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mmu_circAtxn1_447
Basic information of circular RNA
PanCircBase ID:
mmu_circAtxn1_447
mm39_Chr. Position ID:
chr13|45851296|46005932|-
Gene name:
Atxn1
Transcript:
ENSMUST00000091628.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,37294,97688,154507
Genomic length:
154636
Exon/intron sizes in nt:
125,64,129,129
Flanking exon/introns:
chr13:45722056-45851296|chr13:46005932-46109930
Splice length:
447
Other database IDs:
CIRCpedia: MMU_CIRCpedia_20657, circAtlas: mmu-Atxn1_0008
Human Ortholog IDs:
Mature spliced Sequence:
ATTGCAGCATCCTGGAACAGAATGAAAGGATCTGTGTTGAAACAGCTACAGTAGGGTTACAGTAGACCCTGAGAAAAACAGAGTGGACTTCAGCCTGCACGGATGAGCTTGAAGCAGGAATGGTTTGGGGTTCAGGCCTCTTACACTGAATTTCTCTACTGCCACCCTTTCTACTCAAGCAACATCTTCAGGAAAAGATCTCCCGGGAAGGAAGTGGCTGCTTGTGGCTTTGCACTGTGATGAAGGCAAATGGTACAGTTTTCCAAAGAAAATAGACCAAAACTTTCTTCTTGAGAAGAAACAAACCTGCTGTTGGCAGAGGGTATTTCTAACCTCTCTGCGAAAGAAAGAAAGACACCACCAGAACCTGGGCATCCCAGCTGCTGAGGGAAGTTTCCATGGTGAAGTCTCAGGGAGGCTTCCTGGGAGCAGAGCATAGTGAATGCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCTGAGGGAAGTTTCC
59.96
GCAGGCTGAAGTCCACTCTG
60.67
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCTGAGGGAAGTTTCC
59.96
CAGGCTGAAGTCCACTCTGT
59.32
166
PCR template sequence:
AAGAAAGACACCACCAGAACCTGGGCATCCCAGCTGCTGAGGGAAGTTTCCATGGTGAAGTCTCAGGGAGGCTTCCTGGGAGCAGAGCATAGTGAATGCTATTGCAGCATCCTGGAACAGAATGAAAGGATCTGTGTTGAAACAGCTACAGTAGGGTTACAGTAGACCCTGAGAAAAACAGAGTGGACTTCAGCCTGCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-19b-3p(1), mmu-miR-205-5p(1), mmu-miR-130a-3p(1), mmu-miR-19a-3p(1), mmu-miR-125b-5p(1), mmu-miR-125a-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATAGTGAATGCTATTGCAGCATCCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATXN1_447_ORF_3
0.4399
0.06012894
0.033006138
114
ORF sequence:
ATGGTGAAGTCTCAGGGAGGCTTCCTGGGAGCAGAGCATAGTGAATGCTATTGCAGCATCCTGGAACAGAATGAAAGGATCTGTGTTGAAACAGCTACAGTAGGGTTACAGTAG
Peptide sequence:
MVKSQGGFLGAEHSECYCSILEQNERICVETATVGLQ
IRESfinder result
IRESfinder score
0.683211823
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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