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mmu_circAtrnl1_1616
Basic information of circular RNA
PanCircBase ID:
mmu_circAtrnl1_1616
mm39_Chr. Position ID:
chr19|57680198|57766377|+
Gene name:
Atrnl1
Transcript:
ENSMUST00000077282.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
14,15,16,17,18,19,20,21,22,23,24,25
Exon/intron offsets:
0,4407,7750,10221,15148,22819,39785,48413,59863,61458,63694,86117
Genomic length:
86179
Exon/intron sizes in nt:
133,182,214,189,219,138,94,53,95,79,158,62
Flanking exon/introns:
chr19:57675209-57680198|chr19:57766377-57785856
Splice length:
1616
Other database IDs:
circBase: mmu_circ_0007929, CIRCpedia: MMU_CIRCpedia_23915, circAtlas: mmu-Atrnl1_0055
Human Ortholog IDs:
Mature spliced Sequence:
TCTGTCAGAAACTACACTAAATGTCATATAAGAAATGAGCAGATTTGTAACAAACTTACAAGCTGTAAAAGCTGTTCACTCAACTTGAATTGCCAGTGGGATCAGCGGCAGCAGGAATGTCAGGCTTTGCCAGCTCACCTTTGTGGAGAAGGCTGGAATCATGTTGGGGACGCTTGTCTTCGAATCAATTCCAGTCGAGAAAGCTATGATAATGCCAAACTTTATTGCTATAACCTCAGTGGAAATCTCGCCTCCCTGACCACGTCCAAGGAGGTGGAGTTTGTGTTGGATGAAATACAGAAGTTCACACAGCAGAAAGTGTCACCGTGGGTAGGCCTACGCAAGATCAACATATCCTACTGGGGATGGGAGGACATGTCTCCTTTCACAAATACAAGCCTGCAGTGGCTTCCTGGTGAGCCAAATGACTCTGGATTCTGTGCCTACTTAGAAAGGGCTGCAGTGGCAGGGTTAAAAGCAAACCCTTGCACATCCATGGCAGATGGACTCGTTTGTGAAAAGCCTGTAGTAAGCCCAAATCAGAACGCGAGGCCGTGCAAGAAGCCGTGCTCCCTGAGGACCTCCTGCGCCAACTGCACGAGCAGCGGCATGGAGTGCATGTGGTGCAGCAGCACGAAGCGCTGCGTGGACTCCAACGCTTACATCATCTCCTTTCCCTACGGACAGTGCCTGGAGTGGCAGACTGCCACCTGCTCGCCTCAAAATTGTTCTGGGTTAAGAACCTGTGGACAGTGCTTGGAGCAGCCTGGGTGTGGCTGGTGCAACGATCCTAGTAACACAGGAAGAGGCTATTGCATCGAAGGGTCTTCCCGGGGCCCAATGAAACTCGCGGGGGTCCACAACAGTGACGTGGTTCTTGACACCAGCCTCTGCCCCAAGGAGAAGAACTACGAGTGGTCTTTTATCCAGTGTCCAGCTTGCCAGTGTAATGGACACAGCACGTGCATCAACAACAACGTCTGTGAGCAGTGTAAGAATCTCACCACTGGGCGACAGTGTCAGGAATGCATGCCAGGGTACTATGGAGACCCAACCAACGGTGGGCAGTGCACAGCTTGCACGTGCGGCGGCCATGCGAACGTCTGTCACCTGCACACGGGAAAGTGTTTTTGCACAACCAAGGGGATCAAGGGTGACCAGTGCCAGCTATGTGACTCTGAAAATCGCTATGTTGGTAATCCACTTAGGGGGACATGCTATTACAGTCTTCTGATTGACTACCAGTTTACCTTCAGCTTGCTGCAGGAAGATGACCGGCACCACACTGCCATCAACTTCATCGCCAACCCAGAGCAGTCAAACAAAAACTTGGACATTTCGATTAATGCTTCCAACAACTTTAATCTCAACATTACGTGGTCAGTTGGCTCAACAGGTGGAACCATATCTGGGGAAGAGACTCCTATAGTTTCTAAGACAAATATAAAGGAATACAGAGACAGCTTTTCCTATGAAAAATTTAACTTCAGAAGCAATCCTAATATCACATTTTATGTGTATGTCAGCAACTTCTCCTGGCCTATTAAAATACAGATTGCGTTTTCACAACACAACACAATCATGGATCTCGTGCAGTTCTTTGTCACCTTCTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAATCATGGATCTCGTGCAGT
60.09
CCCACTGGCAATTCAAGTTGA
59.04
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAATCATGGATCTCGTGCAGT
60.09
CCCACTGGCAATTCAAGTTGAG
60.03
141
PCR template sequence:
