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mmu_circPdia3_1040
Basic information of circular RNA
PanCircBase ID:
mmu_circPdia3_1040
mm39_Chr. Position ID:
chr2|121257075|121266895|+
Gene name:
Pdia3
Transcript:
ENSMUST00000028683.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,2859,5057,5679,6922,7390,8194,9326,9762
Genomic length:
9820
Exon/intron sizes in nt:
108,130,117,126,183,109,129,80,58
Flanking exon/introns:
chr2:121255123-121257075|chr2:121266895-121268066
Splice length:
1040
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_14494
Human Ortholog IDs:
Mature spliced Sequence:
ATGGAATTGTCAGCCACTTGAAGAAACAAGCAGGACCAGCTTCAGTTCCTCTCAGGACTGAGGAAGAATTTAAGAAGTTCATTAGTGATAAAGATGCCTCAGTGGTGGGTTTTTTCAGGGATTTATTCAGTGATGGGCACTCTGAATTCCTAAAAGCAGCCAGCAACTTGAGAGATAACTACCGATTTGCACACACCAACATTGAGTCTCTGGTGAAGGAGTACGATGATAATGGAGAGGGGATCACTATATTCCGTCCATTACATCTTGCTAACAAGTTTGAAGACAAAACTGTGGCATATACTGAAAAGAAAATGACCAGTGGCAAGATCAAGAAATTTATTCAGGATAGCATTTTTGGTCTCTGTCCTCATATGACGGAAGATAATAAAGATTTGATACAAGGCAAGGACTTACTCACCGCTTACTATGATGTGGACTATGAAAAGAATGCTAAAGGTTCTAACTACTGGAGAAACAGGGTCATGATGGTGGCAAAGAAATTCCTTGATGCTGGACACAAACTCAACTTTGCTGTAGCTAGCCGTAAAACCTTTAGCCATGAACTGTCAGATTTTGGCTTAGAAAGCACTACTGGAGAGGTTCCTGTTGTGGCTATCAGAACTGCTAAAGGAGAGAAGTTTGTCATGCAGGAGGAGTTCTCGCGAGATGGCAAGGCTCTTGAACAGTTCCTGCAAGAATACTTTGATGGCAACTTGAAGAGATACCTGAAGTCTGAACCCATCCCAGAGTCCAACGAAGGGCCTGTCAAGGTTGTGGTAGCAGAGAATTTTGATGACATAGTGAATGAAGAAGATAAGGACGTGCTGATTGAATTTTACGCCCCTTGGTGTGGCCACTGTAAGAATCTGGAACCCAAGTATAAAGAGCTGGGAGAAAAACTCAGCAAAGATCCAAATATTGTCATAGCCAAGATGGATGCCACAGCCAATGATGTGCCTTCTCCATATGAAGTCAAGGGTTTTCCTACCATCTACTTCTCACCAGCCAACAAGAAGCTAACTCCAAAGAAGTATGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAATGATGTGCCTTCTCC
59.26
GAACTGAAGCTGGTCCTGCT
59.96
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGCCAATGATGTGCCTTC
58.82
GAACTGAAGCTGGTCCTGCT
59.96
144
PCR template sequence:
TGCCACAGCCAATGATGTGCCTTCTCCATATGAAGTCAAGGGTTTTCCTACCATCTACTTCTCACCAGCCAACAAGAAGCTAACTCCAAAGAAGTATGAAATGGAATTGTCAGCCACTTGAAGAAACAAGCAGGACCAGCTTCAGTTCCTCTCAGGACTGAGGAAGAATTTAAGAAGTTCATTAGTGATAAAGATGCCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-19b-3p(1), mmu-miR-19a-3p(1), mmu-miR-7a-5p(1), mmu-miR-184-3p(1), mmu-miR-10a-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-541-5p(1), mmu-miR-544-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGAAGTATGAAATGGAATTGTCAG
siRNA sets
AATTCCATTTCATACTTCT, CAATTCCATTTCATACTTC, ATTCCATTTCATACTTCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDIA3_1040_ORF_1
1.1338
0.29839979
0.968549048
747
ORF sequence:
ATGACCAGTGGCAAGATCAAGAAATTTATTCAGGATAGCATTTTTGGTCTCTGTCCTCATATGACGGAAGATAATAAAGATTTGATACAAGGCAAGGACTTACTCACCGCTTACTATGATGTGGACTATGAAAAGAATGCTAAAGGTTCTAACTACTGGAGAAACAGGGTCATGATGGTGGCAAAGAAATTCCTTGATGCTGGACACAAACTCAACTTTGCTGTAGCTAGCCGTAAAACCTTTAGCCATGAACTGTCAGATTTTGGCTTAGAAAGCACTACTGGAGAGGTTCCTGTTGTGGCTATCAGAACTGCTAAAGGAGAGAAGTTTGTCATGCAGGAGGAGTTCTCGCGAGATGGCAAGGCTCTTGAACAGTTCCTGCAAGAATACTTTGATGGCAACTTGAAGAGATACCTGAAGTCTGAACCCATCCCAGAGTCCAACGAAGGGCCTGTCAAGGTTGTGGTAGCAGAGAATTTTGATGACATAGTGAATGAAGAAGATAAGGACGTGCTGATTGAATTTTACGCCCCTTGGTGTGGCCACTGTAAGAATCTGGAACCCAAGTATAAAGAGCTGGGAGAAAAACTCAGCAAAGATCCAAATATTGTCATAGCCAAGATGGATGCCACAGCCAATGATGTGCCTTCTCCATATGAAGTCAAGGGTTTTCCTACCATCTACTTCTCACCAGCCAACAAGAAGCTAACTCCAAAGAAGTATGAAATGGAATTGTCAGCCACTTGA
Peptide sequence:
MTSGKIKKFIQDSIFGLCPHMTEDNKDLIQGKDLLTAYYDVDYEKNAKGSNYWRNRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTTGEVPVVAIRTAKGEKFVMQEEFSRDGKALEQFLQEYFDGNLKRYLKSEPIPESNEGPVKVVVAENFDDIVNEEDKDVLIEFYAPWCGHCKNLEPKYKELGEKLSKDPNIVIAKMDATANDVPSPYEVKGFPTIYFSPANKKLTPKKYEMELSAT
IRESfinder result
IRESfinder score
0.505634727
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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