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mmu_circPafah1b1_295
Basic information of circular RNA
PanCircBase ID:
mmu_circPafah1b1_295
mm39_Chr. Position ID:
chr11|74581351|74590346|-
Gene name:
Pafah1b1
Transcript:
ENSMUST00000126341.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,8785
Genomic length:
8995
Exon/intron sizes in nt:
85,210
Flanking exon/introns:
chr11:74581110-74581351|chr11:74590346-74614824
Splice length:
295
Other database IDs:
CIRCpedia: MMU_CIRCpedia_227219, circAtlas: mmu-Pafah1b1_0016
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTGGAATGAACCTTACTTGTTGACTGGTTGCTGATTGGATTCACTTGAAAAAAAGAATCATTTTTCCCTCTGTGGAAGCCACATAGTGGCATATTTAATTCAAATCCAGGGATCACAACTTTTGATTTTTCTGGAGGGACATACCACTATATCAAATAAGCTTGACATTACAGCCAAAATGGTGCTGTCCCAGAGACAACGAGATGAACTAAATCGAGCTATAGCAGATTATCTTCGTTCAAATGGCTATGAAGAGGCATATTCCGTTTTTAAAAAGGAAGCTGAACTAGATATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTTCAAATGGCTATGAAGAGGC
60.24
TGGCTTCCACAGAGGGAAAA
59.15
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGTTCAAATGGCTATGAAGAGGC
60.24
TGGCTTCCACAGAGGGAAAAA
59.78
141
PCR template sequence:
ACAACGAGATGAACTAAATCGAGCTATAGCAGATTATCTTCGTTCAAATGGCTATGAAGAGGCATATTCCGTTTTTAAAAAGGAAGCTGAACTAGATATGGTGGAATGAACCTTACTTGTTGACTGGTTGCTGATTGGATTCACTTGAAAAAAAGAATCATTTTTCCCTCTGTGGAAGCCACATAGTGGCATATTTAATT
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-29b-3p(1), mmu-miR-29c-3p(1), mmu-miR-382-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAACTAGATATGGTGGAATGAACCT
siRNA sets
TTCATTCCACCATATCTAG, ATTCCACCATATCTAGTTC, TCATTCCACCATATCTAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPAFAH1B1_295_ORF_1
1.1592
0.183738798
0.191434888
126
ORF sequence:
ATGGTGCTGTCCCAGAGACAACGAGATGAACTAAATCGAGCTATAGCAGATTATCTTCGTTCAAATGGCTATGAAGAGGCATATTCCGTTTTTAAAAAGGAAGCTGAACTAGATATGGTGGAATGA
Peptide sequence:
MVLSQRQRDELNRAIADYLRSNGYEEAYSVFKKEAELDMVE
IRESfinder result
IRESfinder score
0.841032576
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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