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mmu_circAtg2b_707
Basic information of circular RNA
PanCircBase ID:
mmu_circAtg2b_707
mm39_Chr. Position ID:
chr12|105620267|105625247|-
Gene name:
Atg2b
Transcript:
ENSMUST00000041055.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
15,14,13,12
Exon/intron offsets:
0,3958,4259,4829
Genomic length:
4980
Exon/intron sizes in nt:
274,189,93,151
Flanking exon/introns:
chr12:105618890-105620267|chr12:105625247-105627258
Splice length:
707
Other database IDs:
circAtlas: mmu-Atg2b_0042
Human Ortholog IDs:
Mature spliced Sequence:
GTTTATAGGTACTGGCATCAAAGTGTCCTATGAGCAGAGACAAAGGTCAGCTTCCCGGCACTTTAGCACCGACATGTCCGTTGGGCAAATGGAGTTTTTGGAGTGTCTGTTTCCAACAGATTGTCATTCTGTCCCTTCTCACTACACCGAGCTTCTAACGTTCCATTCCAAAGAAGGGACGGATGCCCACCTTCCCGTTTGTCTTCAGCTTCACTATAAACACTCAGAGACTAGAGGACCCCAGGGTAATCAAGCAAGACTTAGTTCAGTTCCTCAAAAGGCAGAATTACAAATTAAATTAAACCCCGTGTGTTGCGAGCTGGATATCAGTATTGTGGATAGGTTAAATTCCTTGCTTCAACCTCAGAAACTCACTACCGTGGAGATGATGGCCTCGCACATGTATGCGTCCTATAACAAGCATATTAGTTTGCACAAGGCTTTCACGGAAGTGTTCCTAGATGACTCACACAGTCCTGCAAACCGTCGGGTGTCCGTACAAGTTGCCACCCCAGCCCTGCACCTGTCTGTTCGCTTCCCTATTCCTGATCTAAGATCAGACCAGGAAAGAGGACCCTGGTTTAAGAAGTCACTTCAGAAGGAGACCCTTCATTTAGAATTTACGGATCTGGAGTCCAAGACAGAGTTCGTGGGAGGATCCACCCCAGAACAAACTAAACTGGAGCTGACTTTTCGAGAGCTATCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGACAGAGTTCGTGGGAGGA
59.89
CCATTTGCCCAACGGACATG
60.11
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGACAGAGTTCGTGGGAGGA
59.89
AACTCCATTTGCCCAACGGA
60.18
165
PCR template sequence:
CTTCATTTAGAATTTACGGATCTGGAGTCCAAGACAGAGTTCGTGGGAGGATCCACCCCAGAACAAACTAAACTGGAGCTGACTTTTCGAGAGCTATCTGGTTTATAGGTACTGGCATCAAAGTGTCCTATGAGCAGAGACAAAGGTCAGCTTCCCGGCACTTTAGCACCGACATGTCCGTTGGGCAAATGGAGTTTTTG
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-19a-3p(1), mmu-miR-136-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGAGAGCTATCTGGTTTATAGGTACT
siRNA sets
TACCTATAAACCAGATAGC, ACCTATAAACCAGATAGCT, TATAAACCAGATAGCTCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATG2B_707_ORF_1
1.0033
0.072946178
0.820649123
642
ORF sequence:
ATGTCCGTTGGGCAAATGGAGTTTTTGGAGTGTCTGTTTCCAACAGATTGTCATTCTGTCCCTTCTCACTACACCGAGCTTCTAACGTTCCATTCCAAAGAAGGGACGGATGCCCACCTTCCCGTTTGTCTTCAGCTTCACTATAAACACTCAGAGACTAGAGGACCCCAGGGTAATCAAGCAAGACTTAGTTCAGTTCCTCAAAAGGCAGAATTACAAATTAAATTAAACCCCGTGTGTTGCGAGCTGGATATCAGTATTGTGGATAGGTTAAATTCCTTGCTTCAACCTCAGAAACTCACTACCGTGGAGATGATGGCCTCGCACATGTATGCGTCCTATAACAAGCATATTAGTTTGCACAAGGCTTTCACGGAAGTGTTCCTAGATGACTCACACAGTCCTGCAAACCGTCGGGTGTCCGTACAAGTTGCCACCCCAGCCCTGCACCTGTCTGTTCGCTTCCCTATTCCTGATCTAAGATCAGACCAGGAAAGAGGACCCTGGTTTAAGAAGTCACTTCAGAAGGAGACCCTTCATTTAGAATTTACGGATCTGGAGTCCAAGACAGAGTTCGTGGGAGGATCCACCCCAGAACAAACTAAACTGGAGCTGACTTTTCGAGAGCTATCTGGTTTATAG
Peptide sequence:
MSVGQMEFLECLFPTDCHSVPSHYTELLTFHSKEGTDAHLPVCLQLHYKHSETRGPQGNQARLSSVPQKAELQIKLNPVCCELDISIVDRLNSLLQPQKLTTVEMMASHMYASYNKHISLHKAFTEVFLDDSHSPANRRVSVQVATPALHLSVRFPIPDLRSDQERGPWFKKSLQKETLHLEFTDLESKTEFVGGSTPEQTKLELTFRELSGL
IRESfinder result
IRESfinder score
0.675324603
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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