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mmu_circEcd_277
Basic information of circular RNA
PanCircBase ID:
mmu_circEcd_277
mm39_Chr. Position ID:
chr14|20374440|20377359|-
Gene name:
Ecd
Transcript:
ENSMUST00000022344.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
13,12
Exon/intron offsets:
0,2851
Genomic length:
2919
Exon/intron sizes in nt:
209,68
Flanking exon/introns:
chr14:20371019-20374440|chr14:20377359-20378670
Splice length:
277
Other database IDs:
circAtlas: mmu-Ecd_0013
circBase: hsa_circ_0018779, circAtlas: hsa-ECD_0022, CIRCpedia: HSA_CIRCpedia_2331
Human Ortholog IDs:
Mature spliced Sequence:
AGACCCTTCGGAAGCTCCAATCACTTTTGATGCAGATTCTTTTCTGAATTATTTTGATAAGATTTTAGGAGCAAAGCCTCAGGAGTCAGACTCTGAGGATGACCCGGGTGAGGAGGACGTGGAAGGTGTAGACAGTGATGATGACGTGGGCTTTGAGGCTCAGGAGTCTGAGTCTCTGAAAGGAGCCCTTGGCAGCCTCAAGTCCTACATGGCCCGGATGGACCAGGAACTGGCACACACCAGCATGGGCAGAAGCTTCACCACGCGGGAGCGATTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAAGTCCTACATGGCCCG
60.18
TGACTCCTGAGGCTTTGCTC
59.68
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAAGTCCTACATGGCCCG
60.18
TCTGACTCCTGAGGCTTTGC
59.68
171
PCR template sequence:
GAAAGGAGCCCTTGGCAGCCTCAAGTCCTACATGGCCCGGATGGACCAGGAACTGGCACACACCAGCATGGGCAGAAGCTTCACCACGCGGGAGCGATTGAGACCCTTCGGAAGCTCCAATCACTTTTGATGCAGATTCTTTTCTGAATTATTTTGATAAGATTTTAGGAGCAAAGCCTCAGGAGTCAGACTCTGAGGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-217-5p(1), mmu-miR-138-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCGGGAGCGATTGAGACCCTTCGGAA
siRNA sets
TTCCGAAGGGTCTCAATCG,TCCGAAGGGTCTCAATCGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCECD_277_ORF_1
0.9774
0.243907517
0.150995763
99
ORF sequence:
ATGGCCCGGATGGACCAGGAACTGGCACACACCAGCATGGGCAGAAGCTTCACCACGCGGGAGCGATTGAGACCCTTCGGAAGCTCCAATCACTTTTGA
Peptide sequence:
MARMDQELAHTSMGRSFTTRERLRPFGSSNHF
IRESfinder result
IRESfinder score
0.346965534
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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