top of page
mmu_circHspa4_387
Basic information of circular RNA
PanCircBase ID:
mmu_circHspa4_387
mm39_Chr. Position ID:
chr11|53155860|53157945|-
Gene name:
Hspa4
Transcript:
ENSMUST00000020630.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
16,15,14
Exon/intron offsets:
0,890,1932
Genomic length:
2085
Exon/intron sizes in nt:
10,81,26,153
Flanking exon/introns:
chr11:53153826-53155860|chr11:53157945-53159316
Splice length:
387
Other database IDs:
circAtlas: mmu-Hspa4_0007
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_115796
Human Ortholog IDs:
Mature spliced Sequence:
ACATCTCAAGCTGGATCAAAAGATAAAAAGACGGACCAACCACCTCAAGCAAAGAAGGCAAAAGTGAAGACCAGCACTGTGGACCTGCCCATTGAGAGCCAGCTGCTCTGGCAGCTGGACCGGGAGATGCTCGGCCTGTACACAGAGAATGAGGGTAAGATGATCATGCAGGATAAACTGGAGAAGGAACGGAATGACGCCAAGAATGCTGTGGAAGAGTATGTGTATGAGATGAGAGACAAGCTTAGTGGTGAATATGAGAAGTTTGTGAGTGAAGATGATCGTAATACTTTTACCTTAAAATTAGAGGATACTGAAAATTGGCTGTATGAAGATGGAGAAGATCAACCAAAGCAAGTTTATGTAGACAAATTGGCTGAATTAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGAAGATCAACCAAAGCA
57.49
CTCTCAATGGGCAGGTCCAC
60.39
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCTGTATGAAGATGGAGAAGA
58.97
TCCACAGTGCTGGTCTTCAC
59.89
149
PCR template sequence:
TACTTTTACCTTAAAATTAGAGGATACTGAAAATTGGCTGTATGAAGATGGAGAAGATCAACCAAAGCAAGTTTATGTAGACAAATTGGCTGAATTAAAAACATCTCAAGCTGGATCAAAAGATAAAAAGACGGACCAACCACCTCAAGCAAAGAAGGCAAAAGTGAAGACCAGCACTGTGGACCTGCCCATTGAGAGCC
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-9-5p(1), mmu-miR-128-3p(1), mmu-miR-22-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTGAATTAAAAACATCTCAAGCTG
siRNA sets
TGAGATGTTTTTAATTCAG, AGATGTTTTTAATTCAGCC, GAGATGTTTTTAATTCAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHSPA4_387_ORF_1
1.1549
0.383064295
0.958067596
648
ORF sequence:
ATGCTCGGCCTGTACACAGAGAATGAGGGTAAGATGATCATGCAGGATAAACTGGAGAAGGAACGGAATGACGCCAAGAATGCTGTGGAAGAGTATGTGTATGAGATGAGAGACAAGCTTAGTGGTGAATATGAGAAGTTTGTGAGTGAAGATGATCGTAATACTTTTACCTTAAAATTAGAGGATACTGAAAATTGGCTGTATGAAGATGGAGAAGATCAACCAAAGCAAGTTTATGTAGACAAATTGGCTGAATTAAAAACATCTCAAGCTGGATCAAAAGATAAAAAGACGGACCAACCACCTCAAGCAAAGAAGGCAAAAGTGAAGACCAGCACTGTGGACCTGCCCATTGAGAGCCAGCTGCTCTGGCAGCTGGACCGGGAGATGCTCGGCCTGTACACAGAGAATGAGGGTAAGATGATCATGCAGGATAAACTGGAGAAGGAACGGAATGACGCCAAGAATGCTGTGGAAGAGTATGTGTATGAGATGAGAGACAAGCTTAGTGGTGAATATGAGAAGTTTGTGAGTGAAGATGATCGTAATACTTTTACCTTAAAATTAGAGGATACTGAAAATTGGCTGTATGAAGATGGAGAAGATCAACCAAAGCAAGTTTATGTAGACAAATTGGCTGAATTAAAA
Peptide sequence:
MLGLYTENEGKMIMQDKLEKERNDAKNAVEEYVYEMRDKLSGEYEKFVSEDDRNTFTLKLEDTENWLYEDGEDQPKQVYVDKLAELKTSQAGSKDKKTDQPPQAKKAKVKTSTVDLPIESQLLWQLDREMLGLYTENEGKMIMQDKLEKERNDAKNAVEEYVYEMRDKLSGEYEKFVSEDDRNTFTLKLEDTENWLYEDGEDQPKQVYVDKLAELK
IRESfinder result
IRESfinder score
0.316352154
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page