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mmu_circAtad1_421
Basic information of circular RNA
PanCircBase ID:
mmu_circAtad1_421
mm39_Chr. Position ID:
chr19|32675839|32680038|-
Gene name:
Atad1
Transcript:
ENSMUST00000235412.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,3080,4100
Genomic length:
4199
Exon/intron sizes in nt:
201,121,99
Flanking exon/introns:
chr19:32673298-32675839|chr19:32680038-32684234
Splice length:
421
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216520, circAtlas: mmu-Atad1_0005
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_113201
Human Ortholog IDs:
Mature spliced Sequence:
GCGGAAAAACTGATGAAGCAAATTGGTGTGAAAAATGTGAAGCTTTCAGAATATGAAATGAGTATTGCTGCTCATCTAGTAGACCCTCTTAATATGCATGTTACTTGGAGTGATATAGCAGGTTTAGATGACGTCATTACAGATCTGAAAGACACAGTCATCTTACCTATCAAAAAGAAGCATTTGTTTGAGAATTCCAGACTACTGCAGCCTCCAAAAGGTGTTCTTCTGTATGGACCTCCAGGCTGTGGGAAAACATTAATTGCCAAAGCAACAGCCAAAGAAGCAGGCTGTCGGTTCATTAACCTCCAGCCTTCGACACTGACTGATAAGTGGTATGGAGAATCTCAAAAACTGGCTGCTGCTGTTTTCTCCCTTGCCATAAAGCTACAGCCTTCTATCATATTTATTGATGAAATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGCTGTTTTCTCCCTTGC
60.04
AGGGTCTACTAGATGAGCAGCA
60.09
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAAAACTGGCTGCTGCTGT
59.9
AGGGTCTACTAGATGAGCAGCA
60.09
160
PCR template sequence:
CTGACTGATAAGTGGTATGGAGAATCTCAAAAACTGGCTGCTGCTGTTTTCTCCCTTGCCATAAAGCTACAGCCTTCTATCATATTTATTGATGAAATAGGCGGAAAAACTGATGAAGCAAATTGGTGTGAAAAATGTGAAGCTTTCAGAATATGAAATGAGTATTGCTGCTCATCTAGTAGACCCTCTTAATATGCATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(2), mmu-miR-15a-5p(2), mmu-miR-322-5p(2), mmu-miR-15b-5p(1), mmu-miR-199b-3p(1), mmu-miR-182-5p(1), mmu-miR-199a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTGATGAAATAGGCGGAAAAACTGA
siRNA sets
TTTTCCGCCTATTTCATCA, TTTTTCCGCCTATTTCATC, AGTTTTTCCGCCTATTTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATAD1_421_ORF_1
0.9993
0.027845089
0.516241894
465
ORF sequence:
ATGAAGCAAATTGGTGTGAAAAATGTGAAGCTTTCAGAATATGAAATGAGTATTGCTGCTCATCTAGTAGACCCTCTTAATATGCATGTTACTTGGAGTGATATAGCAGGTTTAGATGACGTCATTACAGATCTGAAAGACACAGTCATCTTACCTATCAAAAAGAAGCATTTGTTTGAGAATTCCAGACTACTGCAGCCTCCAAAAGGTGTTCTTCTGTATGGACCTCCAGGCTGTGGGAAAACATTAATTGCCAAAGCAACAGCCAAAGAAGCAGGCTGTCGGTTCATTAACCTCCAGCCTTCGACACTGACTGATAAGTGGTATGGAGAATCTCAAAAACTGGCTGCTGCTGTTTTCTCCCTTGCCATAAAGCTACAGCCTTCTATCATATTTATTGATGAAATAGGCGGAAAAACTGATGAAGCAAATTGGTGTGAAAAATGTGAAGCTTTCAGAATATGA
Peptide sequence:
MKQIGVKNVKLSEYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKTLIAKATAKEAGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIGGKTDEANWCEKCEAFRI
IRESfinder result
IRESfinder score
0.683168138
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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