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mmu_circAtrnl1_617
Basic information of circular RNA
PanCircBase ID:
mmu_circAtrnl1_617
mm39_Chr. Position ID:
chr19|57703017|57744050|+
Gene name:
Atrnl1
Transcript:
ENSMUST00000077282.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
19,20,21,22,23,24
Exon/intron offsets:
0,16966,25594,37044,38639,40875
Genomic length:
41033
Exon/intron sizes in nt:
1,38,94,53,95,79,158
Flanking exon/introns:
chr19:57695565-57703017|chr19:57744050-57766315
Splice length:
617
Other database IDs:
circAtlas: mmu-Atrnl1_0030
circAtlas: hsa-ATRNL1_0040, CIRCpedia: HSA_CIRCpedia_120054
Human Ortholog IDs:
Mature spliced Sequence:
CTTGCCAGTGTAATGGACACAGCACGTGCATCAACAACAACGTCTGTGAGCAGTGTAAGAATCTCACCACTGGGCGACAGTGTCAGGAATGCATGCCAGGGTACTATGGAGACCCAACCAACGGTGGGCAGTGCACAGCTTGCACGTGCGGCGGCCATGCGAACGTCTGTCACCTGCACACGGGAAAGTGTTTTTGCACAACCAAGGGGATCAAGGGTGACCAGTGCCAGCTATGTGACTCTGAAAATCGCTATGTTGGTAATCCACTTAGGGGGACATGCTATTACAGTCTTCTGATTGACTACCAGTTTACCTTCAGCTTGCTGCAGGAAGATGACCGGCACCACACTGCCATCAACTTCATCGCCAACCCAGAGCAGTCAAACAAAAACTTGGACATTTCGATTAATGCTTCCAACAACTTTAATCTCAACATTACGTGGTCAGTTGGCTCAACAGGTGGAACCATATCTGGGGAAGAGACTCCTATAGTTTCTAAGACAAATATAAAGGAATACAGAGACAGCTTTTCCTATGAAAAATTTAACTTCAGAAGCAATCCTAATATCACATTTTATGTGTATGTCAGCAACTTCTCCTGGCCTATTAAAATACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGTATGTCAGCAACTTCTCCT
59.68
CCTGGCATGCATTCCTGACA
60.68
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGTATGTCAGCAACTTCTCC
58.34
CCTGGCATGCATTCCTGACA
60.68
140
PCR template sequence:
CAGAGACAGCTTTTCCTATGAAAAATTTAACTTCAGAAGCAATCCTAATATCACATTTTATGTGTATGTCAGCAACTTCTCCTGGCCTATTAAAATACAGCTTGCCAGTGTAATGGACACAGCACGTGCATCAACAACAACGTCTGTGAGCAGTGTAAGAATCTCACCACTGGGCGACAGTGTCAGGAATGCATGCCAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-382-5p(1), mmu-miR-541-5p(1), mmu-miR-324-3p(1), mmu-miR-34b-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TATTAAAATACAGCTTGCCAGTGTAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATRNL1_617_ORF_1
0.7382
0.097420747
0.91915685
822
ORF sequence:
ATGCCAGGGTACTATGGAGACCCAACCAACGGTGGGCAGTGCACAGCTTGCACGTGCGGCGGCCATGCGAACGTCTGTCACCTGCACACGGGAAAGTGTTTTTGCACAACCAAGGGGATCAAGGGTGACCAGTGCCAGCTATGTGACTCTGAAAATCGCTATGTTGGTAATCCACTTAGGGGGACATGCTATTACAGTCTTCTGATTGACTACCAGTTTACCTTCAGCTTGCTGCAGGAAGATGACCGGCACCACACTGCCATCAACTTCATCGCCAACCCAGAGCAGTCAAACAAAAACTTGGACATTTCGATTAATGCTTCCAACAACTTTAATCTCAACATTACGTGGTCAGTTGGCTCAACAGGTGGAACCATATCTGGGGAAGAGACTCCTATAGTTTCTAAGACAAATATAAAGGAATACAGAGACAGCTTTTCCTATGAAAAATTTAACTTCAGAAGCAATCCTAATATCACATTTTATGTGTATGTCAGCAACTTCTCCTGGCCTATTAAAATACAGCTTGCCAGTGTAATGGACACAGCACGTGCATCAACAACAACGTCTGTGAGCAGTGTAAGAATCTCACCACTGGGCGACAGTGTCAGGAATGCATGCCAGGGTACTATGGAGACCCAACCAACGGTGGGCAGTGCACAGCTTGCACGTGCGGCGGCCATGCGAACGTCTGTCACCTGCACACGGGAAAGTGTTTTTGCACAACCAAGGGGATCAAGGGTGACCAGTGCCAGCTATGTGACTCTGAAAATCGCTATGTTGGTAATCCACTTAGGGGGACATGCTATTACAGTCTTCTGA
Peptide sequence:
MPGYYGDPTNGGQCTACTCGGHANVCHLHTGKCFCTTKGIKGDQCQLCDSENRYVGNPLRGTCYYSLLIDYQFTFSLLQEDDRHHTAINFIANPEQSNKNLDISINASNNFNLNITWSVGSTGGTISGEETPIVSKTNIKEYRDSFSYEKFNFRSNPNITFYVYVSNFSWPIKIQLASVMDTARASTTTSVSSVRISPLGDSVRNACQGTMETQPTVGSAQLARAAAMRTSVTCTRESVFAQPRGSRVTSASYVTLKIAMLVIHLGGHAITVF
IRESfinder result
IRESfinder score
0.542053965
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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