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mmu_ciHspa5_293

Basic information of circular RNA
PanCircBase ID:

mmu_ciHspa5_293

mm39_Chr. Position ID:

chr2|34665245|34665538|+

Gene name:

Hspa5

Transcript:

ENSMUST00000028222.13

CircRNA type:

Circular intronic (ci)RNA

Exon/Intron count:

1

Exon/intron indexes:

8

Exon/intron offsets:

0

Genomic length:

293

Exon/intron sizes in nt:

293

Flanking exon/introns:

chr2:34665245-34665562

Splice length:

293

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

GTAATTAAACGTTCACAAATATTGTATGTTTTGAAAGGATGTGATCTGGGTTTCACAATATTATTAAACAATATTATTAAATAAGTTAAACTATTATCCTCCCAGGGAAAGAAGTATGTTTTGTAACTCAAATGAAGAGGTTCTTAGTTGAACCAGTGTTGAATTTTTTTCATGTTAACTAGCTTTTGTAATACAAGGTCAGAGGGGCTTACAATGCTTTGAAGAGTTGAAATTAAGAGCAGTAGCACCCAGTGAGTTAATGTAGGGATCCCAGTGCCCTGGCTTTGTCAATA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CAAGGTCAGAGGGGCTTACA

59.02

GTGAAACCCAGATCACATCCT

57.64

156

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GTCAGAGGGGCTTACAATGCT

60.07

GTGAAACCCAGATCACATCCT

57.64

152

PCR template sequence:

CAAGGTCAGAGGGGCTTACAATGCTTTGAAGAGTTGAAATTAAGAGCAGTAGCACCCAGTGAGTTAATGTAGGGATCCCAGTGCCCTGGCTTTGTCAATAGTAATTAAACGTTCACAAATATTGTATGTTTTGAAAGGATGTGATCTGGGTTTCACAATATTATTAAACAATATTATTAAATAAGTTAAACTATTATCCT

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

6

Interacting miRNAs (#binding sites)

mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-221-3p(1), mmu-miR-335-5p(1), mmu-miR-222-3p(1), mmu-miR-3087-3p(1)

siRNAs for circular RNA silencing
Junction sequence

GGCTTTGTCAATAGTAATTAAACGTT

siRNA sets

AACGTTTAATTACTATTGA,AATTACTATTGACAAAGCC,TAATTACTATTGACAAAGC

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

0.904264908

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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