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mmu_circHspa4_199
Basic information of circular RNA
PanCircBase ID:
mmu_circHspa4_199
mm39_Chr. Position ID:
chr11|53179850|53183141|-
Gene name:
Hspa4
Transcript:
ENSMUST00000020630.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,3233
Genomic length:
3291
Exon/intron sizes in nt:
141,58
Flanking exon/introns:
chr11:53177802-53179850|chr11:53183141-53190886
Splice length:
199
Other database IDs:
CIRCpedia: MMU_CIRCpedia_22597, circAtlas: mmu-Hspa4_0005
circBase: hsa_circ_0007802, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_50165
Human Ortholog IDs:
Mature spliced Sequence:
GGCATGTGTTTCTTTTGGTCCTAAGAATCGTTCAATTGGAGCAGCAGCTAAGAGCCAGGTAATTTCTAATGCCAAGAACACAGTTCAAGGCTTTAAAAGATTCCATGGGCGTGCATTCTCCGATCCATTTGTGGAAGCAGAAAAATCTAATCTTGCATATGATATTGTGCAGTTGCCCACTGGATTAACGGGCATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGTGCATTCTCCGATCCAT
60.88
GCTGCTGCTCCAATTGAACG
60.46
139
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCCATGGGCGTGCATTCT
60
GCTGCTGCTCCAATTGAACG
60.46
147
PCR template sequence:
TTCCATGGGCGTGCATTCTCCGATCCATTTGTGGAAGCAGAAAAATCTAATCTTGCATATGATATTGTGCAGTTGCCCACTGGATTAACGGGCATAAAGGGCATGTGTTTCTTTTGGTCCTAAGAATCGTTCAATTGGAGCAGCAGCTAAGAGCCAGGTAATTTCTAATGCCAAGAACACAGTTCAAGGCTTTAAAAG
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-363-3p(1), mmu-miR-1904(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AACGGGCATAAAGGGCATGTGTTTCT
siRNA sets
AAACACATGCCCTTTATGC, GAAACACATGCCCTTTATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.718498987
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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