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mmu_circAbca5_416
Basic information of circular RNA
PanCircBase ID:
mmu_circAbca5_416
mm39_Chr. Position ID:
chr11|110176519|110179002|-
Gene name:
Abca5
Transcript:
ENSMUST00000043961.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
28,27,26,25
Exon/intron offsets:
0,1070,1888,2369
Genomic length:
2483
Exon/intron sizes in nt:
9,27,51,35,114
Flanking exon/introns:
chr11:110170578-110176519|chr11:110179002-110180616
Splice length:
416
Other database IDs:
circBase: hsa_circ_0107589, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_22233
Human Ortholog IDs:
Mature spliced Sequence:
GTGTTTTGCCTCATTGCTTATGTGCCCTCCGTCATTCTGTTCACGTACATAGCTTCGTTCACTTTCAAGAAAATTTTAAATACCAAGGAATTTTGGTCATTTATCTATTCTGTGACCGCATTGGCTTGTGTGGCAATCACGGAAACAACTTTCTTTCTGCAATATGCAGTTACGGCTGTCTTTCATTACACCTTCTGCATAGCCATTCCAATCTACCCTCTCCTGGGTTGTCTGATTTCTTTCATAAAGGGTTCTTGGAAGAATATGCCAAAAAATGAGAATACCTACAATCCCTGGGATAGACTTTTAGTTGCTGTAATCATGCCCTACCTGCAGTGTATACTGTGGATTTTCCTCTTACAACACTATGAGAAAATACATGGAGGCAGATCTATAAGAAAGGATCCATTTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATCATGCCCTACCTGCAGTG
59.82
GAACAGAATGACGGAGGGCA
60.04
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCATGCCCTACCTGCAGTG
59.82
TGAACAGAATGACGGAGGGC
60.04
141
PCR template sequence:
TAATCATGCCCTACCTGCAGTGTATACTGTGGATTTTCCTCTTACAACACTATGAGAAAATACATGGAGGCAGATCTATAAGAAAGGATCCATTTTTCAGGTGTTTTGCCTCATTGCTTATGTGCCCTCCGTCATTCTGTTCACGTACATAGCTTCGTTCACTTTCAAGAAAATTTTAAATACCAAGGAATTTTGGTCAT
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-382-5p(1), mmu-miR-541-5p(1), mmu-miR-802-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCCATTTTTCAGGTGTTTTGCCTCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCA5_416_ORF_1
0.4192
-0.285848254
0.015073811
204
ORF sequence:
ATGCCAAAAAATGAGAATACCTACAATCCCTGGGATAGACTTTTAGTTGCTGTAATCATGCCCTACCTGCAGTGTATACTGTGGATTTTCCTCTTACAACACTATGAGAAAATACATGGAGGCAGATCTATAAGAAAGGATCCATTTTTCAGGTGTTTTGCCTCATTGCTTATGTGCCCTCCGTCATTCTGTTCACGTACATAG
Peptide sequence:
MPKNENTYNPWDRLLVAVIMPYLQCILWIFLLQHYEKIHGGRSIRKDPFFRCFASLLMCPPSFCSRT
IRESfinder result
IRESfinder score
0.865158466
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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