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mmu_circAtrnl1_1394
Basic information of circular RNA
PanCircBase ID:
mmu_circAtrnl1_1394
mm39_Chr. Position ID:
chr19|57617516|57661705|+
Gene name:
Atrnl1
Transcript:
ENSMUST00000077282.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
2,3,4,5,6,7,8,9,10
Exon/intron offsets:
0,1141,9367,13335,21173,23838,25686,27970,44034
Genomic length:
44189
Exon/intron sizes in nt:
84,11,41,29,20,91,75,80,00,00,00,000
Flanking exon/introns:
chr19:57600075-57617516|chr19:57661705-57670802
Splice length:
1394
Other database IDs:
CIRCpedia: MMU_CIRCpedia_36948, circAtlas: mmu-Atrnl1_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_113215
Human Ortholog IDs:
Mature spliced Sequence:
GTTAACAGAACCTTCTGGATATTTAACAGATGGACCAATTAACTATAAATATAAAACAAAGTGTACATGGCTAATTGAAGGCTATCCAAATGCAGTGCTAAGGTTAAGATTCAATCATTTTGCTACAGAATGCAGCTGGGATCATATGTATGTTTATGATGGAGATTCTATATACGCACCTTTAGTAGCTGTACTTAGTGGCTTGATCGTTCCTGAAGTGAGGGGTAACGAGACCGTGCCTGAGGTGGTCACGACGTCTGGCTACGCGCTGCTCCACTTTTTCAGCGATGCTGCATATAACCTAACTGGCTTCAACATTTTTTATTCGATCAATTCCTGTCCTAACAACTGCTCTGGTCATGGAAAGTGTACAACCAGTGTCTCTGTTGCAAGTCAAGTGTATTGTGAATGCGACAAATACTGGAAAGGGGAAGCATGTGACATTCCTTACTGTAAAGCCAATTGTGGGAGTCCAGATCATGGCTACTGTGACCTAACAGGAGAGAAACTCTGTGTCTGCAACGATAGTTGGCAAGGCCCAGATTGTTCTCTGAATGTCCCTTCTACTGAGTCTTACTGGATTTTGCCAAATGTTAAACCCTTCAGCCCTTCCGTAGGTCGGGCCTCACATAAAGCAGTTTTACATGGGAAATTCATGTGGGTGATTGGAGGATATACTTTTAACTACAGTTCTTTTCAAATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAGGAAAACATCTTTATGTACGGAGGCAGAATGGAGACCAGTGATGGCAACGTCACCGATGAATTATGGGTGTTTAACGTACGCAGTCAATCATGGAGCACGAAAACCCCCACTGTCCTTGGCCACAGTCAGCAGTACGCTGTGGAGGGACACTCGGCACACATCATGGAGCTGGACAGTAGAGACGTGGTCATGATTGTCATATTTGGATATTCTGCAATATATGGCTATACCAGCAGCATACAGGAATACCATATCTCCTCAAACACTTGGCTAGTTCCAGAAACGAAAGGAGCCATTGTGCAAGGTGGATATGGCCACACAAGTGTGTATGACGAAGTGACCAAGTCCATCTATGTTCACGGAGGCTACAAAGCATTGCCTGGCAATAAGTACGGGCTGGTGGACGACCTCTATAAGTACGAAGTCAACACCAGGACTTGGACTATTTTGAAAGAAAGTGGGTTTGCCAGATACCTTCACTCAGCTGTTCTTATCAATGGAGCTATGCTTATTTTTGGAGGAAATACCCATAATGATACTTCCCTGAGTAACGGTGCAAAATGTTTTTCTGCCGATTTCCTGGCATATGACATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCCCTGAGTAACGGTGCA
59.68
AGCACTGCATTTGGATAGCCT
60.06
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTCCCTGAGTAACGGTGC
59.68
AGCACTGCATTTGGATAGCCT
60.06
157
PCR template sequence:
