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mmu_circAtp9a_388
Basic information of circular RNA
PanCircBase ID:
mmu_circAtp9a_388
mm39_Chr. Position ID:
chr2|168480989|168485937|-
Gene name:
Atp9a
Transcript:
ENSMUST00000109175.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
26,25,24,23
Exon/intron offsets:
0,812,1561,4792
Genomic length:
4948
Exon/intron sizes in nt:
5,81,09,65,156
Flanking exon/introns:
chr2:168479624-168480989|chr2:168485937-168489604
Splice length:
388
Other database IDs:
circAtlas: mmu-Atp9a_0009
Human Ortholog IDs:
Mature spliced Sequence:
GAAGGGAAGCAGGCCTCGCTGGCAGCGGACTTCTCCATCACCCAGTTCAAGCATCTCGGCCGCTTGCTCATGGTGCACGGTCGGAACAGCTACAAGCGCTCGGCGGCCCTCAGTCAGTTTGTGATCCACAGGAGCCTCTGCATCAGCACCATGCAGGCTGTCTTCTCGTCTGTGTTCTACTTTGCATCCGTTCCTCTCTACCAAGGCTTCCTGATCATTGGGTATTCTACCATCTACACGATGTTTCCCGTGTTCTCCCTGGTTTTGGACAAAGACGTGAAGTCGGAAGTCGCCATGTTGTATCCTGAGCTCTACAAGGACCTGCTTAAGGGGCGGCCACTGTCCTACAAGACGTTCTTAATTTGGGTGTTAATCAGCATCTATCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCACTGTCCTACAAGACGT
59.68
CTTGTAGCTGTTCCGACCGT
60.04
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCACTGTCCTACAAGACG
60.39
CTTGTAGCTGTTCCGACCGT
60.04
150
PCR template sequence:
GTCGCCATGTTGTATCCTGAGCTCTACAAGGACCTGCTTAAGGGGCGGCCACTGTCCTACAAGACGTTCTTAATTTGGGTGTTAATCAGCATCTATCAAGGAAGGGAAGCAGGCCTCGCTGGCAGCGGACTTCTCCATCACCCAGTTCAAGCATCTCGGCCGCTTGCTCATGGTGCACGGTCGGAACAGCTACAAGCGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
AGCATCTATCAAGGAAGGGAAGCAGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATP9A_388_ORF_1
0.8383
0.103273253
0.77635498
627
ORF sequence:
ATGGTGCACGGTCGGAACAGCTACAAGCGCTCGGCGGCCCTCAGTCAGTTTGTGATCCACAGGAGCCTCTGCATCAGCACCATGCAGGCTGTCTTCTCGTCTGTGTTCTACTTTGCATCCGTTCCTCTCTACCAAGGCTTCCTGATCATTGGGTATTCTACCATCTACACGATGTTTCCCGTGTTCTCCCTGGTTTTGGACAAAGACGTGAAGTCGGAAGTCGCCATGTTGTATCCTGAGCTCTACAAGGACCTGCTTAAGGGGCGGCCACTGTCCTACAAGACGTTCTTAATTTGGGTGTTAATCAGCATCTATCAAGGAAGGGAAGCAGGCCTCGCTGGCAGCGGACTTCTCCATCACCCAGTTCAAGCATCTCGGCCGCTTGCTCATGGTGCACGGTCGGAACAGCTACAAGCGCTCGGCGGCCCTCAGTCAGTTTGTGATCCACAGGAGCCTCTGCATCAGCACCATGCAGGCTGTCTTCTCGTCTGTGTTCTACTTTGCATCCGTTCCTCTCTACCAAGGCTTCCTGATCATTGGGTATTCTACCATCTACACGATGTTTCCCGTGTTCTCCCTGGTTTTGGACAAAGACGTGAAGTCGGAAGTCGCCATGTTGTATCCTGA
Peptide sequence:
MVHGRNSYKRSAALSQFVIHRSLCISTMQAVFSSVFYFASVPLYQGFLIIGYSTIYTMFPVFSLVLDKDVKSEVAMLYPELYKDLLKGRPLSYKTFLIWVLISIYQGREAGLAGSGLLHHPVQASRPLAHGARSEQLQALGGPQSVCDPQEPLHQHHAGCLLVCVLLCIRSSLPRLPDHWVFYHLHDVSRVLPGFGQRREVGSRHVVS
IRESfinder result
IRESfinder score
0.516141259
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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