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mmu_circUsp34_1891
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_1891
mm39_Chr. Position ID:
chr11|23338433|23371366|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
16
Exon/intron indexes:
26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41
Exon/intron offsets:
0,230,4408,5318,13019,15126,15378,17433,23781,26302,29029,29215,30545,31606,32664,32812
Genomic length:
32933
Exon/intron sizes in nt:
12,71,48,10,12,10,12,60,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr11:23335172-23338433|chr11:23371366-23376061
Splice length:
1891
Other database IDs:
CIRCpedia: MMU_CIRCpedia_13841, circAtlas: mmu-Usp34_0153
Human Ortholog IDs:
Mature spliced Sequence:
GTTTGCATATCATCTGAGACAGTGGCAGATTGAGGGCACCGGTATTAGCAGTCACTTGAAAGCACTGAGTGACAAACAGTCTTTGCCTCTAAGGGTTGTATGTCAGCCTGCTGGACTTCCCGACAAGATGACTATTGAAATGTATCCAAGTGACCAGGTAGCAGATCTTCGTGCTGAAGTAACTCACTGGTATGAAAACTTACAGAAAGAACAAATAAATCAACAAGCTCAGCTTCAGGAGTTTGGTCAAAGCAGCAGAAAGGGAGAGTTTCCTGGTGGCCTCATGGGGCCTGTCAGGATGATCTCCTCTGGACATGAATTAACAACAGACTATGATGAAAAAGCACTTCATGAACTTGGTTTTAAAGATATGCAGATGGTGTTTGTATCTTTGGGTGCACCAAGAAGAGAAAGAAAAGGAGAAGGGGTTCAACTGCCTGCATCTTGCCTCCCACCACCTCAGAAGGACAACATTCCGATGCTTTTGCTGTTACAAGAACCTCATTTAACTACTCTCTTTGATTTATTAGAAATGCTTGCTTCATTTAAACCACCCTCAGGAAAAGTTGCAGTTGATGACAGTGAGAGTTTAAAATGTGAAGAACTTCATCTTCATGCAGAAAATCTTTCAAGGCGTGTCTGGGAGTTGCTGATGCTTCTTCCGACTTGTCCCAACATGCTGACGGCATTCCAGAATGTCTCAGACGAGCAGAGCAATGATGGACTTAATTGGAAGGAACTTCTCAAAATTAAGAGTGCTCATAAGTTGTTATATGCTCTTGAGATTATTGAAGCACTAGGAAAACCTAACAGAAGAATAAGAAGAGAGTCAACGGGAAGTTACAGTGATCTTTATCCAGATTCTGATGATTCAAGTGAAGATCAAGTGGAAAACAGTAAAAATTCCTGGACTTGCAAGTTTGTTGCTGCTGGCGGGCTTCAGCAGTTACTAGAAATTTTTAATTCTGCGATTCTAGAGCCTAAAGAGCAAGAATCATGGACTGTGTGGCAGCTGGATTGTCTTGCTTGCTTGCTGAAATTAATCTGCCAGTTTGCAGTAGATCCGTCAGATTTGGATTTAGCTTATCATGATGTTTTTGCCTGGTCTGGCATAGCCGAAAGCCATAGGAAAAGAACCTGGCCTGGAAAATCAAGAAAGGCTGCTGGTGATCATGCCAAGAGTCTTCATATACCACGATTAACAGAGGTGTTTCTTGTGCTTGTCCAAGGAACCAGTTTGATTCAGCGACTTATGTCTGTTGCTTATACGTATGATAATCTGGCTCCTAGAGTTTTGAAAGCTCAGTCTGATCATAGGTCTAGACATGAAGTGTCCCATTATTCAATGTGGCTCTTGGTGAGCTGGGCTCATTGCTGCTCTTTAGTCAAGTCTAGTCTTGCCGACAGTGATCATTTACAAGATTGGCTAAAACAGCTGACTCTCCTTATTCCCGAGACTGCAGTTCGCCATGAATCTTGCAATGGTCTCTATAAGCTATCTCTGTCAGGCCTAGATGGAGGAGACTCAATCCATCGATCCTTCCTTCTTTTGGCTGCCTCAACATTATTGAAATTCCTTCCTGATGCTCAAGCACTCAAACCTCCAAGGATAGATGATTATGAAGAAGAACCACTGTTAAAACCTGGATGTAAAGAATATTTTTGGTTATTATGCAAGTTAGTGGACAACATACACATAAAGGACGCTAGTCAGACAACACTCCTTGATTTAGATGCTTTGGCAAGACATTTGGCTGACTGTATTCGCAGTAGAGAAATCCTGGACCACCTAGATGGCAGTATAGAAGATGATGGGCTTTCGGGGCTCCTGAGACTGGCAACAAGTGTTATTAAACACAAGCCACCCTTCAAATTCTCAAGAGAGGGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGATGATGGGCTTTCGGGG
60.11
TGACTGCTAATACCGGTGCC
59.82
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGATGATGGGCTTTCGGGG
60.11
AGTGACTGCTAATACCGGTGC
60.13
142
PCR template sequence:
AGATGGCAGTATAGAAGATGATGGGCTTTCGGGGCTCCTGAGACTGGCAACAAGTGTTATTAAACACAAGCCACCCTTCAAATTCTCAAGAGAGGGACAGGTTTGCATATCATCTGAGACAGTGGCAGATTGAGGGCACCGGTATTAGCAGTCACTTGAAAGCACTGAGTGACAAACAGTCTTTGCCTCTAAGGGTTGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
28
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(2), mmu-miR-335-5p(2), mmu-miR-214-3p(2), mmu-miR-1904(2), mmu-miR-140-5p(1), mmu-miR-134-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-221-3p(1), mmu-miR-135a-5p(1), mmu-miR-31-5p(1), mmu-miR-122-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-29a-3p(1), mmu-miR-222-3p(1), mmu-miR-433-3p(1), mmu-miR-431-5p(1), mmu-miR-153-3p(1), mmu-miR-194-5p(1), mmu-miR-215-5p(1), mmu-miR-362-5p(1), mmu-miR-297a-5p(1), mmu-miR-705(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-207(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGAGAGGGACAGGTTTGCATATCAT
siRNA sets
TATGCAAACCTGTCCCTCT, ATGCAAACCTGTCCCTCTC, ATATGCAAACCTGTCCCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_1891_ORF_1
0.9914
-0.034817891
0.999911954
1797
ORF sequence:
ATGACTATTGAAATGTATCCAAGTGACCAGGTAGCAGATCTTCGTGCTGAAGTAACTCACTGGTATGAAAACTTACAGAAAGAACAAATAAATCAACAAGCTCAGCTTCAGGAGTTTGGTCAAAGCAGCAGAAAGGGAGAGTTTCCTGGTGGCCTCATGGGGCCTGTCAGGATGATCTCCTCTGGACATGAATTAACAACAGACTATGATGAAAAAGCACTTCATGAACTTGGTTTTAAAGATATGCAGATGGTGTTTGTATCTTTGGGTGCACCAAGAAGAGAAAGAAAAGGAGAAGGGGTTCAACTGCCTGCATCTTGCCTCCCACCACCTCAGAAGGACAACATTCCGATGCTTTTGCTGTTACAAGAACCTCATTTAACTACTCTCTTTGATTTATTAGAAATGCTTGCTTCATTTAAACCACCCTCAGGAAAAGTTGCAGTTGATGACAGTGAGAGTTTAAAATGTGAAGAACTTCATCTTCATGCAGAAAATCTTTCAAGGCGTGTCTGGGAGTTGCTGATGCTTCTTCCGACTTGTCCCAACATGCTGACGGCATTCCAGAATGTCTCAGACGAGCAGAGCAATGATGGACTTAATTGGAAGGAACTTCTCAAAATTAAGAGTGCTCATAAGTTGTTATATGCTCTTGAGATTATTGAAGCACTAGGAAAACCTAACAGAAGAATAAGAAGAGAGTCAACGGGAAGTTACAGTGATCTTTATCCAGATTCTGATGATTCAAGTGAAGATCAAGTGGAAAACAGTAAAAATTCCTGGACTTGCAAGTTTGTTGCTGCTGGCGGGCTTCAGCAGTTACTAGAAATTTTTAATTCTGCGATTCTAGAGCCTAAAGAGCAAGAATCATGGACTGTGTGGCAGCTGGATTGTCTTGCTTGCTTGCTGAAATTAATCTGCCAGTTTGCAGTAGATCCGTCAGATTTGGATTTAGCTTATCATGATGTTTTTGCCTGGTCTGGCATAGCCGAAAGCCATAGGAAAAGAACCTGGCCTGGAAAATCAAGAAAGGCTGCTGGTGATCATGCCAAGAGTCTTCATATACCACGATTAACAGAGGTGTTTCTTGTGCTTGTCCAAGGAACCAGTTTGATTCAGCGACTTATGTCTGTTGCTTATACGTATGATAATCTGGCTCCTAGAGTTTTGAAAGCTCAGTCTGATCATAGGTCTAGACATGAAGTGTCCCATTATTCAATGTGGCTCTTGGTGAGCTGGGCTCATTGCTGCTCTTTAGTCAAGTCTAGTCTTGCCGACAGTGATCATTTACAAGATTGGCTAAAACAGCTGACTCTCCTTATTCCCGAGACTGCAGTTCGCCATGAATCTTGCAATGGTCTCTATAAGCTATCTCTGTCAGGCCTAGATGGAGGAGACTCAATCCATCGATCCTTCCTTCTTTTGGCTGCCTCAACATTATTGAAATTCCTTCCTGATGCTCAAGCACTCAAACCTCCAAGGATAGATGATTATGAAGAAGAACCACTGTTAAAACCTGGATGTAAAGAATATTTTTGGTTATTATGCAAGTTAGTGGACAACATACACATAAAGGACGCTAGTCAGACAACACTCCTTGATTTAGATGCTTTGGCAAGACATTTGGCTGACTGTATTCGCAGTAGAGAAATCCTGGACCACCTAGATGGCAGTATAGAAGATGATGGGCTTTCGGGGCTCCTGAGACTGGCAACAAGTGTTATTAAACACAAGCCACCCTTCAAATTCTCAAGAGAGGGACAGGTTTGCATATCATCTGAGACAGTGGCAGATTGA
Peptide sequence:
MTIEMYPSDQVADLRAEVTHWYENLQKEQINQQAQLQEFGQSSRKGEFPGGLMGPVRMISSGHELTTDYDEKALHELGFKDMQMVFVSLGAPRRERKGEGVQLPASCLPPPQKDNIPMLLLLQEPHLTTLFDLLEMLASFKPPSGKVAVDDSESLKCEELHLHAENLSRRVWELLMLLPTCPNMLTAFQNVSDEQSNDGLNWKELLKIKSAHKLLYALEIIEALGKPNRRIRRESTGSYSDLYPDSDDSSEDQVENSKNSWTCKFVAAGGLQQLLEIFNSAILEPKEQESWTVWQLDCLACLLKLICQFAVDPSDLDLAYHDVFAWSGIAESHRKRTWPGKSRKAAGDHAKSLHIPRLTEVFLVLVQGTSLIQRLMSVAYTYDNLAPRVLKAQSDHRSRHEVSHYSMWLLVSWAHCCSLVKSSLADSDHLQDWLKQLTLLIPETAVRHESCNGLYKLSLSGLDGGDSIHRSFLLLAASTLLKFLPDAQALKPPRIDDYEEEPLLKPGCKEYFWLLCKLVDNIHIKDASQTTLLDLDALARHLADCIRSREILDHLDGSIEDDGLSGLLRLATSVIKHKPPFKFSREGQVCISSETVAD
IRESfinder result
IRESfinder score
0.73667192
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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