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mmu_circXrn1_447
Basic information of circular RNA
PanCircBase ID:
mmu_circXrn1_447
mm39_Chr. Position ID:
chr9|95863827|95871059|+
Gene name:
Xrn1
Transcript:
ENSMUST00000034981.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
14,15,16
Exon/intron offsets:
0,3409,7062
Genomic length:
7232
Exon/intron sizes in nt:
15,71,20,170
Flanking exon/introns:
chr9:95861277-95863827|chr9:95871059-95873028
Splice length:
447
Other database IDs:
CIRCpedia: MMU_CIRCpedia_35230, circAtlas: mmu-Xrn1_0030
circAtlas: hsa-XRN1_0138, CIRCpedia: HSA_CIRCpedia_374719
Human Ortholog IDs:
Mature spliced Sequence:
GTACTATCCCTATCATTACGCACCCTTCCTATCTGATATCCGCAGTATCAGTACACTCAAAATCCATTTTGAACTCGGAAAACCCTTCAAGCCATTCGAGCAGCTGCTTGCTGTACTTCCATCGGCTAGTAAAAATTTGCTTCCTACATGCTACCAGCATTTGATGACCAGTGAAGACTCGCCAATTATAGAATATTATCCACCTGATTTCAAAACTGATCTAAATGGGAAACAACAGGAATGGGAAGCTGTGGTATTAATACCGTTTATTGATGAGACGCGATTATTGGAAGCCATGGAGACATGTAACCACTCCCTCAAAAAAGAAGAGAGGAAAAGAAACCAGCACAGTGAGTGCCTGATGTGCTGGTATGACAGAGACACAGAGTTCACCTACTCCTCTCCATGGCCAGAAAAGTTCCCTGCCATAGAACGATGTTGTACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCCTCTCCATGGCCAGAA
60.25
TGGCTTGAAGGGTTTTCCGA
59.82
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTACTCCTCTCCATGGCCA
60.4
TGGCTTGAAGGGTTTTCCGA
59.82
149
PCR template sequence:
ACAGTGAGTGCCTGATGTGCTGGTATGACAGAGACACAGAGTTCACCTACTCCTCTCCATGGCCAGAAAAGTTCCCTGCCATAGAACGATGTTGTACAAGGTACTATCCCTATCATTACGCACCCTTCCTATCTGATATCCGCAGTATCAGTACACTCAAAATCCATTTTGAACTCGGAAAACCCTTCAAGCCATTCGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGTTGTACAAGGTACTATCCCTAT
siRNA sets
ATAGTACCTTGTACAACAT,GATAGTACCTTGTACAACA,TAGTACCTTGTACAACATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXRN1_447_ORF_1
0.5803
0.091026825
0.809686998
729
ORF sequence:
ATGACCAGTGAAGACTCGCCAATTATAGAATATTATCCACCTGATTTCAAAACTGATCTAAATGGGAAACAACAGGAATGGGAAGCTGTGGTATTAATACCGTTTATTGATGAGACGCGATTATTGGAAGCCATGGAGACATGTAACCACTCCCTCAAAAAAGAAGAGAGGAAAAGAAACCAGCACAGTGAGTGCCTGATGTGCTGGTATGACAGAGACACAGAGTTCACCTACTCCTCTCCATGGCCAGAAAAGTTCCCTGCCATAGAACGATGTTGTACAAGGTACTATCCCTATCATTACGCACCCTTCCTATCTGATATCCGCAGTATCAGTACACTCAAAATCCATTTTGAACTCGGAAAACCCTTCAAGCCATTCGAGCAGCTGCTTGCTGTACTTCCATCGGCTAGTAAAAATTTGCTTCCTACATGCTACCAGCATTTGATGACCAGTGAAGACTCGCCAATTATAGAATATTATCCACCTGATTTCAAAACTGATCTAAATGGGAAACAACAGGAATGGGAAGCTGTGGTATTAATACCGTTTATTGATGAGACGCGATTATTGGAAGCCATGGAGACATGTAACCACTCCCTCAAAAAAGAAGAGAGGAAAAGAAACCAGCACAGTGAGTGCCTGATGTGCTGGTATGACAGAGACACAGAGTTCACCTACTCCTCTCCATGGCCAGAAAAGTTCCCTGCCATAGAACGATGTTGTACA
Peptide sequence:
MTSEDSPIIEYYPPDFKTDLNGKQQEWEAVVLIPFIDETRLLEAMETCNHSLKKEERKRNQHSECLMCWYDRDTEFTYSSPWPEKFPAIERCCTRYYPYHYAPFLSDIRSISTLKIHFELGKPFKPFEQLLAVLPSASKNLLPTCYQHLMTSEDSPIIEYYPPDFKTDLNGKQQEWEAVVLIPFIDETRLLEAMETCNHSLKKEERKRNQHSECLMCWYDRDTEFTYSSPWPEKFPAIERCCT
IRESfinder result
IRESfinder score
0.589403251
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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