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mmu_circAtrnl1_263
Basic information of circular RNA
PanCircBase ID:
mmu_circAtrnl1_263
mm39_Chr. Position ID:
chr19|57638689|57641442|+
Gene name:
Atrnl1
Transcript:
ENSMUST00000077282.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
6,7
Exon/intron offsets:
0,2665
Genomic length:
2753
Exon/intron sizes in nt:
175,88
Flanking exon/introns:
chr19:57631060-57638689|chr19:57641442-57643202
Splice length:
263
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215722, circAtlas: mmu-Atrnl1_0078
Human Ortholog IDs:
Mature spliced Sequence:
GCCCAGATTGTTCTCTGAATGTCCCTTCTACTGAGTCTTACTGGATTTTGCCAAATGTTAAACCCTTCAGCCCTTCCGTAGGTCGGGCCTCACATAAAGCAGTTTTACATGGGAAATTCATGTGGGTGATTGGAGGATATACTTTTAACTACAGTTCTTTTCAAATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGGGCCCTCTTCAGAGAT
59.95
GCTTTATGTGAGGCCCGACC
61.1
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCAAGGGGCCCTCTTCAGA
60.25
GCTTTATGTGAGGCCCGACC
61.1
149
PCR template sequence:
AATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAGGCCCAGATTGTTCTCTGAATGTCCCTTCTACTGAGTCTTACTGGATTTTGCCAAATGTTAAACCCTTCAGCCCTTCCGTAGGTCGGGCCTCACATAAAGC
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-182-5p(1), mmu-miR-499-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCCCTCTATCAGGCCCAGATTGTTC
siRNA sets
AACAATCTGGGCCTGATAG, AATCTGGGCCTGATAGAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATRNL1_263_ORF_1
0.5148
-0.141993835
0.076050498
330
ORF sequence:
ATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAGGCCCAGATTGTTCTCTGAATGTCCCTTCTACTGAGTCTTACTGGATTTTGCCAAATGTTAAACCCTTCAGCCCTTCCGTAGGTCGGGCCTCACATAAAGCAGTTTTACATGGGAAATTCATGTGGGTGATTGGAGGATATACTTTTAACTACAGTTCTTTTCAAATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAG
Peptide sequence:
MECRCCIKGPSSEIRTFSCPLSGPDCSLNVPSTESYWILPNVKPFSPSVGRASHKAVLHGKFMWVIGGYTFNYSSFQMVLNYNLESSIWNVGAVSRGPLQRYGHSLALYQ
IRESfinder result
IRESfinder score
0.855134184
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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