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mmu_circAgps_396
Basic information of circular RNA
PanCircBase ID:
mmu_circAgps_396
mm39_Chr. Position ID:
chr2|75689242|75698757|+
Gene name:
Agps
Transcript:
ENSMUST00000047232.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,8,9,10
Exon/intron offsets:
0,3035,7848,9406
Genomic length:
9515
Exon/intron sizes in nt:
8,08,11,26,109
Flanking exon/introns:
chr2:75687432-75689242|chr2:75698757-75707814
Splice length:
396
Other database IDs:
circAtlas: mmu-Agps_0029
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_38730
Human Ortholog IDs:
Mature spliced Sequence:
GAGGAACAAGTGTGTCCTATGGCTTGATGTGTCCTGCAGACGAGACAAGAACAATAATTTCTTTGGACACTTCACAAATGAACCGGATTCTCTGGGTTGATGAGAACAATCTGACAGCTCACGTAGAGGCTGGGATAACAGGACAAGATTTGGAAAGACAGCTTAAAGAAAGTGGTTATTGTACAGGTCATGAACCGGACTCCCTGGAATTCAGCACCGTGGGAGGATGGATATCTACTCGAGCGTCAGGCATGAAGAAAAATATCTATGGCAATATTGAGGACCTGGTGGTTCATATGAAAATGGTAACACCTAGAGGTGTAATAGAGAAAAGCTCCCAAGGACCTCGTATGTCAACGGGCCCTGATATCCATCACTTCATTATGGGATCTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTCCCAAGGACCTCGTAT
60.03
CAACCCAGAGAATCCGGTTCA
60
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAGCTCCCAAGGACCTCG
59.96
CAACCCAGAGAATCCGGTTCA
60
166
PCR template sequence:
ATGAAAATGGTAACACCTAGAGGTGTAATAGAGAAAAGCTCCCAAGGACCTCGTATGTCAACGGGCCCTGATATCCATCACTTCATTATGGGATCTGAAGGAGGAACAAGTGTGTCCTATGGCTTGATGTGTCCTGCAGACGAGACAAGAACAATAATTTCTTTGGACACTTCACAAATGAACCGGATTCTCTGGGTTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGGGATCTGAAGGAGGAACAAGTGT
siRNA sets
TGTTCCTCCTTCAGATCCC, CTTGTTCCTCCTTCAGATC, TTGTTCCTCCTTCAGATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGPS_396_ORF_1
0.9035
0.091247802
0.90987569
765
ORF sequence:
ATGTGTCCTGCAGACGAGACAAGAACAATAATTTCTTTGGACACTTCACAAATGAACCGGATTCTCTGGGTTGATGAGAACAATCTGACAGCTCACGTAGAGGCTGGGATAACAGGACAAGATTTGGAAAGACAGCTTAAAGAAAGTGGTTATTGTACAGGTCATGAACCGGACTCCCTGGAATTCAGCACCGTGGGAGGATGGATATCTACTCGAGCGTCAGGCATGAAGAAAAATATCTATGGCAATATTGAGGACCTGGTGGTTCATATGAAAATGGTAACACCTAGAGGTGTAATAGAGAAAAGCTCCCAAGGACCTCGTATGTCAACGGGCCCTGATATCCATCACTTCATTATGGGATCTGAAGGAGGAACAAGTGTGTCCTATGGCTTGATGTGTCCTGCAGACGAGACAAGAACAATAATTTCTTTGGACACTTCACAAATGAACCGGATTCTCTGGGTTGATGAGAACAATCTGACAGCTCACGTAGAGGCTGGGATAACAGGACAAGATTTGGAAAGACAGCTTAAAGAAAGTGGTTATTGTACAGGTCATGAACCGGACTCCCTGGAATTCAGCACCGTGGGAGGATGGATATCTACTCGAGCGTCAGGCATGAAGAAAAATATCTATGGCAATATTGAGGACCTGGTGGTTCATATGAAAATGGTAACACCTAGAGGTGTAATAGAGAAAAGCTCCCAAGGACCTCGTATGTCAACGGGCCCTGATATCCATCACTTCATTATGGGATCTGAA
Peptide sequence:
MCPADETRTIISLDTSQMNRILWVDENNLTAHVEAGITGQDLERQLKESGYCTGHEPDSLEFSTVGGWISTRASGMKKNIYGNIEDLVVHMKMVTPRGVIEKSSQGPRMSTGPDIHHFIMGSEGGTSVSYGLMCPADETRTIISLDTSQMNRILWVDENNLTAHVEAGITGQDLERQLKESGYCTGHEPDSLEFSTVGGWISTRASGMKKNIYGNIEDLVVHMKMVTPRGVIEKSSQGPRMSTGPDIHHFIMGSE
IRESfinder result
IRESfinder score
0.572874764
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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