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mmu_circAp3d1_380
Basic information of circular RNA
PanCircBase ID:
mmu_circAp3d1_380
mm39_Chr. Position ID:
chr10|80554842|80555222|-
Gene name:
Ap3d1
Transcript:
ENSMUST00000020420.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
13
Exon/intron offsets:
0
Genomic length:
380
Exon/intron sizes in nt:
380
Flanking exon/introns:
chr10:80553764-80554842|chr10:80555222-80555500
Splice length:
380
Other database IDs:
circAtlas: hsa-AP3D1_0014, CIRCpedia: HSA_CIRCpedia_25330
Human Ortholog IDs:
Mature spliced Sequence:
GTGTCCAAGAAGAACCTGATGGAGATTGTGAAGAAGCTCATGACTCACGTGGACAAGGCTGAGGGCACCACCTATCGCGATGAACTGCTCACCAAGATCATTGACATCTGTAGCCAGTCCAACTACCAGCACATCACCAACTTCGAGTGGTACATCAGCATCCTTGTGGAGCTGACAAGGCTGGAGGGCACCCGCCATGGCCACCTCATTGCTGCACAGATGCTGGACGTGGCTATCCGGGTCAAGGCCATTCGCAAATTTGCTGTGTCGCAGATGTCCTCACTGCTTGACAGTGCTCACCTGGTAGCCAGCAGCACCCAACGCAATGGTATCTGTGAGGTGCTCTATGCTGCTGCCTGGATCTGCGGGGAGTTCTCAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCACCCAACGCAATGGTATC
59.9
CTTGGTGAGCAGTTCATCGC
59.55
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGAGGTGCTCTATGCTGC
60.11
CTTGGTGAGCAGTTCATCGC
59.55
143
PCR template sequence:
CACTGCTTGACAGTGCTCACCTGGTAGCCAGCAGCACCCAACGCAATGGTATCTGTGAGGTGCTCTATGCTGCTGCCTGGATCTGCGGGGAGTTCTCAGAGTGTCCAAGAAGAACCTGATGGAGATTGTGAAGAAGCTCATGACTCACGTGGACAAGGCTGAGGGCACCACCTATCGCGATGAACTGCTCACCAAGATCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-680(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGAGTTCTCAGAGTGTCCAAGAAGA
siRNA sets
TTGGACACTCTGAGAACTC, GGACACTCTGAGAACTCCC, TGGACACTCTGAGAACTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAP3D1_380_ORF_1
1.1599
0.511815116
0.850448608
381
ORF sequence:
ATGGAGATTGTGAAGAAGCTCATGACTCACGTGGACAAGGCTGAGGGCACCACCTATCGCGATGAACTGCTCACCAAGATCATTGACATCTGTAGCCAGTCCAACTACCAGCACATCACCAACTTCGAGTGGTACATCAGCATCCTTGTGGAGCTGACAAGGCTGGAGGGCACCCGCCATGGCCACCTCATTGCTGCACAGATGCTGGACGTGGCTATCCGGGTCAAGGCCATTCGCAAATTTGCTGTGTCGCAGATGTCCTCACTGCTTGACAGTGCTCACCTGGTAGCCAGCAGCACCCAACGCAATGGTATCTGTGAGGTGCTCTATGCTGCTGCCTGGATCTGCGGGGAGTTCTCAGAGTGTCCAAGAAGAACCTGA
Peptide sequence:
MEIVKKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQHITNFEWYISILVELTRLEGTRHGHLIAAQMLDVAIRVKAIRKFAVSQMSSLLDSAHLVASSTQRNGICEVLYAAAWICGEFSECPRRT
IRESfinder result
IRESfinder score
0.340888707
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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