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mmu_circApc_434
Basic information of circular RNA
PanCircBase ID:
mmu_circApc_434
mm39_Chr. Position ID:
chr18|34394057|34402307|+
Gene name:
Apc
Transcript:
ENSMUST00000115781.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,7293,8051
Genomic length:
8250
Exon/intron sizes in nt:
1,53,82,199
Flanking exon/introns:
chr18:34354329-34394057|chr18:34402307-34405491
Splice length:
434
Other database IDs:
circAtlas: mmu-Apc_0003
circBase: hsa_circ_0073585, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_101476
Human Ortholog IDs:
Mature spliced Sequence:
GTCCAAGGGTAGCCAAGGATGGCTGCAGCTTCATATGATCAGTTGTTAAAGCAAGTTGAGGCACTGAAGATGGAGAACTCAAATCTTCGACAAGAGCTAGAAGATAATTCCAATCATCTTACAAAACTGGAAACTGAGGCATCTAATATGAAGGAAGTACTTAAGCAGCTACAGGGAAGTATTGAAGATGAGACTATGACTTCTGGACAGATTGACTTACTAGAGCGTCTTAAAGAATTTAACTTAGATAGTAATTTCCCCGGAGTGAAACTACGCTCAAAAATGTCCCTTCGCTCCTACGGAAGTCGGGAAGGATCTGTATCCAGCCGTTCAGGAGAATGCAGTCCTGTCCCCATGGGGTCATTCCCAAGAAGAACATTTGTAAATGGAAGCAGAGAGAGTACTGGGTATCTAGAAGAGCTTGAAAAAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATGCAGTCCTGTCCCCATG
60.03
TCTTCAGTGCCTCAACTTGCT
59.86
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGAATGCAGTCCTGTCCCC
60.11
TCTTCAGTGCCTCAACTTGCT
59.86
170
PCR template sequence:
GAGAATGCAGTCCTGTCCCCATGGGGTCATTCCCAAGAAGAACATTTGTAAATGGAAGCAGAGAGAGTACTGGGTATCTAGAAGAGCTTGAAAAAGAAAGGTCCAAGGGTAGCCAAGGATGGCTGCAGCTTCATATGATCAGTTGTTAAAGCAAGTTGAGGCACTGAAGATGGAGAACTCAAATCTTCGACAAGAGCTAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-217-5p(1), mmu-miR-127-5p(1), mmu-miR-362-5p(1), mmu-miR-452-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGAAAAAGAAAGGTCCAAGGGTAGC
siRNA sets
TTGGACCTTTCTTTTTCAA, CTTGGACCTTTCTTTTTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPC_434_ORF_1
0.7803
0.048265458
0.435508806
465
ORF sequence:
ATGGCTGCAGCTTCATATGATCAGTTGTTAAAGCAAGTTGAGGCACTGAAGATGGAGAACTCAAATCTTCGACAAGAGCTAGAAGATAATTCCAATCATCTTACAAAACTGGAAACTGAGGCATCTAATATGAAGGAAGTACTTAAGCAGCTACAGGGAAGTATTGAAGATGAGACTATGACTTCTGGACAGATTGACTTACTAGAGCGTCTTAAAGAATTTAACTTAGATAGTAATTTCCCCGGAGTGAAACTACGCTCAAAAATGTCCCTTCGCTCCTACGGAAGTCGGGAAGGATCTGTATCCAGCCGTTCAGGAGAATGCAGTCCTGTCCCCATGGGGTCATTCCCAAGAAGAACATTTGTAAATGGAAGCAGAGAGAGTACTGGGTATCTAGAAGAGCTTGAAAAAGAAAGGTCCAAGGGTAGCCAAGGATGGCTGCAGCTTCATATGATCAGTTGTTAA
Peptide sequence:
MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDETMTSGQIDLLERLKEFNLDSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRTFVNGSRESTGYLEELEKERSKGSQGWLQLHMISC
IRESfinder result
IRESfinder score
0.543023012
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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