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mmu_circUsp34_2458
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_2458
mm39_Chr. Position ID:
chr11|23299150|23331379|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
16
Exon/intron indexes:
7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
Exon/intron offsets:
0,2441,5694,5855,12128,12436,13426,13907,14640,18188,21088,21293,24170,25850,28404,32074
Genomic length:
32229
Exon/intron sizes in nt:
19,36,28,29,31,26,13,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr11:23295217-23299150|chr11:23331379-23332553
Splice length:
2458
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTATTTATGCAAGCTCTCTGATCAGGAGTTACGACAGAGTGCGGCTCGTAATATGGCTGACCTAATGTGGAGTACAGTGAAAGAGCCATTGGATACAACACTGTGCTTTGATAAGGAAAGTCTAGACCTTGCATTTAAATACTTTATGTCACCAACTCTGACCATGAGGTTGGCTGGATTGAGTCAGATAACAAATCAGCTCCATACTTTCAATGATGTGTGCAATAACGAATCATTGGTATCAGACACAGAAACGTCCATTGCAAAAGAACTTGCAGACTGGCTTATTAGCAACAATGTAGTAGAACATATATTTGGACCAAATTTACATATTGAGATTATTAAACAGTGCCAAGTGATTTTGAATTTCTTGGCAGCAGAGGGACGACTGAGTACTCAGCATATTGACTGCATTTGGGCTGCAGCACAGCTGAAGCACTGTAGTCGATATATTCATGACTTATTCCCTTCACTCATCAAGAATCTGGATCCTGTGCCACTTAGACATTTACTTAATCTGGTCTCAGCTCTTGAACCAGGTGTTCATACTGAACAGACACTGTACTTGGCATCCATGTTAATTAAAGCTTTGTGGAATAATGCACTTGCAGCTAAGGCTCAGCTGTCTAAACAGAGTTCTTTTGCATCTTTATTAAACACTAATATGCCCATTGGAAACAAGAAAGAGGAAGAAGAGCTTAGAAGAGCAGCTCCTTCACCTTGGTCCCCAGCAGCGAGTCCTCAAAGTAGTGATAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAGGAATCCATGCAAGGAAGTTCTGATGAAACTGCCAACAGTGGTGAAGATGGAAGCAGTGGCCCTGGTAGCAGTAGTGGGCATAGTGATGGATCTAGCAATGAAGTTAATTCAAGCCATGCAAGCCAGTCTGCTGGGAGCCCTGGAAGTGAGGTGCAATCAGAAGACATTGCAGACATCGAGGCCCTTAAAGAAGAAGAGGAAGAGGAGGAGGAAGAAGAAGAAGAGGAAGAGGAAGAAGATGATGAAGAAGAAGAAGATGAAGAAGAAGATGATGATGACGACGATGATCATGGTCACAATCCTGCCAAAAATACTTGTGGTACAGAACTTCGAAACAGAAAGTTAGAAAATCCAGCAGGCATTTGCTTGGGGGAATCCCAAGGCACATCTGAAAGGAATGGGACAAATAGTGGAACTGGAAAGGACCTGGTTTTTAATACTGAGCCATTGCCATCTGTAGATAACCGAATACGAATGCTAGATGCCTGTGCTCACTCTGAAGACCCAGAACATGGCATTTCAGGGGAAGTGAGTTCTGCTCACTTAGCACAAGGTTCTCAGGAGGCTTGTATCACACGAAGTGGGGACTTCCTTGGGGAGACTATTGGGAATGAGTTGTTTAATTGTCGGCAGTTTATTGGTCCACAGCATCACCACCACCACCACCACCACCACCACCATCATCACCATCACCACCACCACCACCACCACCACCACGATGGACATATGGTTGATGATATGCTAAGTGCAGATGATGTCAGTTGCAGTAGCTCCCAGGTCAGTGCAAAATCAGAAAAAAATATGGCTGATTTTGATGGTGAAGAATCTGGATGTGAAGAGGAACTAGTTCAGATAAATTCACATGCAGAACTAACATCTCATCTCCAACAACATCTTCCCAATTTAGCATCTATTTATCATGAACATCTTAGTCAAGGACCTGCAGTTCATAAACATCAATTCAGTAGTAATGCTGTGACAGATATTAATTTGGATAATGTTTGCAAGAAAGGAAATACTTTATTATGGGATATAGTGCAAGATGATGATGCAATTAATCTTTCTGAAGGATTAATAAATGAAGCAGAGAAACTTCTCTGTTCTTTGGTTTGTTGGTTTACGGATAGACAAATTCGAATGAGATTCATTGAAGGCTGCCTTGAAAATTTAGGGAACAACAGATCAGTGGTGATTTCACTTCGTCTTCTTCCAAAACTGTTTGGTACTTTTCAGCAGTTTGGAAGCAGTTATGATACTCATTGGATTACAATGTGGGCAGAGAAAGAACTGAACATGATGAAGCTTTTCTTTGACAATCTGGTGTATTACATTCAAGGTATAAGGGAAGGCAGACAAAAGCATGCACTGTACAGCCATAGTGCCGAAGTTCAAGTTCGACTTCAGTTCCTGACCTGTGTGTTTTCAACCCTGGGATCCCCTGATCACTTCAGGTTAAGTTTAGAGCAAGTGGACATTTTATGGCATTGTTTGGTAGAAGACTCTGAGTGCTATGATGATGCACTTCATTGGTTTTTAAATCAAGTTCGAAGTAAAGATCAACATGCAATGGGAATGGAAACCTATAAACATCTTTTCCTGGAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTATGATGATGCACTTCATTGG
59.72
ATTACGAGCCGCACTCTGTC
60.18
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTATGATGATGCACTTCATTGGT
59.72
ATTACGAGCCGCACTCTGTC
60.18
150
PCR template sequence:
GTGCTATGATGATGCACTTCATTGGTTTTTAAATCAAGTTCGAAGTAAAGATCAACATGCAATGGGAATGGAAACCTATAAACATCTTTTCCTGGAGAAGGTATTTATGCAAGCTCTCTGATCAGGAGTTACGACAGAGTGCGGCTCGTAATATGGCTGACCTAATGTGGAGTACAGTGAAAGAGCCATTGGATACAACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(2), mmu-miR-221-3p(1), mmu-miR-92a-3p(1), mmu-miR-152-3p(1), mmu-miR-25-3p(1), mmu-miR-139-5p(1), mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-363-3p(1), mmu-miR-22-3p(1), mmu-miR-758-3p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-300-3p(1), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTCCTGGAGAAGGTATTTATGCAAG
siRNA sets
TTGCATAAATACCTTCTCC, CATAAATACCTTCTCCAGG, CTTGCATAAATACCTTCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_2458_ORF_1
1.1059
0.055497714
0.999999688
2502
ORF sequence:
ATGCAATGGGAATGGAAACCTATAAACATCTTTTCCTGGAGAAGGTATTTATGCAAGCTCTCTGATCAGGAGTTACGACAGAGTGCGGCTCGTAATATGGCTGACCTAATGTGGAGTACAGTGAAAGAGCCATTGGATACAACACTGTGCTTTGATAAGGAAAGTCTAGACCTTGCATTTAAATACTTTATGTCACCAACTCTGACCATGAGGTTGGCTGGATTGAGTCAGATAACAAATCAGCTCCATACTTTCAATGATGTGTGCAATAACGAATCATTGGTATCAGACACAGAAACGTCCATTGCAAAAGAACTTGCAGACTGGCTTATTAGCAACAATGTAGTAGAACATATATTTGGACCAAATTTACATATTGAGATTATTAAACAGTGCCAAGTGATTTTGAATTTCTTGGCAGCAGAGGGACGACTGAGTACTCAGCATATTGACTGCATTTGGGCTGCAGCACAGCTGAAGCACTGTAGTCGATATATTCATGACTTATTCCCTTCACTCATCAAGAATCTGGATCCTGTGCCACTTAGACATTTACTTAATCTGGTCTCAGCTCTTGAACCAGGTGTTCATACTGAACAGACACTGTACTTGGCATCCATGTTAATTAAAGCTTTGTGGAATAATGCACTTGCAGCTAAGGCTCAGCTGTCTAAACAGAGTTCTTTTGCATCTTTATTAAACACTAATATGCCCATTGGAAACAAGAAAGAGGAAGAAGAGCTTAGAAGAGCAGCTCCTTCACCTTGGTCCCCAGCAGCGAGTCCTCAAAGTAGTGATAACAGTGACACACATCAGAGTGGAGCCAGTGACATTGAAATGGATGAGCAGCTTATTAATAGAAATAAACATGTGCAGCAGCGACTGTCTGACACTGAGGAATCCATGCAAGGAAGTTCTGATGAAACTGCCAACAGTGGTGAAGATGGAAGCAGTGGCCCTGGTAGCAGTAGTGGGCATAGTGATGGATCTAGCAATGAAGTTAATTCAAGCCATGCAAGCCAGTCTGCTGGGAGCCCTGGAAGTGAGGTGCAATCAGAAGACATTGCAGACATCGAGGCCCTTAAAGAAGAAGAGGAAGAGGAGGAGGAAGAAGAAGAAGAGGAAGAGGAAGAAGATGATGAAGAAGAAGAAGATGAAGAAGAAGATGATGATGACGACGATGATCATGGTCACAATCCTGCCAAAAATACTTGTGGTACAGAACTTCGAAACAGAAAGTTAGAAAATCCAGCAGGCATTTGCTTGGGGGAATCCCAAGGCACATCTGAAAGGAATGGGACAAATAGTGGAACTGGAAAGGACCTGGTTTTTAATACTGAGCCATTGCCATCTGTAGATAACCGAATACGAATGCTAGATGCCTGTGCTCACTCTGAAGACCCAGAACATGGCATTTCAGGGGAAGTGAGTTCTGCTCACTTAGCACAAGGTTCTCAGGAGGCTTGTATCACACGAAGTGGGGACTTCCTTGGGGAGACTATTGGGAATGAGTTGTTTAATTGTCGGCAGTTTATTGGTCCACAGCATCACCACCACCACCACCACCACCACCACCATCATCACCATCACCACCACCACCACCACCACCACCACGATGGACATATGGTTGATGATATGCTAAGTGCAGATGATGTCAGTTGCAGTAGCTCCCAGGTCAGTGCAAAATCAGAAAAAAATATGGCTGATTTTGATGGTGAAGAATCTGGATGTGAAGAGGAACTAGTTCAGATAAATTCACATGCAGAACTAACATCTCATCTCCAACAACATCTTCCCAATTTAGCATCTATTTATCATGAACATCTTAGTCAAGGACCTGCAGTTCATAAACATCAATTCAGTAGTAATGCTGTGACAGATATTAATTTGGATAATGTTTGCAAGAAAGGAAATACTTTATTATGGGATATAGTGCAAGATGATGATGCAATTAATCTTTCTGAAGGATTAATAAATGAAGCAGAGAAACTTCTCTGTTCTTTGGTTTGTTGGTTTACGGATAGACAAATTCGAATGAGATTCATTGAAGGCTGCCTTGAAAATTTAGGGAACAACAGATCAGTGGTGATTTCACTTCGTCTTCTTCCAAAACTGTTTGGTACTTTTCAGCAGTTTGGAAGCAGTTATGATACTCATTGGATTACAATGTGGGCAGAGAAAGAACTGAACATGATGAAGCTTTTCTTTGACAATCTGGTGTATTACATTCAAGGTATAAGGGAAGGCAGACAAAAGCATGCACTGTACAGCCATAGTGCCGAAGTTCAAGTTCGACTTCAGTTCCTGACCTGTGTGTTTTCAACCCTGGGATCCCCTGATCACTTCAGGTTAAGTTTAGAGCAAGTGGACATTTTATGGCATTGTTTGGTAGAAGACTCTGAGTGCTATGATGATGCACTTCATTGGTTTTTAAATCAAGTTCGAAGTAAAGATCAACATGCAATGGGAATGGAAACCTATAAACATCTTTTCCTGGAGAAG
Peptide sequence:
MQWEWKPINIFSWRRYLCKLSDQELRQSAARNMADLMWSTVKEPLDTTLCFDKESLDLAFKYFMSPTLTMRLAGLSQITNQLHTFNDVCNNESLVSDTETSIAKELADWLISNNVVEHIFGPNLHIEIIKQCQVILNFLAAEGRLSTQHIDCIWAAAQLKHCSRYIHDLFPSLIKNLDPVPLRHLLNLVSALEPGVHTEQTLYLASMLIKALWNNALAAKAQLSKQSSFASLLNTNMPIGNKKEEEELRRAAPSPWSPAASPQSSDNSDTHQSGASDIEMDEQLINRNKHVQQRLSDTEESMQGSSDETANSGEDGSSGPGSSSGHSDGSSNEVNSSHASQSAGSPGSEVQSEDIADIEALKEEEEEEEEEEEEEEEEDDEEEEDEEEDDDDDDDHGHNPAKNTCGTELRNRKLENPAGICLGESQGTSERNGTNSGTGKDLVFNTEPLPSVDNRIRMLDACAHSEDPEHGISGEVSSAHLAQGSQEACITRSGDFLGETIGNELFNCRQFIGPQHHHHHHHHHHHHHHHHHHHHHHHDGHMVDDMLSADDVSCSSSQVSAKSEKNMADFDGEESGCEEELVQINSHAELTSHLQQHLPNLASIYHEHLSQGPAVHKHQFSSNAVTDINLDNVCKKGNTLLWDIVQDDDAINLSEGLINEAEKLLCSLVCWFTDRQIRMRFIEGCLENLGNNRSVVISLRLLPKLFGTFQQFGSSYDTHWITMWAEKELNMMKLFFDNLVYYIQGIREGRQKHALYSHSAEVQVRLQFLTCVFSTLGSPDHFRLSLEQVDILWHCLVEDSECYDDALHWFLNQVRSKDQHAMGMETYKHLFLEK
IRESfinder result
IRESfinder score
0.684888705
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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