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mmu_circApc_588
Basic information of circular RNA
PanCircBase ID:
mmu_circApc_588
mm39_Chr. Position ID:
chr18|34401350|34412405|+
Gene name:
Apc
Transcript:
ENSMUST00000115781.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,758,4141,8266,10971
Genomic length:
11055
Exon/intron sizes in nt:
82,199,109,114,84
Flanking exon/introns:
chr18:34394210-34401350|chr18:34412405-34415059
Splice length:
588
Other database IDs:
circBase: mmu_circ_0007249, CIRCpedia: MMU_CIRCpedia_17194, circAtlas: mmu-Apc_0002
circBase: hsa_circ_0127612, circAtlas: hsa-APC_0002, CIRCpedia: HSA_CIRCpedia_49841
Human Ortholog IDs:
Mature spliced Sequence:
GAAGTACTTAAGCAGCTACAGGGAAGTATTGAAGATGAGACTATGACTTCTGGACAGATTGACTTACTAGAGCGTCTTAAAGAATTTAACTTAGATAGTAATTTCCCCGGAGTGAAACTACGCTCAAAAATGTCCCTTCGCTCCTACGGAAGTCGGGAAGGATCTGTATCCAGCCGTTCAGGAGAATGCAGTCCTGTCCCCATGGGGTCATTCCCAAGAAGAACATTTGTAAATGGAAGCAGAGAGAGTACTGGGTATCTAGAAGAGCTTGAAAAAGAAAGATCATTACTCCTTGCTGATCTTGACAAAGAAGAGAAGGAAAAGGACTGGTATTATGCTCAACTTCAGAACCTCACAAAAAGAATAGATAGCCTGCCTTTAACTGAAAATTTTTCCTTACAGACAGACATGACAAGACGGCAGCTGGAGTATGAAGCAAGGCAGATCAGGGCTGCAATGGAGGAGCAGCTTGGCACCTGCCAGGACATGGAGAAGCGTGCACAGCGAAGAATAGCCAGGATCCAGCAAATAGAAAAGGACATACTGCGCGTGCGCCAGCTTTTACAGTCCCAGGCGGCGGAAGCGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGCACAGCGAAGAATAGC
59.97
CGCTCTAGTAAGTCAATCTGTCCA
59.9
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGTGCACAGCGAAGAATAG
59.97
CGCTCTAGTAAGTCAATCTGTCCA
59.9
168
PCR template sequence:
GGAGAAGCGTGCACAGCGAAGAATAGCCAGGATCCAGCAAATAGAAAAGGACATACTGCGCGTGCGCCAGCTTTTACAGTCCCAGGCGGCGGAAGCGGAGGAAGTACTTAAGCAGCTACAGGGAAGTATTGAAGATGAGACTATGACTTCTGGACAGATTGACTTACTAGAGCGTCTTAAAGAATTTAACTTAGATAGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-217-5p(1), mmu-miR-136-5p(1), mmu-miR-452-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCGGAAGCGGAGGAAGTACTTAAGC
siRNA sets
TACTTCCTCCGCTTCCGCC, AAGTACTTCCTCCGCTTCC, TAAGTACTTCCTCCGCTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPC_588_ORF_1
0.856
0.158250106
0.994243052
1134
ORF sequence:
ATGACTTCTGGACAGATTGACTTACTAGAGCGTCTTAAAGAATTTAACTTAGATAGTAATTTCCCCGGAGTGAAACTACGCTCAAAAATGTCCCTTCGCTCCTACGGAAGTCGGGAAGGATCTGTATCCAGCCGTTCAGGAGAATGCAGTCCTGTCCCCATGGGGTCATTCCCAAGAAGAACATTTGTAAATGGAAGCAGAGAGAGTACTGGGTATCTAGAAGAGCTTGAAAAAGAAAGATCATTACTCCTTGCTGATCTTGACAAAGAAGAGAAGGAAAAGGACTGGTATTATGCTCAACTTCAGAACCTCACAAAAAGAATAGATAGCCTGCCTTTAACTGAAAATTTTTCCTTACAGACAGACATGACAAGACGGCAGCTGGAGTATGAAGCAAGGCAGATCAGGGCTGCAATGGAGGAGCAGCTTGGCACCTGCCAGGACATGGAGAAGCGTGCACAGCGAAGAATAGCCAGGATCCAGCAAATAGAAAAGGACATACTGCGCGTGCGCCAGCTTTTACAGTCCCAGGCGGCGGAAGCGGAGGAAGTACTTAAGCAGCTACAGGGAAGTATTGAAGATGAGACTATGACTTCTGGACAGATTGACTTACTAGAGCGTCTTAAAGAATTTAACTTAGATAGTAATTTCCCCGGAGTGAAACTACGCTCAAAAATGTCCCTTCGCTCCTACGGAAGTCGGGAAGGATCTGTATCCAGCCGTTCAGGAGAATGCAGTCCTGTCCCCATGGGGTCATTCCCAAGAAGAACATTTGTAAATGGAAGCAGAGAGAGTACTGGGTATCTAGAAGAGCTTGAAAAAGAAAGATCATTACTCCTTGCTGATCTTGACAAAGAAGAGAAGGAAAAGGACTGGTATTATGCTCAACTTCAGAACCTCACAAAAAGAATAGATAGCCTGCCTTTAACTGAAAATTTTTCCTTACAGACAGACATGACAAGACGGCAGCTGGAGTATGAAGCAAGGCAGATCAGGGCTGCAATGGAGGAGCAGCTTGGCACCTGCCAGGACATGGAGAAGCGTGCACAGCGAAGAATAGCCAGGATCCAGCAAATAGAAAAGGACATACTGCGCGTGCGCCAGCTTTTACAGTCCCAGGCGGCGGAAGCGGAG
Peptide sequence:
MTSGQIDLLERLKEFNLDSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRTFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRAAMEEQLGTCQDMEKRAQRRIARIQQIEKDILRVRQLLQSQAAEAEEVLKQLQGSIEDETMTSGQIDLLERLKEFNLDSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRTFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRAAMEEQLGTCQDMEKRAQRRIARIQQIEKDILRVRQLLQSQAAEAE
IRESfinder result
IRESfinder score
0.536536534
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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