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mmu_circUsp34_921
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_921
mm39_Chr. Position ID:
chr11|23295149|23313188|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
6,7,8,9,10,11,12,13,14
Exon/intron offsets:
0,4001,6442,9695,9856,16129,16437,17427,17908
Genomic length:
18039
Exon/intron sizes in nt:
6,81,93,62,82,93,12,61,00,00,000
Flanking exon/introns:
chr11:23293660-23295149|chr11:23313188-23313790
Splice length:
921
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATTAGGATATGGCTACATATCCCTGCTGTCATGCAGCACATTATTCCTTTTAGAACGTATGTTATCAGGTATTTATGCAAGCTCTCTGATCAGGAGTTACGACAGAGTGCGGCTCGTAATATGGCTGACCTAATGTGGAGTACAGTGAAAGAGCCATTGGATACAACACTGTGCTTTGATAAGGAAAGTCTAGACCTTGCATTTAAATACTTTATGTCACCAACTCTGACCATGAGGTTGGCTGGATTGAGTCAGATAACAAATCAGCTCCATACTTTCAATGATGTGTGCAATAACGAATCATTGGTATCAGACACAGAAACGTCCATTGCAAAAGAACTTGCAGACTGGCTTATTAGCAACAATGTAGTAGAACATATATTTGGACCAAATTTACATATTGAGATTATTAAACAGTGCCAAGTGATTTTGAATTTCTTGGCAGCAGAGGGACGACTGAGTACTCAGCATATTGACTGCATTTGGGCTGCAGCACAGCTGAAGCACTGTAGTCGATATATTCATGACTTATTCCCTTCACTCATCAAGAATCTGGATCCTGTGCCACTTAGACATTTACTTAATCTGGTCTCAGCTCTTGAACCAGGTGTTCATACTGAACAGACACTGTACTTGGCATCCATGTTAATTAAAGCTTTGTGGAATAATGCACTTGCAGCTAAGGCTCAGCTGTCTAAACAGAGTTCTTTTGCATCTTTATTAAACACTAATATGCCCATTGGAAACAAGAAAGAGGAAGAAGAGCTTAGAAGAGCAGCTCCTTCACCTTGGTCCCCAGCAGCGAGTCCTCAAAGTAGTGATAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGAGTGGAGCCAGTGACA
60.47
TCCTGATCAGAGAGCTTGCA
58.43
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGTGGAGCCAGTGACAT
59.39
CTCCTGATCAGAGAGCTTGCA
59.52
180
PCR template sequence:
TAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAGATTAGGATATGGCTACATATCCCTGCTGTCATGCAGCACATTATTCCTTTTAGAACGTATGTTATCAGGTATTTATGCAAGCTCTCTGATCAGGAGTTAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(1), mmu-miR-221-3p(1), mmu-miR-139-5p(1), mmu-miR-214-3p(1), mmu-miR-149-5p(1), mmu-miR-363-3p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-300-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTGACACTGAGATTAGGATATGGC
siRNA sets
ATATCCTAATCTCAGTGTC, TATCCTAATCTCAGTGTCA, ATCCTAATCTCAGTGTCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_921_ORF_1
0.9881
0.01547603
0.999938143
1812
ORF sequence:
