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mmu_circZcchc2_2254
Basic information of circular RNA
PanCircBase ID:
mmu_circZcchc2_2254
mm39_Chr. Position ID:
chr1|105939431|105958963|+
Gene name:
Zcchc2
Transcript:
ENSMUST00000118196.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,4297,6517,8146,10024,11498,11962,15701,18050
Genomic length:
19532
Exon/intron sizes in nt:
11,39,58,45,81,33,65,90,00,00,000
Flanking exon/introns:
chr1:105933816-105939431|chr1:105958963-105959825
Splice length:
2254
Other database IDs:
circAtlas: mmu-Zcchc2_0010
Human Ortholog IDs:
Mature spliced Sequence:
CTTCCAAAGGAATTCTCTTCTGAGAGTTTTGACAAGACCATCTTAAAAGCCCTGAATCAGGGTTCTCTAAGGAGGGAAGAGCGGCGCCACCCTGACCTGGAGCCCATCCTAAGGCAGCTGTTTTCAACCTCACCCCAGGCTTTCCTTCAGAGTCACAAAGTCCGCAGCTTTTTTCGGTCGATCTCATCGGAGTCTCAACACAATTTCAATAACTTACAGTCCTCTCTGAAGACTTCTAAGATATTAGAACACTTAAAAGAAGACAGCTCAGAAGCTTCAAGTCAAGAAGAAGATGTGTTACAGCACACCATCATCCACAAGAAACATGCTGGGAAAAGTCCCGCTCTGAATGTTGCTACAAGCTGTTCTCCATTGGATGGCCTTACCATGCAGTATGCAGAACAAAATGGAATTGTGGATTGGAGGAACCAAGGCTGTGCGGCCATCCAACACTCAGAACACTGTGTGTCCTCAGCTGACCAACACTCTGCTGAAAAACGGAGCTTATCTTCAGGAAATAAGAAGAAAGGGAAGCCACAAGTAGAAAAGGAGAAAGTAAAGAAAACTGAGGACAGATTGAACAGCAGAATAAATGGAATTAGACTCTCTGCTCCACAGCATGTTCATGGCAGTACTGTGAAAGATATGAATTTGGACATTGGATCTGGACATGACACATGTGGAGAAACATCTTCAGAGAGTTACAGCTCTCCGTCTAGTCCACGGCATGATGGAAGAGAGAGTTTGGAAAGTGAAGAAGAGAAGGACAGAGATTCAGACAGCAATTCTGAAGATTCTGTGAATCCGTCGTCAGCCAGGTTTTCAGGTTATGGCTCTGTCGCCCAGACCATCGCAGTCAAGCCGCCTGCTGAGACTGTCTCCCTGGGAACCGAGGACGGGAATCTTTTGGAAGCTGCACTGACCTCACACAAGTACCCGCATATTCCCTTCATGCCAACTCTACACTGTGTCACGCACAACGGTGCCCAGAAGTCGCAAGTTGTCATTCCGTCGCCCAAATCTGCAGATGGCAAAACCTTAGGGATGCTTGTCCCTAATGCGGTGGCTATTTCTGCAGTGATGGAATCCTCAAATTCAGCCCCTGTTGGAATCCTAGGCCCGGCAGCTTCTGGGGAGTCAGAGAAACACCTTGAGTTGTTAGCTTCCCCTTTACCTCTCCCATCAACCTTCCTCCCACACAGCAGTGCGCCTGCTTTGCAGCTGACATTACAGAGTCTAAAGTTACAGCCACCACAGGGATCTTCTGACAGTTGTCCAGTTAGTATCCCACCACAACCAACCGGAAGTCTGAGCATCGGATCACCAAACACTGCCTTTATTCCTGTCCATAACCCAGGTAGTTTCCCAGGGTCTCCTGTGGCTACCACGGATCCCATCACAAAATCCGCACCCCAAGTGGTAGGACTAAATCAAATGGTGCCTCAGATTGAGGGGAACACAGGGACAGTCCCTCAGCCGAGCAATGTGAAGGTAGTTCTTCCGGCAGCGGGCCTCTCAGCTGCACAGCCACCAGCTTCCTTCCCCTTTCCAGGCTCACCCCAGGCTGCCAGTGCACTCCCCACCCAGAATTCCAGTGCGCTCAACGCAGCCACTTCTGCCCAGCCAGCAAGCACAGGCATCAGTCCATCCCAGTCCACAGTTCCCCCTGCTGTTCCCACCCACACCCCAGGCCCTGCCCCGAGCCCCAGCCCTGCCTTGACACACAGTACTGCACAGAGCGACAGCACGTCGTACATCAGTGCTGTGGGGAACACGAATGCTAACGGGACCATAGTGCCACCACAGCAGATGGGTCCCTGTGGTTCTTGTGGGCGAAGGTGCAGCTGCGGGACCAATGGAAACCTCCAGCTAAATAGTTACTATTATCCCAACCCAATGCCTGGACCAATGTACCGACTCCCATCATTCTTCACTCTGCCATCCATTTGCAATGGCAGCTACCTCAACCAAGCACATCAGAGCAATGGAAACCAACTTCCTTTTTTTCTGCCTCAGACTCCATATGCAAATGGACTGGTGCATGACCCAGTCATGGGGAGCCAAGCCAGCTATGGCATGCAGCAGATGGCAGGATTTGGGAGATTGTATCCTGTATATCCAGCACCTAATGTAGTTGCCAACACCAGTGGTTCTGGGCCCAAGAAGAATGGGAATGTCTCATGTTACAATTGTGGTGTAAGCGGACACTATGCACAAGACTGTAAGCAGTCATCCATGGAGGCCAATCAGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCGGACACTATGCACAAGA
59.39
GCCGCTCTTCCCTCCTTAGA
61.04
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCGGACACTATGCACAAGA
60
CCGCTCTTCCCTCCTTAGAG
58.96
140
PCR template sequence:
GGGCCCAAGAAGAATGGGAATGTCTCATGTTACAATTGTGGTGTAAGCGGACACTATGCACAAGACTGTAAGCAGTCATCCATGGAGGCCAATCAGCAAGCTTCCAAAGGAATTCTCTTCTGAGAGTTTTGACAAGACCATCTTAAAAGCCCTGAATCAGGGTTCTCTAAGGAGGGAAGAGCGGCGCCACCCTGACCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
35
Interacting miRNAs (#binding sites)
mmu-miR-210-3p(1), mmu-miR-23b-3p(1), mmu-let-7a-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-150-5p(1), mmu-miR-221-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-101a-3p(1), mmu-let-7c-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-29b-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-222-3p(1), mmu-miR-184-3p(1), mmu-miR-709(1), mmu-miR-324-5p(1), mmu-miR-23a-3p(1), mmu-miR-138-5p(1), mmu-let-7d-5p(1), mmu-miR-136-5p(1), mmu-miR-22-3p(1), mmu-miR-127-5p(1), mmu-miR-34b-5p(1), mmu-miR-342-5p(1), mmu-miR-705(1), mmu-miR-29b-2-5p(1), mmu-miR-669d-5p(1), mmu-miR-3105-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCAATCAGCAAGCTTCCAAAGGAAT
siRNA sets
TTGGAAGCTTGCTGATTGG, ATTCCTTTGGAAGCTTGCT, TGGAAGCTTGCTGATTGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCZCCHC2_2254_ORF_1
0.7806
0.124479314
0.999998141
2298
ORF sequence:
ATGCACAAGACTGTAAGCAGTCATCCATGGAGGCCAATCAGCAAGCTTCCAAAGGAATTCTCTTCTGAGAGTTTTGACAAGACCATCTTAAAAGCCCTGAATCAGGGTTCTCTAAGGAGGGAAGAGCGGCGCCACCCTGACCTGGAGCCCATCCTAAGGCAGCTGTTTTCAACCTCACCCCAGGCTTTCCTTCAGAGTCACAAAGTCCGCAGCTTTTTTCGGTCGATCTCATCGGAGTCTCAACACAATTTCAATAACTTACAGTCCTCTCTGAAGACTTCTAAGATATTAGAACACTTAAAAGAAGACAGCTCAGAAGCTTCAAGTCAAGAAGAAGATGTGTTACAGCACACCATCATCCACAAGAAACATGCTGGGAAAAGTCCCGCTCTGAATGTTGCTACAAGCTGTTCTCCATTGGATGGCCTTACCATGCAGTATGCAGAACAAAATGGAATTGTGGATTGGAGGAACCAAGGCTGTGCGGCCATCCAACACTCAGAACACTGTGTGTCCTCAGCTGACCAACACTCTGCTGAAAAACGGAGCTTATCTTCAGGAAATAAGAAGAAAGGGAAGCCACAAGTAGAAAAGGAGAAAGTAAAGAAAACTGAGGACAGATTGAACAGCAGAATAAATGGAATTAGACTCTCTGCTCCACAGCATGTTCATGGCAGTACTGTGAAAGATATGAATTTGGACATTGGATCTGGACATGACACATGTGGAGAAACATCTTCAGAGAGTTACAGCTCTCCGTCTAGTCCACGGCATGATGGAAGAGAGAGTTTGGAAAGTGAAGAAGAGAAGGACAGAGATTCAGACAGCAATTCTGAAGATTCTGTGAATCCGTCGTCAGCCAGGTTTTCAGGTTATGGCTCTGTCGCCCAGACCATCGCAGTCAAGCCGCCTGCTGAGACTGTCTCCCTGGGAACCGAGGACGGGAATCTTTTGGAAGCTGCACTGACCTCACACAAGTACCCGCATATTCCCTTCATGCCAACTCTACACTGTGTCACGCACAACGGTGCCCAGAAGTCGCAAGTTGTCATTCCGTCGCCCAAATCTGCAGATGGCAAAACCTTAGGGATGCTTGTCCCTAATGCGGTGGCTATTTCTGCAGTGATGGAATCCTCAAATTCAGCCCCTGTTGGAATCCTAGGCCCGGCAGCTTCTGGGGAGTCAGAGAAACACCTTGAGTTGTTAGCTTCCCCTTTACCTCTCCCATCAACCTTCCTCCCACACAGCAGTGCGCCTGCTTTGCAGCTGACATTACAGAGTCTAAAGTTACAGCCACCACAGGGATCTTCTGACAGTTGTCCAGTTAGTATCCCACCACAACCAACCGGAAGTCTGAGCATCGGATCACCAAACACTGCCTTTATTCCTGTCCATAACCCAGGTAGTTTCCCAGGGTCTCCTGTGGCTACCACGGATCCCATCACAAAATCCGCACCCCAAGTGGTAGGACTAAATCAAATGGTGCCTCAGATTGAGGGGAACACAGGGACAGTCCCTCAGCCGAGCAATGTGAAGGTAGTTCTTCCGGCAGCGGGCCTCTCAGCTGCACAGCCACCAGCTTCCTTCCCCTTTCCAGGCTCACCCCAGGCTGCCAGTGCACTCCCCACCCAGAATTCCAGTGCGCTCAACGCAGCCACTTCTGCCCAGCCAGCAAGCACAGGCATCAGTCCATCCCAGTCCACAGTTCCCCCTGCTGTTCCCACCCACACCCCAGGCCCTGCCCCGAGCCCCAGCCCTGCCTTGACACACAGTACTGCACAGAGCGACAGCACGTCGTACATCAGTGCTGTGGGGAACACGAATGCTAACGGGACCATAGTGCCACCACAGCAGATGGGTCCCTGTGGTTCTTGTGGGCGAAGGTGCAGCTGCGGGACCAATGGAAACCTCCAGCTAAATAGTTACTATTATCCCAACCCAATGCCTGGACCAATGTACCGACTCCCATCATTCTTCACTCTGCCATCCATTTGCAATGGCAGCTACCTCAACCAAGCACATCAGAGCAATGGAAACCAACTTCCTTTTTTTCTGCCTCAGACTCCATATGCAAATGGACTGGTGCATGACCCAGTCATGGGGAGCCAAGCCAGCTATGGCATGCAGCAGATGGCAGGATTTGGGAGATTGTATCCTGTATATCCAGCACCTAATGTAGTTGCCAACACCAGTGGTTCTGGGCCCAAGAAGAATGGGAATGTCTCATGTTACAATTGTGGTGTAAGCGGACACTATGCACAAGACTGTAAGCAGTCATCCATGGAGGCCAATCAGCAA
Peptide sequence:
MHKTVSSHPWRPISKLPKEFSSESFDKTILKALNQGSLRREERRHPDLEPILRQLFSTSPQAFLQSHKVRSFFRSISSESQHNFNNLQSSLKTSKILEHLKEDSSEASSQEEDVLQHTIIHKKHAGKSPALNVATSCSPLDGLTMQYAEQNGIVDWRNQGCAAIQHSEHCVSSADQHSAEKRSLSSGNKKKGKPQVEKEKVKKTEDRLNSRINGIRLSAPQHVHGSTVKDMNLDIGSGHDTCGETSSESYSSPSSPRHDGRESLESEEEKDRDSDSNSEDSVNPSSARFSGYGSVAQTIAVKPPAETVSLGTEDGNLLEAALTSHKYPHIPFMPTLHCVTHNGAQKSQVVIPSPKSADGKTLGMLVPNAVAISAVMESSNSAPVGILGPAASGESEKHLELLASPLPLPSTFLPHSSAPALQLTLQSLKLQPPQGSSDSCPVSIPPQPTGSLSIGSPNTAFIPVHNPGSFPGSPVATTDPITKSAPQVVGLNQMVPQIEGNTGTVPQPSNVKVVLPAAGLSAAQPPASFPFPGSPQAASALPTQNSSALNAATSAQPASTGISPSQSTVPPAVPTHTPGPAPSPSPALTHSTAQSDSTSYISAVGNTNANGTIVPPQQMGPCGSCGRRCSCGTNGNLQLNSYYYPNPMPGPMYRLPSFFTLPSICNGSYLNQAHQSNGNQLPFFLPQTPYANGLVHDPVMGSQASYGMQQMAGFGRLYPVYPAPNVVANTSGSGPKKNGNVSCYNCGVSGHYAQDCKQSSMEANQQ
IRESfinder result
IRESfinder score
0.51806747
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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