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mmu_circHells_334
Basic information of circular RNA
PanCircBase ID:
mmu_circHells_334
mm39_Chr. Position ID:
chr19|38948112|38953927|+
Gene name:
Hells
Transcript:
ENSMUST00000025965.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
19,20,21
Exon/intron offsets:
0,4928,5738
Genomic length:
5815
Exon/intron sizes in nt:
160,97,77
Flanking exon/introns:
chr19:38947604-38948112|chr19:38953927-38956176
Splice length:
334
Other database IDs:
circAtlas: mmu-Hells_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_76684
Human Ortholog IDs:
Mature spliced Sequence:
AATCCTCAGTCTGATCTCCAGGCTCAAGATAGATGTCATAGAATTGGTCAGACAAAGCCAGTTGTTGTGTATCGTCTTGTAACAGCAAATACTATTGACCAGAAAATTGTGGAAAGAGCAGCTGCTAAAAGAAAGTTGGAGAAGTTGATAATCCATAAAAATCATTTCAAAGGTGGTCAGTCTGGGTTAAGTCAATCTAAGAATTTCTTAGATGCAAAGGAATTAATGGAGTTATTAAAATCTAGAGATTATGAAAGGGAAGTAAAAGGATCCAGAGAGAAGGTCATTAGTGACGAAGATCTAGAATTACTGTTGGATCGAAGTGATCTCATTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGATCCAGAGAGAAGGTCA
56.76
AGACGATACACAACAACTGGCT
59.96
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGATCCAGAGAGAAGGTCA
57.52
AGACGATACACAACAACTGGCT
59.96
146
PCR template sequence:
TTAAAATCTAGAGATTATGAAAGGGAAGTAAAAGGATCCAGAGAGAAGGTCATTAGTGACGAAGATCTAGAATTACTGTTGGATCGAAGTGATCTCATTGAATCCTCAGTCTGATCTCCAGGCTCAAGATAGATGTCATAGAATTGGTCAGACAAAGCCAGTTGTTGTGTATCGTCTTGTAACAGCAAATACTATTGACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-136-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
AGTGATCTCATTGAATCCTCAGTCTG
siRNA sets
TGAGGATTCAATGAGATCA, AGACTGAGGATTCAATGAG, GAGGATTCAATGAGATCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHELLS_334_ORF_1
0.7695
0.091272111
0.071294404
123
ORF sequence:
ATGGAGTTATTAAAATCTAGAGATTATGAAAGGGAAGTAAAAGGATCCAGAGAGAAGGTCATTAGTGACGAAGATCTAGAATTACTGTTGGATCGAAGTGATCTCATTGAATCCTCAGTCTGA
Peptide sequence:
MELLKSRDYEREVKGSREKVISDEDLELLLDRSDLIESSV
IRESfinder result
IRESfinder score
0.549147056
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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