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mmu_circPdia5_301
Basic information of circular RNA
PanCircBase ID:
mmu_circPdia5_301
mm39_Chr. Position ID:
chr16|35243235|35250354|-
Gene name:
Pdia5
Transcript:
ENSMUST00000023550.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
11,10,9
Exon/intron offsets:
0,6867,7027
Genomic length:
7119
Exon/intron sizes in nt:
137,72,92
Flanking exon/introns:
chr16:35231367-35243235|chr16:35250354-35258482
Splice length:
301
Other database IDs:
circBase: hsa_circ_0121654, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_43214
Human Ortholog IDs:
Mature spliced Sequence:
GTCCTGGCTGGGATGAACGTCTACCCATCAGAGTTCGAGAACATCAAGGAAGAGTACAATGTCCGCGGCTACCCTACCATCTGCTATTTCGAGAAGGGGCGGTTTCTGTTCCCGTATGAGAACTATGGGTCCACGGCCGAGGACATCGTGGAGTGGTTGAAGAATCCACTGCCACCACAGCCCCAGGTCCCCGAGACTCCCTGGGCAGATGAGGGCGGCTCCGTTTATCACCTGACCGATGAAGACTTTGACCAGTTTGTGAAGGAGCACTCCTCTGTCCTCGTCATGTTCCACGCCCCAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGCTCCGTTTATCACCTGA
59.83
TAGCCGCGGACATTGTACTC
59.9
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGCTCCGTTTATCACCTGA
59.83
GTAGCCGCGGACATTGTACT
60.18
158
PCR template sequence:
TGGGCAGATGAGGGCGGCTCCGTTTATCACCTGACCGATGAAGACTTTGACCAGTTTGTGAAGGAGCACTCCTCTGTCCTCGTCATGTTCCACGCCCCATGTCCTGGCTGGGATGAACGTCTACCCATCAGAGTTCGAGAACATCAAGGAAGAGTACAATGTCCGCGGCTACCCTACCATCTGCTATTTCGAGAAGGGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-34a-5p(1), mmu-miR-298-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCCACGCCCCATGTCCTGGCTGGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDIA5_301_ORF_1
1.0133
0.340231202
0.723621475
408
ORF sequence:
ATGAACGTCTACCCATCAGAGTTCGAGAACATCAAGGAAGAGTACAATGTCCGCGGCTACCCTACCATCTGCTATTTCGAGAAGGGGCGGTTTCTGTTCCCGTATGAGAACTATGGGTCCACGGCCGAGGACATCGTGGAGTGGTTGAAGAATCCACTGCCACCACAGCCCCAGGTCCCCGAGACTCCCTGGGCAGATGAGGGCGGCTCCGTTTATCACCTGACCGATGAAGACTTTGACCAGTTTGTGAAGGAGCACTCCTCTGTCCTCGTCATGTTCCACGCCCCATGTCCTGGCTGGGATGAACGTCTACCCATCAGAGTTCGAGAACATCAAGGAAGAGTACAATGTCCGCGGCTACCCTACCATCTGCTATTTCGAGAAGGGGCGGTTTCTGTTCCCGTATGA
Peptide sequence:
MNVYPSEFENIKEEYNVRGYPTICYFEKGRFLFPYENYGSTAEDIVEWLKNPLPPQPQVPETPWADEGGSVYHLTDEDFDQFVKEHSSVLVMFHAPCPGWDERLPIRVREHQGRVQCPRLPYHLLFREGAVSVPV
IRESfinder result
IRESfinder score
0.47659743
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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