AATGGAGCTATGCTTATTTTTGGAGGAAATACCCATAATGATACTTCCCTGAGTAACGGTGCAAAATGTTTTTCTGCCGATTTCCTGGCATATGACATAGGTTAACAGAACCTTCTGGATATTTAACAGATGGACCAATTAACTATAAATATAAAACAAAGTGTACATGGCTAATTGAAGGCTATCCAAATGCAGTGCTA
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-18a-5p(1), mmu-miR-136-5p(1), mmu-miR-382-3p(1), mmu-miR-182-5p(1), mmu-miR-499-5p(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCATATGACATAGGTTAACAGAACCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATRNL1_1394_ORF_1
0.9996
0.08528871
0.997397364
1254
ORF sequence:
ATGTATGTTTATGATGGAGATTCTATATACGCACCTTTAGTAGCTGTACTTAGTGGCTTGATCGTTCCTGAAGTGAGGGGTAACGAGACCGTGCCTGAGGTGGTCACGACGTCTGGCTACGCGCTGCTCCACTTTTTCAGCGATGCTGCATATAACCTAACTGGCTTCAACATTTTTTATTCGATCAATTCCTGTCCTAACAACTGCTCTGGTCATGGAAAGTGTACAACCAGTGTCTCTGTTGCAAGTCAAGTGTATTGTGAATGCGACAAATACTGGAAAGGGGAAGCATGTGACATTCCTTACTGTAAAGCCAATTGTGGGAGTCCAGATCATGGCTACTGTGACCTAACAGGAGAGAAACTCTGTGTCTGCAACGATAGTTGGCAAGGCCCAGATTGTTCTCTGAATGTCCCTTCTACTGAGTCTTACTGGATTTTGCCAAATGTTAAACCCTTCAGCCCTTCCGTAGGTCGGGCCTCACATAAAGCAGTTTTACATGGGAAATTCATGTGGGTGATTGGAGGATATACTTTTAACTACAGTTCTTTTCAAATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAGGAAAACATCTTTATGTACGGAGGCAGAATGGAGACCAGTGATGGCAACGTCACCGATGAATTATGGGTGTTTAACGTACGCAGTCAATCATGGAGCACGAAAACCCCCACTGTCCTTGGCCACAGTCAGCAGTACGCTGTGGAGGGACACTCGGCACACATCATGGAGCTGGACAGTAGAGACGTGGTCATGATTGTCATATTTGGATATTCTGCAATATATGGCTATACCAGCAGCATACAGGAATACCATATCTCCTCAAACACTTGGCTAGTTCCAGAAACGAAAGGAGCCATTGTGCAAGGTGGATATGGCCACACAAGTGTGTATGACGAAGTGACCAAGTCCATCTATGTTCACGGAGGCTACAAAGCATTGCCTGGCAATAAGTACGGGCTGGTGGACGACCTCTATAAGTACGAAGTCAACACCAGGACTTGGACTATTTTGAAAGAAAGTGGGTTTGCCAGATACCTTCACTCAGCTGTTCTTATCAATGGAGCTATGCTTATTTTTGGAGGAAATACCCATAATGATACTTCCCTGAGTAACGGTGCAAAATGTTTTTCTGCCGATTTCCTGGCATATGACATAGGTTAA
Peptide sequence:
MYVYDGDSIYAPLVAVLSGLIVPEVRGNETVPEVVTTSGYALLHFFSDAAYNLTGFNIFYSINSCPNNCSGHGKCTTSVSVASQVYCECDKYWKGEACDIPYCKANCGSPDHGYCDLTGEKLCVCNDSWQGPDCSLNVPSTESYWILPNVKPFSPSVGRASHKAVLHGKFMWVIGGYTFNYSSFQMVLNYNLESSIWNVGAVSRGPLQRYGHSLALYQENIFMYGGRMETSDGNVTDELWVFNVRSQSWSTKTPTVLGHSQQYAVEGHSAHIMELDSRDVVMIVIFGYSAIYGYTSSIQEYHISSNTWLVPETKGAIVQGGYGHTSVYDEVTKSIYVHGGYKALPGNKYGLVDDLYKYEVNTRTWTILKESGFARYLHSAVLINGAMLIFGGNTHNDTSLSNGAKCFSADFLAYDIG
IRESfinder result
IRESfinder score
0.619139004
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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