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mmu_circUsp34_660
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_660
mm39_Chr. Position ID:
chr11|23301591|23313188|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,9,10,11,12,13,14
Exon/intron offsets:
0,3253,3414,9687,9995,10985,11466
Genomic length:
11597
Exon/intron sizes in nt:
62,82,93,12,61,30,36,100
Flanking exon/introns:
chr11:23299343-23301591|chr11:23313188-23313790
Splice length:
660
Other database IDs:
CIRCpedia: MMU_CIRCpedia_214421, circAtlas: mmu-Usp34_0147
Human Ortholog IDs:
Mature spliced Sequence:
AATCAGCTCCATACTTTCAATGATGTGTGCAATAACGAATCATTGGTATCAGACACAGAAACGTCCATTGCAAAAGAACTTGCAGACTGGCTTATTAGCAACAATGTAGTAGAACATATATTTGGACCAAATTTACATATTGAGATTATTAAACAGTGCCAAGTGATTTTGAATTTCTTGGCAGCAGAGGGACGACTGAGTACTCAGCATATTGACTGCATTTGGGCTGCAGCACAGCTGAAGCACTGTAGTCGATATATTCATGACTTATTCCCTTCACTCATCAAGAATCTGGATCCTGTGCCACTTAGACATTTACTTAATCTGGTCTCAGCTCTTGAACCAGGTGTTCATACTGAACAGACACTGTACTTGGCATCCATGTTAATTAAAGCTTTGTGGAATAATGCACTTGCAGCTAAGGCTCAGCTGTCTAAACAGAGTTCTTTTGCATCTTTATTAAACACTAATATGCCCATTGGAAACAAGAAAGAGGAAGAAGAGCTTAGAAGAGCAGCTCCTTCACCTTGGTCCCCAGCAGCGAGTCCTCAAAGTAGTGATAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACACATCAGAGTGGAGCCA
59.68
TGCAATGGACGTTTCTGTGTC
59.4
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACACATCAGAGTGGAGCC
59.68
TGCAATGGACGTTTCTGTGTC
59.4
164
PCR template sequence:
TAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAGAATCAGCTCCATACTTTCAATGATGTGTGCAATAACGAATCATTGGTATCAGACACAGAAACGTCCATTGCAAAAGAACTTGCAGACTGGCTTATTAGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(1), mmu-miR-221-3p(1), mmu-miR-139-5p(1), mmu-miR-149-5p(1), mmu-miR-363-3p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTGACACTGAGAATCAGCTCCATA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_660_ORF_1
1.0705
0.037957379
0.974620839
939
ORF sequence:
ATGTTAATTAAAGCTTTGTGGAATAATGCACTTGCAGCTAAGGCTCAGCTGTCTAAACAGAGTTCTTTTGCATCTTTATTAAACACTAATATGCCCATTGGAAACAAGAAAGAGGAAGAAGAGCTTAGAAGAGCAGCTCCTTCACCTTGGTCCCCAGCAGCGAGTCCTCAAAGTAGTGATAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAGAATCAGCTCCATACTTTCAATGATGTGTGCAATAACGAATCATTGGTATCAGACACAGAAACGTCCATTGCAAAAGAACTTGCAGACTGGCTTATTAGCAACAATGTAGTAGAACATATATTTGGACCAAATTTACATATTGAGATTATTAAACAGTGCCAAGTGATTTTGAATTTCTTGGCAGCAGAGGGACGACTGAGTACTCAGCATATTGACTGCATTTGGGCTGCAGCACAGCTGAAGCACTGTAGTCGATATATTCATGACTTATTCCCTTCACTCATCAAGAATCTGGATCCTGTGCCACTTAGACATTTACTTAATCTGGTCTCAGCTCTTGAACCAGGTGTTCATACTGAACAGACACTGTACTTGGCATCCATGTTAATTAAAGCTTTGTGGAATAATGCACTTGCAGCTAAGGCTCAGCTGTCTAAACAGAGTTCTTTTGCATCTTTATTAAACACTAATATGCCCATTGGAAACAAGAAAGAGGAAGAAGAGCTTAGAAGAGCAGCTCCTTCACCTTGGTCCCCAGCAGCGAGTCCTCAAAGTAGTGATAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAG
Peptide sequence:
MLIKALWNNALAAKAQLSKQSSFASLLNTNMPIGNKKEEEELRRAAPSPWSPAASPQSSDNSDTHQSGASDIEMDEQLINRNKHVQQRLSDTENQLHTFNDVCNNESLVSDTETSIAKELADWLISNNVVEHIFGPNLHIEIIKQCQVILNFLAAEGRLSTQHIDCIWAAAQLKHCSRYIHDLFPSLIKNLDPVPLRHLLNLVSALEPGVHTEQTLYLASMLIKALWNNALAAKAQLSKQSSFASLLNTNMPIGNKKEEEELRRAAPSPWSPAASPQSSDNSDTHQSGASDIEMDEQLINRNKHVQQRLSDTE
IRESfinder result
IRESfinder score
0.812421436
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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