ATGCAGCACATTATTCCTTTTAGAACGTATGTTATCAGGTATTTATGCAAGCTCTCTGATCAGGAGTTACGACAGAGTGCGGCTCGTAATATGGCTGACCTAATGTGGAGTACAGTGAAAGAGCCATTGGATACAACACTGTGCTTTGATAAGGAAAGTCTAGACCTTGCATTTAAATACTTTATGTCACCAACTCTGACCATGAGGTTGGCTGGATTGAGTCAGATAACAAATCAGCTCCATACTTTCAATGATGTGTGCAATAACGAATCATTGGTATCAGACACAGAAACGTCCATTGCAAAAGAACTTGCAGACTGGCTTATTAGCAACAATGTAGTAGAACATATATTTGGACCAAATTTACATATTGAGATTATTAAACAGTGCCAAGTGATTTTGAATTTCTTGGCAGCAGAGGGACGACTGAGTACTCAGCATATTGACTGCATTTGGGCTGCAGCACAGCTGAAGCACTGTAGTCGATATATTCATGACTTATTCCCTTCACTCATCAAGAATCTGGATCCTGTGCCACTTAGACATTTACTTAATCTGGTCTCAGCTCTTGAACCAGGTGTTCATACTGAACAGACACTGTACTTGGCATCCATGTTAATTAAAGCTTTGTGGAATAATGCACTTGCAGCTAAGGCTCAGCTGTCTAAACAGAGTTCTTTTGCATCTTTATTAAACACTAATATGCCCATTGGAAACAAGAAAGAGGAAGAAGAGCTTAGAAGAGCAGCTCCTTCACCTTGGTCCCCAGCAGCGAGTCCTCAAAGTAGTGATAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAGATTAGGATATGGCTACATATCCCTGCTGTCATGCAGCACATTATTCCTTTTAGAACGTATGTTATCAGGTATTTATGCAAGCTCTCTGATCAGGAGTTACGACAGAGTGCGGCTCGTAATATGGCTGACCTAATGTGGAGTACAGTGAAAGAGCCATTGGATACAACACTGTGCTTTGATAAGGAAAGTCTAGACCTTGCATTTAAATACTTTATGTCACCAACTCTGACCATGAGGTTGGCTGGATTGAGTCAGATAACAAATCAGCTCCATACTTTCAATGATGTGTGCAATAACGAATCATTGGTATCAGACACAGAAACGTCCATTGCAAAAGAACTTGCAGACTGGCTTATTAGCAACAATGTAGTAGAACATATATTTGGACCAAATTTACATATTGAGATTATTAAACAGTGCCAAGTGATTTTGAATTTCTTGGCAGCAGAGGGACGACTGAGTACTCAGCATATTGACTGCATTTGGGCTGCAGCACAGCTGAAGCACTGTAGTCGATATATTCATGACTTATTCCCTTCACTCATCAAGAATCTGGATCCTGTGCCACTTAGACATTTACTTAATCTGGTCTCAGCTCTTGAACCAGGTGTTCATACTGAACAGACACTGTACTTGGCATCCATGTTAATTAAAGCTTTGTGGAATAATGCACTTGCAGCTAAGGCTCAGCTGTCTAAACAGAGTTCTTTTGCATCTTTATTAAACACTAATATGCCCATTGGAAACAAGAAAGAGGAAGAAGAGCTTAGAAGAGCAGCTCCTTCACCTTGGTCCCCAGCAGCGAGTCCTCAAAGTAGTGATAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAG
Peptide sequence:
MQHIIPFRTYVIRYLCKLSDQELRQSAARNMADLMWSTVKEPLDTTLCFDKESLDLAFKYFMSPTLTMRLAGLSQITNQLHTFNDVCNNESLVSDTETSIAKELADWLISNNVVEHIFGPNLHIEIIKQCQVILNFLAAEGRLSTQHIDCIWAAAQLKHCSRYIHDLFPSLIKNLDPVPLRHLLNLVSALEPGVHTEQTLYLASMLIKALWNNALAAKAQLSKQSSFASLLNTNMPIGNKKEEEELRRAAPSPWSPAASPQSSDNSDTHQSGASDIEMDEQLINRNKHVQQRLSDTEIRIWLHIPAVMQHIIPFRTYVIRYLCKLSDQELRQSAARNMADLMWSTVKEPLDTTLCFDKESLDLAFKYFMSPTLTMRLAGLSQITNQLHTFNDVCNNESLVSDTETSIAKELADWLISNNVVEHIFGPNLHIEIIKQCQVILNFLAAEGRLSTQHIDCIWAAAQLKHCSRYIHDLFPSLIKNLDPVPLRHLLNLVSALEPGVHTEQTLYLASMLIKALWNNALAAKAQLSKQSSFASLLNTNMPIGNKKEEEELRRAAPSPWSPAASPQSSDNSDTHQSGASDIEMDEQLINRNKHVQQRLSDTE
IRESfinder result
IRESfinder score
0.759466229
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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