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mmu_circAlpk1_386
Basic information of circular RNA
PanCircBase ID:
mmu_circAlpk1_386
mm39_Chr. Position ID:
chr3|127518023|127523150|-
Gene name:
Alpk1
Transcript:
ENSMUST00000029662.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,4896
Genomic length:
5127
Exon/intron sizes in nt:
155,231
Flanking exon/introns:
chr3:127489401-127518023|chr3:127523150-127573809
Splice length:
386
Other database IDs:
CIRCpedia: MMU_CIRCpedia_220024, circAtlas: mmu-Alpk1_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTACCTCAGCCTTCAAGGGCCTTCTTTATTGAGAATCAATGCCTCTCCTAGGTAATTGATCACCATAGACCCAGGGAGACTCAATTCATCCTGGAGGGTGGGTAATCGTCATGAATAATCAAGATGCCGTGGCTTCGATACTGCATGAGTGCAAGCAAGTGCTGGATCGTCTCTTGTTGGAAACGCCAGATGTGTCTACAGAGGACAAGAGTGAGGACCAGCGGTGCAGAGCTTCACTCCCCAGCGAGTTAAGGACCCTGATCCAGGAGGCAGAGGAAATGAAGTGGCCCTTCGTGCCTGAAAAGTGGCAATACAAACAAGCCATGAGCCCAGAGGACAAAACAAACCTGCAAGATGTGATTGGCGCCGGGCTGCAGCAGTTACTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAACAAGCCATGAGCCCAGA
59.89
TCTCCCTGGGTCTATGGTGA
58.98
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAACAAGCCATGAGCCCAGA
59.89
AGTCTCCCTGGGTCTATGGT
58.98
153
PCR template sequence:
GCCCTTCGTGCCTGAAAAGTGGCAATACAAACAAGCCATGAGCCCAGAGGACAAAACAAACCTGCAAGATGTGATTGGCGCCGGGCTGCAGCAGTTACTGGTACCTCAGCCTTCAAGGGCCTTCTTTATTGAGAATCAATGCCTCTCCTAGGTAATTGATCACCATAGACCCAGGGAGACTCAATTCATCCTGGAGGGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-127-5p(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGCAGTTACTGGTACCTCAGCCTT
siRNA sets
CTGAGGTACCAGTAACTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCALPK1_386_ORF_1
1.0259
0.247421086
0.504494836
327
ORF sequence:
ATGAATAATCAAGATGCCGTGGCTTCGATACTGCATGAGTGCAAGCAAGTGCTGGATCGTCTCTTGTTGGAAACGCCAGATGTGTCTACAGAGGACAAGAGTGAGGACCAGCGGTGCAGAGCTTCACTCCCCAGCGAGTTAAGGACCCTGATCCAGGAGGCAGAGGAAATGAAGTGGCCCTTCGTGCCTGAAAAGTGGCAATACAAACAAGCCATGAGCCCAGAGGACAAAACAAACCTGCAAGATGTGATTGGCGCCGGGCTGCAGCAGTTACTGGTACCTCAGCCTTCAAGGGCCTTCTTTATTGAGAATCAATGCCTCTCCTAG
Peptide sequence:
MNNQDAVASILHECKQVLDRLLLETPDVSTEDKSEDQRCRASLPSELRTLIQEAEEMKWPFVPEKWQYKQAMSPEDKTNLQDVIGAGLQQLLVPQPSRAFFIENQCLS
IRESfinder result
IRESfinder score
0.472879988
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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