAGGCCAAAAGATCTATGGAAGCGATTAATGATAAAATTTCGTGGAGAAGAAGGTCTTGACTATGGAGGAGTTGCCAGAACAAAGGACAACGCAGCAGGGTCAGGTATATTTCTTACATACTCAGACTGGTGTGAGCACATGGCATGATCCACGAGTGCCTAGGGATCTTAGCAACAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-181b-5p(1), mmu-miR-434-3p(1), mmu-miR-96-5p(1), mmu-miR-183-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGGAGTTGCCAGAACAAAGGACAAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMURF2_544_1_ORF_1
1.0005
0.086093833
0.725267712
558
ORF sequence:
ATGGAGGAGTTGCCAGAACAAAGGACAACGCAGCAGGGTCAGGTATATTTCTTACATACTCAGACTGGTGTGAGCACATGGCATGATCCACGAGTGCCTAGGGATCTTAGCAACATCAATTGTGAAGAGCTCGGTCCTTTGCCTCCTGGATGGGAGATCCGCAATACCGCAACAGGAAGAGTTTATTTCGTTGACCATAACAACAGAACAACACAATTTACAGATCCCCGGCTCTCTGCTAACTTGCATTTAGTTTTAAATCGTCAGAACCAGTTGAAAGACCAACAGCAACAGCAAGTGGTGCCATTGTGTCCCGATGACACTGAGTGTCTGACAGTGCCAAGATACAAGCGAGATTTGGTTCAAAAACTAAAAATCTTGCGGCAAGAACTTTCCCAACAGCAGCCTCAAGCTGGCCACTGCCGTATTGAGGTGTCTAGGGAAGAGATTTTTGAGGAATCATATAGACAGGTCATGAAAATGAGGCCAAAAGATCTATGGAAGCGATTAATGATAAAATTTCGTGGAGAAGAAGGTCTTGACTATGGAGGAGTTGCC
Peptide sequence:
MEELPEQRTTQQGQVYFLHTQTGVSTWHDPRVPRDLSNINCEELGPLPPGWEIRNTATGRVYFVDHNNRTTQFTDPRLSANLHLVLNRQNQLKDQQQQQVVPLCPDDTECLTVPRYKRDLVQKLKILRQELSQQQPQAGHCRIEVSREEIFEESYRQVMKMRPKDLWKRLMIKFRGEEGLDYGGVA
IRESfinder result
IRESfinder score
0.549970683
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page