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mmu_circParn_509
Basic information of circular RNA
PanCircBase ID:
mmu_circParn_509
mm39_Chr. Position ID:
chr16|13458116|13472457|-
Gene name:
Parn
Transcript:
ENSMUST00000058884.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
13,12,11,10,9,8,7
Exon/intron offsets:
0,6990,8166,10382,11545,12392,14196
Genomic length:
14341
Exon/intron sizes in nt:
78,57,81,43,39,66,145
Flanking exon/introns:
chr16:13449437-13458116|chr16:13472457-13474779
Splice length:
509
Other database IDs:
circBase: hsa_circ_0105047, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_80920
Human Ortholog IDs:
Mature spliced Sequence:
GGATTCCATATCTGAATCAGGAAGAAGAAAGGCAGCTGAGAGAGCAATTCGATGAAAAACGGTCTCAAGCCAATGGGGCAGGAGCTCTGGCAAAATGTCCTGTGACCATCCCTGAGGATCAGAAGAAGTTTATTGACCAAGTAATAGAGAAGATAGAGGATTTCCTACAAAGTGAAGAGAAGAGGAGCCTGGAACTTGACCCATGCACTGGGTTCCAAAGAAAACTTATTTATCAGACTTTGAGTTGGAAGTATCCTAAAGGCATTCATGTTGAGACATTAGAGACTGACAAGAAGGAAAGACATATAGTTATCAGCAAGGTGGATGAAGAAGAACGCAAAAGGAGAGAGCAGGAGAAGTACACAAAGGAGCAGGAGGAGCTGAATGATGCTGTGGGGTTTTCAAGAGTCATCCATGCCATTGCTAATTCGGGGAAGCTGGTTGTGGGACACAACATGCTCTTGGATGTCATGCATACGATTCATCAGTTCTACTGCCCCCTGCCTGCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTAATTCGGGGAAGCTGGT
60.11
CCCATTGGCTTGAGACCGTT
60.61
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTAATTCGGGGAAGCTGG
60.11
CCCATTGGCTTGAGACCGTT
60.61
165
PCR template sequence:
CATCCATGCCATTGCTAATTCGGGGAAGCTGGTTGTGGGACACAACATGCTCTTGGATGTCATGCATACGATTCATCAGTTCTACTGCCCCCTGCCTGCGGGATTCCATATCTGAATCAGGAAGAAGAAAGGCAGCTGAGAGAGCAATTCGATGAAAAACGGTCTCAAGCCAATGGGGCAGGAGCTCTGGCAAAATGTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-152-3p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-532-5p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCCCTGCCTGCGGGATTCCATATCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPARN_509_ORF_1
1.0447
-0.132629231
0.071263226
180
ORF sequence:
ATGATGCTGTGGGGTTTTCAAGAGTCATCCATGCCATTGCTAATTCGGGGAAGCTGGTTGTGGGACACAACATGCTCTTGGATGTCATGCATACGATTCATCAGTTCTACTGCCCCCTGCCTGCGGGATTCCATATCTGAATCAGGAAGAAGAAAGGCAGCTGAGAGAGCAATTCGATGA
Peptide sequence:
MMLWGFQESSMPLLIRGSWLWDTTCSWMSCIRFISSTAPCLRDSISESGRRKAAERAIR
IRESfinder result
IRESfinder score
0.39859692
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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