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mmu_circUsp34_1065
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_1065
mm39_Chr. Position ID:
chr11|23382618|23399293|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
47,48,49,50,51,52,53,54,55,56,57,58
Exon/intron offsets:
0,561,3288,6248,8481,11528,11687,13813,13960,14125,14299,16594
Genomic length:
16675
Exon/intron sizes in nt:
78,95,173,154,79,54,96,65,76,48,66,81
Flanking exon/introns:
chr11:23382534-23382618|chr11:23399293-23401995
Splice length:
1065
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GATTGTGAACATGTTAGTCAAACTGCTGAAGAATTTTATACTGTGAGGTGCCAGGTGGCAGATATGAAGAATATTTATGAGTCTCTGGATGAAGTTACTATTAAAGACACCTTAGAAGGGGACAACATGTACACCTGTTCTCACTGTGGGAAGAAAGTCCGAGCTGAAAAGAGGGCTTGTTTTAAGAAATTACCTCGTATTCTGAGTTTCAATACTATGAGATATACATTTAATATGGTCACGATGATGAAAGAGAAAGTGAATACACACTTTTCTTTCCCTTTACGTTTGGATATGACGCCCTATACAGAAGATTTTCTAATGGGGAAGAGCGACAGGAAAGAAGGTTTCAAAGATGTTGGTGATCGTTCGAAAGACACAGAGAGCTATGAGTATGACTTGATTGGAGTGACTGTTCACACAGGAACAGCAGACGGTGGGCACTATTACAGTTTCATCAGAGACATAGTCAATCCACATGCCTATAAGAACAATAAGTGGTACCTTTTTAATGATGCTGAGGTGAAGCCCTTTGATTCTGCTCAACTTGCTTCTGAATGCTTTGGTGGTGAGATGACCACAAAAACCTATGATTCGGTTACAGATAAATTCATGGACTTTTCCTTTGAAAAGACACATAGTGCATATATGCTGTTTTACAAACGCATGGAACCAGAAGAAGAAAATGGCAGAGAATACAAATTTGATGTTTCATCAGAGTTACTAGAGTGGATTTGGCATGATAACATGCAATTTTTACAAGACAAAAACATTTTTGAACACACTTATTTTGGGTTTATGTGGCAGCTGTGCAGTTGTATTCCAAGTACATTACCAGATCCTAAAGCTGTGTCCCTCATGACAGCAAAGTTAAGTACTTCCTTTGTTTTAGAGACATTCATTCATTCAAAAGAGAAGCCAACAATGCTTCAGTGGATTGAACTACTGACCAAACAATTTAATAATAGTCAAGCAGCCTGTGAGTGGTTTTTAGACCGCATGGCTGATGATGACTGGTGGCCAATGCAGATACTAATTAAGTGTCCCAATCAGATTGTGAGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAGCCTGTGAGTGGTTTT
60.11
CACCTGGCACCTCACAGTAT
59.38
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCAGCCTGTGAGTGGTTT
60.11
CACCTGGCACCTCACAGTAT
59.38
152
PCR template sequence:
TAGTCAAGCAGCCTGTGAGTGGTTTTTAGACCGCATGGCTGATGATGACTGGTGGCCAATGCAGATACTAATTAAGTGTCCCAATCAGATTGTGAGACAGGATTGTGAACATGTTAGTCAAACTGCTGAAGAATTTTATACTGTGAGGTGCCAGGTGGCAGATATGAAGAATATTTATGAGTCTCTGGATGAAGTTACTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-128-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-22-3p(1), mmu-miR-212-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATTGTGAGACAGGATTGTGAACATG
siRNA sets
ATGTTCACAATCCTGTCTC, TTCACAATCCTGTCTCACA, CATGTTCACAATCCTGTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_1065_ORF_1
0.9275
0.054098944
0.999990548
2067
ORF sequence:
