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mmu_circCpsf3_544
Basic information of circular RNA
PanCircBase ID:
mmu_circCpsf3_544
mm39_Chr. Position ID:
chr12|21355303|21360285|+
Gene name:
Cpsf3
Transcript:
ENSMUST00000067284.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
11,12,13,14,15
Exon/intron offsets:
0,1470,2690,3601,4894
Genomic length:
4982
Exon/intron sizes in nt:
153,109,99,95,88
Flanking exon/introns:
chr12:21352506-21355303|chr12:21360285-21362298
Splice length:
544
Other database IDs:
circBase: mmu_circ_0003838, CIRCpedia: MMU_CIRCpedia_36320, circAtlas: mmu-Cpsf3_0001
circBase: hsa_circ_0006443, circAtlas: hsa-CPSF3_0001, CIRCpedia: HSA_CIRCpedia_69510
Human Ortholog IDs:
Mature spliced Sequence:
ATTTTAGTCCATGGGGAACAGAATGAAATGGCCAGGCTGAAAGCAGCGCTGATCCGAGAATATGAAGATAATGATGAAGTTCACATCGAGGTTCACAATCCTCGGAACACAGAGGCCGTGACCTTAAACTTCAGGGGAGAGAAGCTCGCCAAGGTCATGGGCTTTTTGGCAGACAAGAAACCAGAACAGGGCCAGCGGGTCTCTGGAATTCTTGTTAAAAGAAACTTTAATTACCACATACTCTCTCCCTGTGACCTCTCCAATTACACTGACCTGGCCATGAGCACTGTGAAACAGACCCAGGCCATCCCGTACACCGGGCCCTTTTACCTGCTCTACTACCAGCTCCAGAAATTGACGGGTGATGTAGAAGAATTAGAAATTCAAGAAAAGCCTGCTCTGAAGGTGTTCAAAAGCATCACTGTGGTGCAGGAGCCGGGCATGGTGGTTCTGGAGTGGCTGGCGAACCCCTCTAACGACATGTATGCAGACACAGTGACCACCGTGATATTGGAAGTTCAGTCAAATCCAAAGATAAGGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGAACCCCTCTAACGACAT
59.82
TATTCTCGGATCAGCGCTGC
60.32
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGTTCTGGAGTGGCTGG
60.3
GCTTTCAGCCTGGCCATTTC
60.11
144
PCR template sequence:
GTGGTTCTGGAGTGGCTGGCGAACCCCTCTAACGACATGTATGCAGACACAGTGACCACCGTGATATTGGAAGTTCAGTCAAATCCAAAGATAAGGAAAGATTTTAGTCCATGGGGAACAGAATGAAATGGCCAGGCTGAAAGCAGCGCTGATCCGAGAATATGAAGATAATGATGAAGTTCACATCGAGGTTCACAATC
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-27b-3p(1), mmu-miR-27a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGATAAGGAAAGATTTTAGTCCATG
siRNA sets
TAAAATCTTTCCTTATCTT,CTAAAATCTTTCCTTATCT,ACTAAAATCTTTCCTTATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCPSF3_544_ORF_1
1.2263
0.323025447
0.904747423
543
ORF sequence:
ATGGCCAGGCTGAAAGCAGCGCTGATCCGAGAATATGAAGATAATGATGAAGTTCACATCGAGGTTCACAATCCTCGGAACACAGAGGCCGTGACCTTAAACTTCAGGGGAGAGAAGCTCGCCAAGGTCATGGGCTTTTTGGCAGACAAGAAACCAGAACAGGGCCAGCGGGTCTCTGGAATTCTTGTTAAAAGAAACTTTAATTACCACATACTCTCTCCCTGTGACCTCTCCAATTACACTGACCTGGCCATGAGCACTGTGAAACAGACCCAGGCCATCCCGTACACCGGGCCCTTTTACCTGCTCTACTACCAGCTCCAGAAATTGACGGGTGATGTAGAAGAATTAGAAATTCAAGAAAAGCCTGCTCTGAAGGTGTTCAAAAGCATCACTGTGGTGCAGGAGCCGGGCATGGTGGTTCTGGAGTGGCTGGCGAACCCCTCTAACGACATGTATGCAGACACAGTGACCACCGTGATATTGGAAGTTCAGTCAAATCCAAAGATAAGGAAAGATTTTAGTCCATGGGGAACAGAATGA
Peptide sequence:
MARLKAALIREYEDNDEVHIEVHNPRNTEAVTLNFRGEKLAKVMGFLADKKPEQGQRVSGILVKRNFNYHILSPCDLSNYTDLAMSTVKQTQAIPYTGPFYLLYYQLQKLTGDVEELEIQEKPALKVFKSITVVQEPGMVVLEWLANPSNDMYADTVTTVILEVQSNPKIRKDFSPWGTE
IRESfinder result
IRESfinder score
0.627464587
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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