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mmu_circAlkbh1_557
Basic information of circular RNA
PanCircBase ID:
mmu_circAlkbh1_557
mm39_Chr. Position ID:
chr12|87478169|87487184|-
Gene name:
Alkbh1
Transcript:
ENSMUST00000162961.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,2719,6997,8906
Genomic length:
9015
Exon/intron sizes in nt:
194,91,163,109
Flanking exon/introns:
chr12:87476040-87478169|chr12:87487184-87490411
Splice length:
557
Other database IDs:
circAtlas: mmu-Alkbh1_0004
Human Ortholog IDs:
Mature spliced Sequence:
GTGGTCAGGTTTCCTCTGAATGTGTCCTCTGTCACTGAGCGTGATGCCGAGAGGGTGGGACTTGAACCTGTGAGCAAGTGGAGGGCCTATGGACTCGAAGGCTATCCTGGATTTATTTTCATTCCAAACCCCTTCCTCCCGGGATGCCAGAGGCACTGGGTAAAACAGTGCCTTAAGTTGTACTCCCAGAAACCTAATGTGTGTAACCTGGACAAGCACATGACTAAAGAAGAGACCCAAGGACTGTGGGAACAGAGCAAAGAGGTCCTAAGGTCTAAAGAAGTGACTAAGCGAAGACCCCGAAGTTTACTAGAGAGACTGCGTTGGGTCACCCTGGGCTACCATTATAACTGGGACAGTAAGAAATACTCAGCAGATCATTATACACCTTTCCCTTCTGACCTGGCTTTCCTCTCAGAGCAAGTCGCCACTGCCTGTGGATTTCAGGGTTTCCAAGCAGAAGCAGGGATCCTGAATTACTATCGCCTAGACTCCACACTGGGAATCCACGTGGACAGATCTGAGCTAGATCACTCCAAACCCTTGCTGTCCTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCCACACTGGGAATCCACG
60.39
AGTCCATAGGCCCTCCACTT
59.96
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCCACACTGGGAATCCACG
60.39
GCTCACAGGTTCAAGTCCCA
59.89
141
PCR template sequence:
CAGAAGCAGGGATCCTGAATTACTATCGCCTAGACTCCACACTGGGAATCCACGTGGACAGATCTGAGCTAGATCACTCCAAACCCTTGCTGTCCTTCAGGTGGTCAGGTTTCCTCTGAATGTGTCCTCTGTCACTGAGCGTGATGCCGAGAGGGTGGGACTTGAACCTGTGAGCAAGTGGAGGGCCTATGGACTCGAAG
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-199a-5p(1), mmu-miR-324-5p(1), mmu-miR-218-5p(1), mmu-miR-34b-5p(1), mmu-miR-452-3p(1), mmu-miR-188-3p(1), mmu-miR-344-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCTGTCCTTCAGGTGGTCAGGTTTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCALKBH1_557_ORF_1
0.5749
0.128123574
0.249738067
357
ORF sequence:
ATGACTAAAGAAGAGACCCAAGGACTGTGGGAACAGAGCAAAGAGGTCCTAAGGTCTAAAGAAGTGACTAAGCGAAGACCCCGAAGTTTACTAGAGAGACTGCGTTGGGTCACCCTGGGCTACCATTATAACTGGGACAGTAAGAAATACTCAGCAGATCATTATACACCTTTCCCTTCTGACCTGGCTTTCCTCTCAGAGCAAGTCGCCACTGCCTGTGGATTTCAGGGTTTCCAAGCAGAAGCAGGGATCCTGAATTACTATCGCCTAGACTCCACACTGGGAATCCACGTGGACAGATCTGAGCTAGATCACTCCAAACCCTTGCTGTCCTTCAGGTGGTCAGGTTTCCTCTGA
Peptide sequence:
MTKEETQGLWEQSKEVLRSKEVTKRRPRSLLERLRWVTLGYHYNWDSKKYSADHYTPFPSDLAFLSEQVATACGFQGFQAEAGILNYYRLDSTLGIHVDRSELDHSKPLLSFRWSGFL
IRESfinder result
IRESfinder score
0.617082123
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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