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mmu_circAp3b1_629
Basic information of circular RNA
PanCircBase ID:
mmu_circAp3b1_629
mm39_Chr. Position ID:
chr13|94608183|94616382|+
Gene name:
Ap3b1
Transcript:
ENSMUST00000022196.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
16,17,18,19
Exon/intron offsets:
0,1123,5290,8051
Genomic length:
8199
Exon/intron sizes in nt:
1,87,13,11,63,148
Flanking exon/introns:
chr13:94599080-94608183|chr13:94616382-94619720
Splice length:
629
Other database IDs:
circAtlas: mmu-Ap3b1_0016
Human Ortholog IDs:
Mature spliced Sequence:
ACAAAATTGCTTACCCAGTACATATTAAATCTCGGCAAGTATGATCAAAACTACGACATCAGAGACCGCACACGATTTATTAGGCAGCTTATTGTTCCGAACGAGAAGAGTGGAGCCTTAAGTAAATATGCCAAAAAAATCTTCCTAGCACCGAAGCCTGCGCCACTGCTCGAGTCTCCCTTTAAAGATAGGGATCGCTTCCAGCTTGGCACCTTATCTCATACTCTCAACATTAAAGCGTCCGGGTACCTGGAATTATCTAATTGGCCAGAGGTGGCGCCTGACCCATCGGTTCGCAATGTAGAAGTAATAGAGTCAGCAAAAGAATGGACCCCACTTGGGAAAACAAAGAAAGAAAAACCCATGAAGAAATTTTACTCTGAATCTGAGGAGGAGGAGGACGAGGACGAGGATGAGGACGAGGAGGAGGAAGAAAAGGAAGATGAGGATGAGAACCCCTCTGATAGCAGCAGTGACAGTGAGAGCGGGTCCGGAAGTGAGAGTGGAGACACAGGCACCGAGGACAGCAGTGAGGACTCGTCCAGTGGACAAGACAGCGAGACCGGAAGCCAGGCAGAAGCGGAACGCCAGAAGGTGGCCAAGAGGAACTCCAAAACCAAGAGGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTGGACAAGACAGCGAGA
59.68
ATCGTGTGCGGTCTCTGATG
60.18
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGGACAAGACAGCGAGAC
59.68
ATCGTGTGCGGTCTCTGATG
60.18
162
PCR template sequence:
GTGAGGACTCGTCCAGTGGACAAGACAGCGAGACCGGAAGCCAGGCAGAAGCGGAACGCCAGAAGGTGGCCAAGAGGAACTCCAAAACCAAGAGGAAAAGACAAAATTGCTTACCCAGTACATATTAAATCTCGGCAAGTATGATCAAAACTACGACATCAGAGACCGCACACGATTTATTAGGCAGCTTATTGTTCCGA
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-136-5p(1), mmu-miR-22-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CCAAGAGGAAAAGACAAAATTGCTTA
siRNA sets
AATTTTGTCTTTTCCTCTT,TAAGCAATTTTGTCTTTTC,ATTTTGTCTTTTCCTCTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAP3B1_629_ORF_1
1.1963
0.554696105
0.792766266
294
ORF sequence:
ATGAAGAAATTTTACTCTGAATCTGAGGAGGAGGAGGACGAGGACGAGGATGAGGACGAGGAGGAGGAAGAAAAGGAAGATGAGGATGAGAACCCCTCTGATAGCAGCAGTGACAGTGAGAGCGGGTCCGGAAGTGAGAGTGGAGACACAGGCACCGAGGACAGCAGTGAGGACTCGTCCAGTGGACAAGACAGCGAGACCGGAAGCCAGGCAGAAGCGGAACGCCAGAAGGTGGCCAAGAGGAACTCCAAAACCAAGAGGAAAAGACAAAATTGCTTACCCAGTACATATTAA
Peptide sequence:
MKKFYSESEEEEDEDEDEDEEEEEKEDEDENPSDSSSDSESGSGSESGDTGTEDSSEDSSSGQDSETGSQAEAERQKVAKRNSKTKRKRQNCLPSTY
IRESfinder result
IRESfinder score
0.366727877
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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