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mmu_circUsp34_1290
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_1290
mm39_Chr. Position ID:
chr11|23338433|23364818|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
26,27,28,29,30,31,32,33,34,35
Exon/intron offsets:
0,230,4408,5318,13019,15126,15378,17433,23781,26302
Genomic length:
26385
Exon/intron sizes in nt:
127,148,101,210,126,123,84,87,201,83
Flanking exon/introns:
chr11:23335172-23338433|chr11:23364818-23367462
Splice length:
1290
Other database IDs:
CIRCpedia: MMU_CIRCpedia_13839
Human Ortholog IDs:
Mature spliced Sequence:
GTTTGCATATCATCTGAGACAGTGGCAGATTGAGGGCACCGGTATTAGCAGTCACTTGAAAGCACTGAGTGACAAACAGTCTTTGCCTCTAAGGGTTGTATGTCAGCCTGCTGGACTTCCCGACAAGATGACTATTGAAATGTATCCAAGTGACCAGGTAGCAGATCTTCGTGCTGAAGTAACTCACTGGTATGAAAACTTACAGAAAGAACAAATAAATCAACAAGCTCAGCTTCAGGAGTTTGGTCAAAGCAGCAGAAAGGGAGAGTTTCCTGGTGGCCTCATGGGGCCTGTCAGGATGATCTCCTCTGGACATGAATTAACAACAGACTATGATGAAAAAGCACTTCATGAACTTGGTTTTAAAGATATGCAGATGGTGTTTGTATCTTTGGGTGCACCAAGAAGAGAAAGAAAAGGAGAAGGGGTTCAACTGCCTGCATCTTGCCTCCCACCACCTCAGAAGGACAACATTCCGATGCTTTTGCTGTTACAAGAACCTCATTTAACTACTCTCTTTGATTTATTAGAAATGCTTGCTTCATTTAAACCACCCTCAGGAAAAGTTGCAGTTGATGACAGTGAGAGTTTAAAATGTGAAGAACTTCATCTTCATGCAGAAAATCTTTCAAGGCGTGTCTGGGAGTTGCTGATGCTTCTTCCGACTTGTCCCAACATGCTGACGGCATTCCAGAATGTCTCAGACGAGCAGAGCAATGATGGACTTAATTGGAAGGAACTTCTCAAAATTAAGAGTGCTCATAAGTTGTTATATGCTCTTGAGATTATTGAAGCACTAGGAAAACCTAACAGAAGAATAAGAAGAGAGTCAACGGGAAGTTACAGTGATCTTTATCCAGATTCTGATGATTCAAGTGAAGATCAAGTGGAAAACAGTAAAAATTCCTGGACTTGCAAGTTTGTTGCTGCTGGCGGGCTTCAGCAGTTACTAGAAATTTTTAATTCTGCGATTCTAGAGCCTAAAGAGCAAGAATCATGGACTGTGTGGCAGCTGGATTGTCTTGCTTGCTTGCTGAAATTAATCTGCCAGTTTGCAGTAGATCCGTCAGATTTGGATTTAGCTTATCATGATGTTTTTGCCTGGTCTGGCATAGCCGAAAGCCATAGGAAAAGAACCTGGCCTGGAAAATCAAGAAAGGCTGCTGGTGATCATGCCAAGAGTCTTCATATACCACGATTAACAGAGGTGTTTCTTGTGCTTGTCCAAGGAACCAGTTTGATTCAGCGACTTATGTCTGTTGCTTATACGTATGATAATCTGGCTCCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGCTTGTCCAAGGAACCA
59.74
TCAGTGCTTTCAAGTGACTGC
59.06
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGCTTGTCCAAGGAACCA
59.74
CAGTGCTTTCAAGTGACTGCT
59.05
142
