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mmu_circAtrnl1_601
Basic information of circular RNA
PanCircBase ID:
mmu_circAtrnl1_601
mm39_Chr. Position ID:
chr19|57626883|57641442|+
Gene name:
Atrnl1
Transcript:
ENSMUST00000077282.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
4,5,6,7
Exon/intron offsets:
0,3968,11806,14471
Genomic length:
14559
Exon/intron sizes in nt:
129,209,175,88
Flanking exon/introns:
chr19:57618771-57626883|chr19:57641442-57643202
Splice length:
601
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215721, circAtlas: mmu-Atrnl1_0104
Human Ortholog IDs:
Mature spliced Sequence:
TGGCTTGATCGTTCCTGAAGTGAGGGGTAACGAGACCGTGCCTGAGGTGGTCACGACGTCTGGCTACGCGCTGCTCCACTTTTTCAGCGATGCTGCATATAACCTAACTGGCTTCAACATTTTTTATTCGATCAATTCCTGTCCTAACAACTGCTCTGGTCATGGAAAGTGTACAACCAGTGTCTCTGTTGCAAGTCAAGTGTATTGTGAATGCGACAAATACTGGAAAGGGGAAGCATGTGACATTCCTTACTGTAAAGCCAATTGTGGGAGTCCAGATCATGGCTACTGTGACCTAACAGGAGAGAAACTCTGTGTCTGCAACGATAGTTGGCAAGGCCCAGATTGTTCTCTGAATGTCCCTTCTACTGAGTCTTACTGGATTTTGCCAAATGTTAAACCCTTCAGCCCTTCCGTAGGTCGGGCCTCACATAAAGCAGTTTTACATGGGAAATTCATGTGGGTGATTGGAGGATATACTTTTAACTACAGTTCTTTTCAAATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAGGTGCTGTATCAAGGGGC
59.16
CTGAAAAAGTGGAGCAGCGC
60.39
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAGGTGCTGTATCAAGGGGC
59.16
GCTGAAAAAGTGGAGCAGCG
60.39
147
PCR template sequence:
AATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAGTGGCTTGATCGTTCCTGAAGTGAGGGGTAACGAGACCGTGCCTGAGGTGGTCACGACGTCTGGCTACGCGCTGCTCCACTTTTTCAGCGATGCTGCATAT
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-382-3p(1), mmu-miR-182-5p(1), mmu-miR-499-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCCCTCTATCAGTGGCTTGATCGTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATRNL1_601_ORF_1
0.643
-0.204758675
0.023121603
162
ORF sequence:
ATGTGGGTGATTGGAGGATATACTTTTAACTACAGTTCTTTTCAAATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAGTGGCTTGATCGTTCCTGA
Peptide sequence:
MWVIGGYTFNYSSFQMVLNYNLESSIWNVGAVSRGPLQRYGHSLALYQWLDRS
IRESfinder result
IRESfinder score
0.742958194
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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