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mmu_circAtf2_629
Basic information of circular RNA
PanCircBase ID:
mmu_circAtf2_629
mm39_Chr. Position ID:
chr2|73672703|73681326|-
Gene name:
Atf2
Transcript:
ENSMUST00000112010.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,8,7,6,5
Exon/intron offsets:
0,3079,3837,8229,8504
Genomic length:
8623
Exon/intron sizes in nt:
87,115,179,129,119
Flanking exon/introns:
chr2:73660285-73672703|chr2:73681326-73693512
Splice length:
629
Other database IDs:
CIRCpedia: MMU_CIRCpedia_28544, circAtlas: mmu-Atf2_0007
circBase: hsa_circ_0057150, circAtlas: hsa-ATF2_0006, CIRCpedia: HSA_CIRCpedia_38699
Human Ortholog IDs:
Mature spliced Sequence:
ATCAGACTCCAACGCCAACAAGATTCCTAAAAAACTGTGAAGAAGTGGGTTTGTTCAATGAGTTGGCAAGTCCATTTGAAAATGAATTCAAGAAGGCTTCCGAAGATGACATTAAAAAAATGCCTCTAGATTTGTCCCCTCTTGCAACACCCATCATAAGAAGCAAAATTGAGGAGCCTTCTGTTGTAGAAACAACTCACCAGGACAGCCCTTTACCTCACCCCGAGTCGACTACCAGTGATGAAAAGGAAGTACCATTGGCACAAACTGCACAGCCCACATCAGCTATCGTTCGTCCAGCATCATTACAGGTTCCCAATGTGCTGCTCACAAGTTCTGACTCAAGTGTAATTATTCAACAAGCAGTACCTTCACCAACCTCAAGTACTGTAATCACCCAGGCACCATCCTCTAACAGGCCAATTGTTCCTGTACCAGGCCCATTTCCTCTTCTCTTACATCTTCCTAATGGACAAACCATGCCCGTTGCTATTCCTGCATCAATTACAAGTTCTAATGTGCATGTTCCAGCTGCAGTCCCACTTGTTCGGCCAGTCACCATGGTGCCTAGTGTTCCAGGAATCCCAGGCCCTTCCTCTCCTCAACCAGTCCAGTCAGAAGCAAAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGTCACCATGGTGCCTAG
60.11
GCCAACTCATTGAACAAACCCA
59.9
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGTCACCATGGTGCCTAG
60.11
TGCCAACTCATTGAACAAACCC
59.9
146
PCR template sequence:
AGCTGCAGTCCCACTTGTTCGGCCAGTCACCATGGTGCCTAGTGTTCCAGGAATCCCAGGCCCTTCCTCTCCTCAACCAGTCCAGTCAGAAGCAAAAATGATCAGACTCCAACGCCAACAAGATTCCTAAAAAACTGTGAAGAAGTGGGTTTGTTCAATGAGTTGGCAAGTCCATTTGAAAATGAATTCAAGAAGGCTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-101a-3p(1), mmu-miR-15b-5p(1), mmu-miR-101b-3p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAGCAAAAATGATCAGACTCCAAC
siRNA sets
GAGTCTGATCATTTTTGCT, GGAGTCTGATCATTTTTGC, TCTGATCATTTTTGCTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATF2_629_ORF_1
1.2767
-0.012657287
0.720469405
540
ORF sequence:
ATGCCTCTAGATTTGTCCCCTCTTGCAACACCCATCATAAGAAGCAAAATTGAGGAGCCTTCTGTTGTAGAAACAACTCACCAGGACAGCCCTTTACCTCACCCCGAGTCGACTACCAGTGATGAAAAGGAAGTACCATTGGCACAAACTGCACAGCCCACATCAGCTATCGTTCGTCCAGCATCATTACAGGTTCCCAATGTGCTGCTCACAAGTTCTGACTCAAGTGTAATTATTCAACAAGCAGTACCTTCACCAACCTCAAGTACTGTAATCACCCAGGCACCATCCTCTAACAGGCCAATTGTTCCTGTACCAGGCCCATTTCCTCTTCTCTTACATCTTCCTAATGGACAAACCATGCCCGTTGCTATTCCTGCATCAATTACAAGTTCTAATGTGCATGTTCCAGCTGCAGTCCCACTTGTTCGGCCAGTCACCATGGTGCCTAGTGTTCCAGGAATCCCAGGCCCTTCCTCTCCTCAACCAGTCCAGTCAGAAGCAAAAATGATCAGACTCCAACGCCAACAAGATTCCTAA
Peptide sequence:
MPLDLSPLATPIIRSKIEEPSVVETTHQDSPLPHPESTTSDEKEVPLAQTAQPTSAIVRPASLQVPNVLLTSSDSSVIIQQAVPSPTSSTVITQAPSSNRPIVPVPGPFPLLLHLPNGQTMPVAIPASITSSNVHVPAAVPLVRPVTMVPSVPGIPGPSSPQPVQSEAKMIRLQRQQDS
IRESfinder result
IRESfinder score
0.608260822
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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