TGTATGTCAGCAACTTCTCCTGGCCTATTAAAATACAGATTGCGTTTTCACAACACAACACAATCATGGATCTCGTGCAGTTCTTTGTCACCTTCTTCAGTCTGTCAGAAACTACACTAAATGTCATATAAGAAATGAGCAGATTTGTAACAAACTTACAAGCTGTAAAAGCTGTTCACTCAACTTGAATTGCCAGTGGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-298-5p(1), mmu-miR-138-5p(1), mmu-miR-434-5p(1), mmu-miR-433-5p(1), mmu-miR-363-3p(1), mmu-miR-382-5p(1), mmu-miR-370-3p(1), mmu-miR-541-5p(1), mmu-miR-324-3p(1), mmu-miR-34b-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-190b-5p(1), mmu-miR-129-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCACCTTCTTCAGTCTGTCAGAAACT
siRNA sets
TCTGACAGACTGAAGAAGG, TGACAGACTGAAGAAGGTG, GTTTCTGACAGACTGAAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATRNL1_1616_ORF_1
0.7211
0.14453282
0.996958714
1272
ORF sequence:
ATGTCTCCTTTCACAAATACAAGCCTGCAGTGGCTTCCTGGTGAGCCAAATGACTCTGGATTCTGTGCCTACTTAGAAAGGGCTGCAGTGGCAGGGTTAAAAGCAAACCCTTGCACATCCATGGCAGATGGACTCGTTTGTGAAAAGCCTGTAGTAAGCCCAAATCAGAACGCGAGGCCGTGCAAGAAGCCGTGCTCCCTGAGGACCTCCTGCGCCAACTGCACGAGCAGCGGCATGGAGTGCATGTGGTGCAGCAGCACGAAGCGCTGCGTGGACTCCAACGCTTACATCATCTCCTTTCCCTACGGACAGTGCCTGGAGTGGCAGACTGCCACCTGCTCGCCTCAAAATTGTTCTGGGTTAAGAACCTGTGGACAGTGCTTGGAGCAGCCTGGGTGTGGCTGGTGCAACGATCCTAGTAACACAGGAAGAGGCTATTGCATCGAAGGGTCTTCCCGGGGCCCAATGAAACTCGCGGGGGTCCACAACAGTGACGTGGTTCTTGACACCAGCCTCTGCCCCAAGGAGAAGAACTACGAGTGGTCTTTTATCCAGTGTCCAGCTTGCCAGTGTAATGGACACAGCACGTGCATCAACAACAACGTCTGTGAGCAGTGTAAGAATCTCACCACTGGGCGACAGTGTCAGGAATGCATGCCAGGGTACTATGGAGACCCAACCAACGGTGGGCAGTGCACAGCTTGCACGTGCGGCGGCCATGCGAACGTCTGTCACCTGCACACGGGAAAGTGTTTTTGCACAACCAAGGGGATCAAGGGTGACCAGTGCCAGCTATGTGACTCTGAAAATCGCTATGTTGGTAATCCACTTAGGGGGACATGCTATTACAGTCTTCTGATTGACTACCAGTTTACCTTCAGCTTGCTGCAGGAAGATGACCGGCACCACACTGCCATCAACTTCATCGCCAACCCAGAGCAGTCAAACAAAAACTTGGACATTTCGATTAATGCTTCCAACAACTTTAATCTCAACATTACGTGGTCAGTTGGCTCAACAGGTGGAACCATATCTGGGGAAGAGACTCCTATAGTTTCTAAGACAAATATAAAGGAATACAGAGACAGCTTTTCCTATGAAAAATTTAACTTCAGAAGCAATCCTAATATCACATTTTATGTGTATGTCAGCAACTTCTCCTGGCCTATTAAAATACAGATTGCGTTTTCACAACACAACACAATCATGGATCTCGTGCAGTTCTTTGTCACCTTCTTCAGTCTGTCAGAAACTACACTAAATGTCATATAA
Peptide sequence:
MSPFTNTSLQWLPGEPNDSGFCAYLERAAVAGLKANPCTSMADGLVCEKPVVSPNQNARPCKKPCSLRTSCANCTSSGMECMWCSSTKRCVDSNAYIISFPYGQCLEWQTATCSPQNCSGLRTCGQCLEQPGCGWCNDPSNTGRGYCIEGSSRGPMKLAGVHNSDVVLDTSLCPKEKNYEWSFIQCPACQCNGHSTCINNNVCEQCKNLTTGRQCQECMPGYYGDPTNGGQCTACTCGGHANVCHLHTGKCFCTTKGIKGDQCQLCDSENRYVGNPLRGTCYYSLLIDYQFTFSLLQEDDRHHTAINFIANPEQSNKNLDISINASNNFNLNITWSVGSTGGTISGEETPIVSKTNIKEYRDSFSYEKFNFRSNPNITFYVYVSNFSWPIKIQIAFSQHNTIMDLVQFFVTFFSLSETTLNVI
IRESfinder result
IRESfinder score
0.530870303
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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