PCR template sequence:
TACCACGATTAACAGAGGTGTTTCTTGTGCTTGTCCAAGGAACCAGTTTGATTCAGCGACTTATGTCTGTTGCTTATACGTATGATAATCTGGCTCCTAGGTTTGCATATCATCTGAGACAGTGGCAGATTGAGGGCACCGGTATTAGCAGTCACTTGAAAGCACTGAGTGACAAACAGTCTTTGCCTCTAAGGGTTGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-214-3p(2), mmu-miR-1904(2), mmu-miR-134-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-135a-5p(1), mmu-miR-31-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-322-5p(1), mmu-miR-29a-3p(1), mmu-miR-335-5p(1), mmu-miR-433-3p(1), mmu-miR-194-5p(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
ATCTGGCTCCTAGGTTTGCATATCAT
siRNA sets
ATGATATGCAAACCTAGGA, ATATGCAAACCTAGGAGCC, TATGCAAACCTAGGAGCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_1290_ORF_1
1.0486
-0.015552046
0.999999365
2451
ORF sequence:
ATGACTATTGAAATGTATCCAAGTGACCAGGTAGCAGATCTTCGTGCTGAAGTAACTCACTGGTATGAAAACTTACAGAAAGAACAAATAAATCAACAAGCTCAGCTTCAGGAGTTTGGTCAAAGCAGCAGAAAGGGAGAGTTTCCTGGTGGCCTCATGGGGCCTGTCAGGATGATCTCCTCTGGACATGAATTAACAACAGACTATGATGAAAAAGCACTTCATGAACTTGGTTTTAAAGATATGCAGATGGTGTTTGTATCTTTGGGTGCACCAAGAAGAGAAAGAAAAGGAGAAGGGGTTCAACTGCCTGCATCTTGCCTCCCACCACCTCAGAAGGACAACATTCCGATGCTTTTGCTGTTACAAGAACCTCATTTAACTACTCTCTTTGATTTATTAGAAATGCTTGCTTCATTTAAACCACCCTCAGGAAAAGTTGCAGTTGATGACAGTGAGAGTTTAAAATGTGAAGAACTTCATCTTCATGCAGAAAATCTTTCAAGGCGTGTCTGGGAGTTGCTGATGCTTCTTCCGACTTGTCCCAACATGCTGACGGCATTCCAGAATGTCTCAGACGAGCAGAGCAATGATGGACTTAATTGGAAGGAACTTCTCAAAATTAAGAGTGCTCATAAGTTGTTATATGCTCTTGAGATTATTGAAGCACTAGGAAAACCTAACAGAAGAATAAGAAGAGAGTCAACGGGAAGTTACAGTGATCTTTATCCAGATTCTGATGATTCAAGTGAAGATCAAGTGGAAAACAGTAAAAATTCCTGGACTTGCAAGTTTGTTGCTGCTGGCGGGCTTCAGCAGTTACTAGAAATTTTTAATTCTGCGATTCTAGAGCCTAAAGAGCAAGAATCATGGACTGTGTGGCAGCTGGATTGTCTTGCTTGCTTGCTGAAATTAATCTGCCAGTTTGCAGTAGATCCGTCAGATTTGGATTTAGCTTATCATGATGTTTTTGCCTGGTCTGGCATAGCCGAAAGCCATAGGAAAAGAACCTGGCCTGGAAAATCAAGAAAGGCTGCTGGTGATCATGCCAAGAGTCTTCATATACCACGATTAACAGAGGTGTTTCTTGTGCTTGTCCAAGGAACCAGTTTGATTCAGCGACTTATGTCTGTTGCTTATACGTATGATAATCTGGCTCCTAGGTTTGCATATCATCTGAGACAGTGGCAGATTGAGGGCACCGGTATTAGCAGTCACTTGAAAGCACTGAGTGACAAACAGTCTTTGCCTCTAAGGGTTGTATGTCAGCCTGCTGGACTTCCCGACAAGATGACTATTGAAATGTATCCAAGTGACCAGGTAGCAGATCTTCGTGCTGAAGTAACTCACTGGTATGAAAACTTACAGAAAGAACAAATAAATCAACAAGCTCAGCTTCAGGAGTTTGGTCAAAGCAGCAGAAAGGGAGAGTTTCCTGGTGGCCTCATGGGGCCTGTCAGGATGATCTCCTCTGGACATGAATTAACAACAGACTATGATGAAAAAGCACTTCATGAACTTGGTTTTAAAGATATGCAGATGGTGTTTGTATCTTTGGGTGCACCAAGAAGAGAAAGAAAAGGAGAAGGGGTTCAACTGCCTGCATCTTGCCTCCCACCACCTCAGAAGGACAACATTCCGATGCTTTTGCTGTTACAAGAACCTCATTTAACTACTCTCTTTGATTTATTAGAAATGCTTGCTTCATTTAAACCACCCTCAGGAAAAGTTGCAGTTGATGACAGTGAGAGTTTAAAATGTGAAGAACTTCATCTTCATGCAGAAAATCTTTCAAGGCGTGTCTGGGAGTTGCTGATGCTTCTTCCGACTTGTCCCAACATGCTGACGGCATTCCAGAATGTCTCAGACGAGCAGAGCAATGATGGACTTAATTGGAAGGAACTTCTCAAAATTAAGAGTGCTCATAAGTTGTTATATGCTCTTGAGATTATTGAAGCACTAGGAAAACCTAACAGAAGAATAAGAAGAGAGTCAACGGGAAGTTACAGTGATCTTTATCCAGATTCTGATGATTCAAGTGAAGATCAAGTGGAAAACAGTAAAAATTCCTGGACTTGCAAGTTTGTTGCTGCTGGCGGGCTTCAGCAGTTACTAGAAATTTTTAATTCTGCGATTCTAGAGCCTAAAGAGCAAGAATCATGGACTGTGTGGCAGCTGGATTGTCTTGCTTGCTTGCTGAAATTAATCTGCCAGTTTGCAGTAGATCCGTCAGATTTGGATTTAGCTTATCATGATGTTTTTGCCTGGTCTGGCATAGCCGAAAGCCATAGGAAAAGAACCTGGCCTGGAAAATCAAGAAAGGCTGCTGGTGATCATGCCAAGAGTCTTCATATACCACGATTAACAGAGGTGTTTCTTGTGCTTGTCCAAGGAACCAGTTTGATTCAGCGACTTATGTCTGTTGCTTATACGTATGATAATCTGGCTCCT
Peptide sequence:
MTIEMYPSDQVADLRAEVTHWYENLQKEQINQQAQLQEFGQSSRKGEFPGGLMGPVRMISSGHELTTDYDEKALHELGFKDMQMVFVSLGAPRRERKGEGVQLPASCLPPPQKDNIPMLLLLQEPHLTTLFDLLEMLASFKPPSGKVAVDDSESLKCEELHLHAENLSRRVWELLMLLPTCPNMLTAFQNVSDEQSNDGLNWKELLKIKSAHKLLYALEIIEALGKPNRRIRRESTGSYSDLYPDSDDSSEDQVENSKNSWTCKFVAAGGLQQLLEIFNSAILEPKEQESWTVWQLDCLACLLKLICQFAVDPSDLDLAYHDVFAWSGIAESHRKRTWPGKSRKAAGDHAKSLHIPRLTEVFLVLVQGTSLIQRLMSVAYTYDNLAPRFAYHLRQWQIEGTGISSHLKALSDKQSLPLRVVCQPAGLPDKMTIEMYPSDQVADLRAEVTHWYENLQKEQINQQAQLQEFGQSSRKGEFPGGLMGPVRMISSGHELTTDYDEKALHELGFKDMQMVFVSLGAPRRERKGEGVQLPASCLPPPQKDNIPMLLLLQEPHLTTLFDLLEMLASFKPPSGKVAVDDSESLKCEELHLHAENLSRRVWELLMLLPTCPNMLTAFQNVSDEQSNDGLNWKELLKIKSAHKLLYALEIIEALGKPNRRIRRESTGSYSDLYPDSDDSSEDQVENSKNSWTCKFVAAGGLQQLLEIFNSAILEPKEQESWTVWQLDCLACLLKLICQFAVDPSDLDLAYHDVFAWSGIAESHRKRTWPGKSRKAAGDHAKSLHIPRLTEVFLVLVQGTSLIQRLMSVAYTYDNLAP
IRESfinder result
IRESfinder score
0.731407502
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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