ATGAAGAATATTTATGAGTCTCTGGATGAAGTTACTATTAAAGACACCTTAGAAGGGGACAACATGTACACCTGTTCTCACTGTGGGAAGAAAGTCCGAGCTGAAAAGAGGGCTTGTTTTAAGAAATTACCTCGTATTCTGAGTTTCAATACTATGAGATATACATTTAATATGGTCACGATGATGAAAGAGAAAGTGAATACACACTTTTCTTTCCCTTTACGTTTGGATATGACGCCCTATACAGAAGATTTTCTAATGGGGAAGAGCGACAGGAAAGAAGGTTTCAAAGATGTTGGTGATCGTTCGAAAGACACAGAGAGCTATGAGTATGACTTGATTGGAGTGACTGTTCACACAGGAACAGCAGACGGTGGGCACTATTACAGTTTCATCAGAGACATAGTCAATCCACATGCCTATAAGAACAATAAGTGGTACCTTTTTAATGATGCTGAGGTGAAGCCCTTTGATTCTGCTCAACTTGCTTCTGAATGCTTTGGTGGTGAGATGACCACAAAAACCTATGATTCGGTTACAGATAAATTCATGGACTTTTCCTTTGAAAAGACACATAGTGCATATATGCTGTTTTACAAACGCATGGAACCAGAAGAAGAAAATGGCAGAGAATACAAATTTGATGTTTCATCAGAGTTACTAGAGTGGATTTGGCATGATAACATGCAATTTTTACAAGACAAAAACATTTTTGAACACACTTATTTTGGGTTTATGTGGCAGCTGTGCAGTTGTATTCCAAGTACATTACCAGATCCTAAAGCTGTGTCCCTCATGACAGCAAAGTTAAGTACTTCCTTTGTTTTAGAGACATTCATTCATTCAAAAGAGAAGCCAACAATGCTTCAGTGGATTGAACTACTGACCAAACAATTTAATAATAGTCAAGCAGCCTGTGAGTGGTTTTTAGACCGCATGGCTGATGATGACTGGTGGCCAATGCAGATACTAATTAAGTGTCCCAATCAGATTGTGAGACAGGATTGTGAACATGTTAGTCAAACTGCTGAAGAATTTTATACTGTGAGGTGCCAGGTGGCAGATATGAAGAATATTTATGAGTCTCTGGATGAAGTTACTATTAAAGACACCTTAGAAGGGGACAACATGTACACCTGTTCTCACTGTGGGAAGAAAGTCCGAGCTGAAAAGAGGGCTTGTTTTAAGAAATTACCTCGTATTCTGAGTTTCAATACTATGAGATATACATTTAATATGGTCACGATGATGAAAGAGAAAGTGAATACACACTTTTCTTTCCCTTTACGTTTGGATATGACGCCCTATACAGAAGATTTTCTAATGGGGAAGAGCGACAGGAAAGAAGGTTTCAAAGATGTTGGTGATCGTTCGAAAGACACAGAGAGCTATGAGTATGACTTGATTGGAGTGACTGTTCACACAGGAACAGCAGACGGTGGGCACTATTACAGTTTCATCAGAGACATAGTCAATCCACATGCCTATAAGAACAATAAGTGGTACCTTTTTAATGATGCTGAGGTGAAGCCCTTTGATTCTGCTCAACTTGCTTCTGAATGCTTTGGTGGTGAGATGACCACAAAAACCTATGATTCGGTTACAGATAAATTCATGGACTTTTCCTTTGAAAAGACACATAGTGCATATATGCTGTTTTACAAACGCATGGAACCAGAAGAAGAAAATGGCAGAGAATACAAATTTGATGTTTCATCAGAGTTACTAGAGTGGATTTGGCATGATAACATGCAATTTTTACAAGACAAAAACATTTTTGAACACACTTATTTTGGGTTTATGTGGCAGCTGTGCAGTTGTATTCCAAGTACATTACCAGATCCTAAAGCTGTGTCCCTCATGACAGCAAAGTTAAGTACTTCCTTTGTTTTAGAGACATTCATTCATTCAAAAGAGAAGCCAACAATGCTTCAGTGGATTGAACTACTGACCAAACAATTTAATAATAGTCAAGCAGCCTGTGAGTGGTTTTTAGACCGCATGGCTGATGATGACTGGTGGCCAATGCAGATACTAATTAAGTGTCCCAATCAGATTGTGAGACAG
Peptide sequence:
MKNIYESLDEVTIKDTLEGDNMYTCSHCGKKVRAEKRACFKKLPRILSFNTMRYTFNMVTMMKEKVNTHFSFPLRLDMTPYTEDFLMGKSDRKEGFKDVGDRSKDTESYEYDLIGVTVHTGTADGGHYYSFIRDIVNPHAYKNNKWYLFNDAEVKPFDSAQLASECFGGEMTTKTYDSVTDKFMDFSFEKTHSAYMLFYKRMEPEEENGREYKFDVSSELLEWIWHDNMQFLQDKNIFEHTYFGFMWQLCSCIPSTLPDPKAVSLMTAKLSTSFVLETFIHSKEKPTMLQWIELLTKQFNNSQAACEWFLDRMADDDWWPMQILIKCPNQIVRQDCEHVSQTAEEFYTVRCQVADMKNIYESLDEVTIKDTLEGDNMYTCSHCGKKVRAEKRACFKKLPRILSFNTMRYTFNMVTMMKEKVNTHFSFPLRLDMTPYTEDFLMGKSDRKEGFKDVGDRSKDTESYEYDLIGVTVHTGTADGGHYYSFIRDIVNPHAYKNNKWYLFNDAEVKPFDSAQLASECFGGEMTTKTYDSVTDKFMDFSFEKTHSAYMLFYKRMEPEEENGREYKFDVSSELLEWIWHDNMQFLQDKNIFEHTYFGFMWQLCSCIPSTLPDPKAVSLMTAKLSTSFVLETFIHSKEKPTMLQWIELLTKQFNNSQAACEWFLDRMADDDWWPMQILIKCPNQIVRQ
IRESfinder result
IRESfinder score
0.657777534
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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