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mmu_circIrf2_417
Basic information of circular RNA
PanCircBase ID:
mmu_circIrf2_417
mm39_Chr. Position ID:
chr8|47246527|47260786|+
Gene name:
Irf2
Transcript:
ENSMUST00000034041.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,12978,13729,14212
Genomic length:
14259
Exon/intron sizes in nt:
93,100,177,47
Flanking exon/introns:
chr8:47192971-47246527|chr8:47260786-47271825
Splice length:
417
Other database IDs:
circBase: mmu_circ_0001673, CIRCpedia: MMU_CIRCpedia_20959, circAtlas: mmu-Irf2_0001
circAtlas: hsa-IRF2_0003, CIRCpedia: HSA_CIRCpedia_103785
Human Ortholog IDs:
Mature spliced Sequence:
GGTACCATGCCGGTGGAACGGATGCGAATGCGCCCGTGGCTGGAGGAGCAGATAAATTCCAATACGATACCAGGGCTAAAGTGGCTGAACAAGGAGAAGAAGATTTTCCAGATCCCCTGGATGCATGCGGCTCGGCACGGATGGGACGTGGAAAAGGATGCTCCGCTCTTCAGAAACTGGGCGATCCATACAGGAAAGCATCAACCAGGAATAGATAAACCAGATCCAAAAACATGGAAAGCAAATTTTCGATGTGCCATGAATTCCCTGCCCGACATTGAGGAAGTGAAGGACAGAAGCATAAAGAAAGGAAACAACGCCTTCAGAGTCTACCGGATGCTGCCCTTATCCGAACGACCTTCCAAGAAAGGAAAGAAACCAAAGACAGAAAAAGAAGAGAGAGTTAAGCACATCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGATGCTGCCCTTATCCGAA
59.89
TTCAGCCACTTTAGCCCTGG
59.96
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCCTTATCCGAACGACCTT
59.82
TTCAGCCACTTTAGCCCTGG
59.96
165
PCR template sequence:
CGCCTTCAGAGTCTACCGGATGCTGCCCTTATCCGAACGACCTTCCAAGAAAGGAAAGAAACCAAAGACAGAAAAAGAAGAGAGAGTTAAGCACATCAAGGGTACCATGCCGGTGGAACGGATGCGAATGCGCCCGTGGCTGGAGGAGCAGATAAATTCCAATACGATACCAGGGCTAAAGTGGCTGAACAAGGAGAAGA
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-9-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-218-5p(1), mmu-miR-183-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
TAAGCACATCAAGGGTACCATGCCGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCIRF2_417_ORF_1
0.9939
0.289046734
0.976855653
828
ORF sequence:
ATGCCGGTGGAACGGATGCGAATGCGCCCGTGGCTGGAGGAGCAGATAAATTCCAATACGATACCAGGGCTAAAGTGGCTGAACAAGGAGAAGAAGATTTTCCAGATCCCCTGGATGCATGCGGCTCGGCACGGATGGGACGTGGAAAAGGATGCTCCGCTCTTCAGAAACTGGGCGATCCATACAGGAAAGCATCAACCAGGAATAGATAAACCAGATCCAAAAACATGGAAAGCAAATTTTCGATGTGCCATGAATTCCCTGCCCGACATTGAGGAAGTGAAGGACAGAAGCATAAAGAAAGGAAACAACGCCTTCAGAGTCTACCGGATGCTGCCCTTATCCGAACGACCTTCCAAGAAAGGAAAGAAACCAAAGACAGAAAAAGAAGAGAGAGTTAAGCACATCAAGGGTACCATGCCGGTGGAACGGATGCGAATGCGCCCGTGGCTGGAGGAGCAGATAAATTCCAATACGATACCAGGGCTAAAGTGGCTGAACAAGGAGAAGAAGATTTTCCAGATCCCCTGGATGCATGCGGCTCGGCACGGATGGGACGTGGAAAAGGATGCTCCGCTCTTCAGAAACTGGGCGATCCATACAGGAAAGCATCAACCAGGAATAGATAAACCAGATCCAAAAACATGGAAAGCAAATTTTCGATGTGCCATGAATTCCCTGCCCGACATTGAGGAAGTGAAGGACAGAAGCATAAAGAAAGGAAACAACGCCTTCAGAGTCTACCGGATGCTGCCCTTATCCGAACGACCTTCCAAGAAAGGAAAGAAACCAAAGACAGAAAAAGAAGAGAGAGTTAAGCACATCAAG
Peptide sequence:
MPVERMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLPLSERPSKKGKKPKTEKEERVKHIKGTMPVERMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLPLSERPSKKGKKPKTEKEERVKHIK
IRESfinder result
IRESfinder score
0.236032562
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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