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mmu_circErn1_424
Basic information of circular RNA
PanCircBase ID:
mmu_circErn1_424
mm39_Chr. Position ID:
chr11|106317638|106349854|-
Gene name:
Ern1
Transcript:
ENSMUST00000001059.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,2201,8102,10277,32095
Genomic length:
32216
Exon/intron sizes in nt:
1,23,73,73,34,121
Flanking exon/introns:
chr11:106314314-106317638|chr11:106349854-106378442
Splice length:
424
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_79503
Human Ortholog IDs:
Mature spliced Sequence:
AGTTTTGGAAGAACCAGCACAGTTACACTGCCTGAGACCTTGTTGTTTGTCTCGACCCTGGATGGAAGCTTGCATGCTGTTAGCAAGAGGACGGGCTCCATCAAGTGGACTTTAAAAGAAGATCCAGTCCTGCAGGTCCCAACACACGTGGAAGAGCCGGCTTTCCTCCCAGATCCCAATGATGGCAGTCTGTACACACTTGGAGGCAAGAACAACGAAGGCCTGACGAAACTTCCCTTTACCATCCCAGAATTGGTTCAGGCCTCCCCATGCCGAAGTTCAGATGGAATCCTCTACATGGGTAAAAAGCAAGATATTTGGTATGTTATCGACCTCCTGACTGGCGAGAAGCAGCAGACTTTGTCATCGGCCTTTGCTGATAGTCTCTGCCCATCAACTTCCCTTCTATATCTTGGACGGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCAGACTTTGTCATCGGC
59.55
GCATGCAAGCTTCCATCCAG
59.9
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCAGACTTTGTCATCGGC
59.55
CAGCATGCAAGCTTCCATCC
59.9
152
PCR template sequence:
GTTATCGACCTCCTGACTGGCGAGAAGCAGCAGACTTTGTCATCGGCCTTTGCTGATAGTCTCTGCCCATCAACTTCCCTTCTATATCTTGGACGGACAGAGTTTTGGAAGAACCAGCACAGTTACACTGCCTGAGACCTTGTTGTTTGTCTCGACCCTGGATGGAAGCTTGCATGCTGTTAGCAAGAGGACGGGCTCCA
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-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-34b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTGGACGGACAGAGTTTTGGAAGAA
siRNA sets
TTCTTCCAAAACTCTGTCC, TCTTCCAAAACTCTGTCCG, TTCCAAAACTCTGTCCGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCERN1_424_ORF_1
0.6244
0.073635151
0.067125988
162
ORF sequence:
ATGGGTAAAAAGCAAGATATTTGGTATGTTATCGACCTCCTGACTGGCGAGAAGCAGCAGACTTTGTCATCGGCCTTTGCTGATAGTCTCTGCCCATCAACTTCCCTTCTATATCTTGGACGGACAGAGTTTTGGAAGAACCAGCACAGTTACACTGCCTGA
Peptide sequence:
MGKKQDIWYVIDLLTGEKQQTLSSAFADSLCPSTSLLYLGRTEFWKNQHSYTA
IRESfinder result
IRESfinder score
0.594664122
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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