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mmu_circAtp9a_167
Basic information of circular RNA
PanCircBase ID:
mmu_circAtp9a_167
mm39_Chr. Position ID:
chr2|168480989|168481910|-
Gene name:
Atp9a
Transcript:
ENSMUST00000109175.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
26,25
Exon/intron offsets:
0,812
Genomic length:
921
Exon/intron sizes in nt:
58,109
Flanking exon/introns:
chr2:168479624-168480989|chr2:168481910-168482550
Splice length:
167
Other database IDs:
circBase: mmu_circ_0001104, CIRCpedia: MMU_CIRCpedia_11734, circAtlas: mmu-Atp9a_0014
Human Ortholog IDs:
Mature spliced Sequence:
GTATTCTACCATCTACACGATGTTTCCCGTGTTCTCCCTGGTTTTGGACAAAGACGTGAAGTCGGAAGTCGCCATGTTGTATCCTGAGCTCTACAAGGACCTGCTTAAGGGGCGGCCACTGTCCTACAAGACGTTCTTAATTTGGGTGTTAATCAGCATCTATCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCACTGTCCTACAAGACGT
59.68
CGACTTCCGACTTCACGTCT
59.76
124
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCACTGTCCTACAAGACG
60.39
CGACTTCCGACTTCACGTCT
59.76
125
PCR template sequence:
TGAGCTCTACAAGGACCTGCTTAAGGGGCGGCCACTGTCCTACAAGACGTTCTTAATTTGGGTGTTAATCAGCATCTATCAAGGTATTCTACCATCTACACGATGTTTCCCGTGTTCTCCCTGGTTTTGGACAAAGACGTGAAGTCGGAAGTCGCCATGTTGTATC
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
AGCATCTATCAAGGTATTCTACCATC
siRNA sets
AGAATACCTTGATAGATGC, TAGAATACCTTGATAGATG, GAATACCTTGATAGATGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATP9A_167_ORF_1
1.0589
0.047340258
0.16876472
207
ORF sequence:
ATGTTTCCCGTGTTCTCCCTGGTTTTGGACAAAGACGTGAAGTCGGAAGTCGCCATGTTGTATCCTGAGCTCTACAAGGACCTGCTTAAGGGGCGGCCACTGTCCTACAAGACGTTCTTAATTTGGGTGTTAATCAGCATCTATCAAGGTATTCTACCATCTACACGATGTTTCCCGTGTTCTCCCTGGTTTTGGACAAAGACGTGA
Peptide sequence:
MFPVFSLVLDKDVKSEVAMLYPELYKDLLKGRPLSYKTFLIWVLISIYQGILPSTRCFPCSPWFWTKT
IRESfinder result
IRESfinder score
0.663262232
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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