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mmu_circFocad_1090
Basic information of circular RNA
PanCircBase ID:
mmu_circFocad_1090
mm39_Chr. Position ID:
chr4|88221681|88267130|+
Gene name:
Focad
Transcript:
ENSMUST00000097992.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
20,21,22,23,24,25,26,27,28
Exon/intron offsets:
0,6347,22698,27524,32723,35740,38758,41134,45359
Genomic length:
45449
Exon/intron sizes in nt:
186,122,93,89,45,109,117,239,90
Flanking exon/introns:
chr4:88215338-88221681|chr4:88267130-88273604
Splice length:
1090
Other database IDs:
circAtlas: mmu-Focad_0104
circBase: hsa_circ_0002555, circAtlas: hsa-FOCAD_0111, CIRCpedia: HSA_CIRCpedia_63749
Human Ortholog IDs:
Mature spliced Sequence:
CATTGGAAGAATTCTTTACATCTCTTGTGAGACAAGAGATGGTGAATATGCCCCGTGGGATATATCACTCTGCATTGAAAGGAGGCGTGCGCTCAGACCAAGGGAAGACAGTAGCAGGAATCCCGAACTTCATATTGAAGACATACGAAACAAACAAGCAACCAGGATTGAAACCTGGCCTGGCAGGTGGCATGCTGTTTTGCTATGATCTTGCCATGTATCAGAGCAAAGATGGCAAGCCACTGAATCGGCTGATGGCCAGTAGAGGGCGAAGCTTCAAGCAGACAACACTGGCTCTCATTCATGAAGTCCATGTCCAGCTTTCAGAATGGCACCGTGCAATCTTTCTTCCACAGGCCTGGCTTGCATACATGACTCGAGCTTACCATGCCATTTTACAGGGAAGGATAGCAGAGCTGGAGCTGCAGCTGCAGCACGGCAAGGAAGGCCCTGAGGAGGTGCAATACAAACGAAGCACAGCCTGGCTCTGGGTCAGAGACATGCTGACAGATGAGATCACCAAGACAGCTGCAAAAGAGAGTCCGGTGGTGAAAGCCAATGCCCTGTTAGCCTTAAGCAGCCTGGCCGTTGTGGTGTCCAAGCATGAAGCCAGCCTTTGCTCAGACTCCGATGGCGTCCTAGAGATCCAACCTAATTTCCTTCCAGTGAAAGAGTGGGTTTCCATGGTGCTTAATACTCTCCTGGTCATTGTGGATAGCCATTACCACCCCAGTGGACAACTCTTCACCTGCTTTTATCATAAGTCCTATTCTGGCGAGAACACAGCGAGCGCTATTGCGCGCTCTGCTGCCGCCACGGCTTTGTCTCTCCTAGTGCCAGTTTTCATTATCTCATGCAAAGAGAAGGTTGAGGAAATCCTGAACATGCTGACTGCCAGGTTACCTGGGAAACCAAGTGCTGATGAATCTCAGGCCGTGCAAATCCACATGGGCCTTGCGTTGGGGATGTTTCTCTCTCGCTTGTGTGAAGAGAAGCTCAGTGACATGTCTGGACAACAGATGAACCTTCTTCTGATGAAGTCCTTGGATGCCCTGGAAAGCTGCTGTTTTGACCCCAGTCTTGAATACAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCTTGGATGCCCTGGAAA
59.96
CACGCCTCCTTTCAATGCAG
59.83
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAGTCCTTGGATGCCCTG
59.67
ACGCCTCCTTTCAATGCAGA
59.96
143
PCR template sequence:
AGAAGCTCAGTGACATGTCTGGACAACAGATGAACCTTCTTCTGATGAAGTCCTTGGATGCCCTGGAAAGCTGCTGTTTTGACCCCAGTCTTGAATACAACATTGGAAGAATTCTTTACATCTCTTGTGAGACAAGAGATGGTGAATATGCCCCGTGGGATATATCACTCTGCATTGAAAGGAGGCGTGCGCTCAGACCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(1), mmu-miR-199a-5p(1), mmu-miR-31-5p(1), mmu-miR-92a-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-25-3p(1), mmu-miR-185-5p(1), mmu-miR-363-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-5101(1), mmu-miR-490-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTTGAATACAACATTGGAAGAATT
siRNA sets
TTCTTCCAATGTTGTATTC, AATTCTTCCAATGTTGTAT, ATTCTTCCAATGTTGTATT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFOCAD_1090_ORF_1
0.9524
0.16708023
0.998078554
1260
ORF sequence:
ATGGTGAATATGCCCCGTGGGATATATCACTCTGCATTGAAAGGAGGCGTGCGCTCAGACCAAGGGAAGACAGTAGCAGGAATCCCGAACTTCATATTGAAGACATACGAAACAAACAAGCAACCAGGATTGAAACCTGGCCTGGCAGGTGGCATGCTGTTTTGCTATGATCTTGCCATGTATCAGAGCAAAGATGGCAAGCCACTGAATCGGCTGATGGCCAGTAGAGGGCGAAGCTTCAAGCAGACAACACTGGCTCTCATTCATGAAGTCCATGTCCAGCTTTCAGAATGGCACCGTGCAATCTTTCTTCCACAGGCCTGGCTTGCATACATGACTCGAGCTTACCATGCCATTTTACAGGGAAGGATAGCAGAGCTGGAGCTGCAGCTGCAGCACGGCAAGGAAGGCCCTGAGGAGGTGCAATACAAACGAAGCACAGCCTGGCTCTGGGTCAGAGACATGCTGACAGATGAGATCACCAAGACAGCTGCAAAAGAGAGTCCGGTGGTGAAAGCCAATGCCCTGTTAGCCTTAAGCAGCCTGGCCGTTGTGGTGTCCAAGCATGAAGCCAGCCTTTGCTCAGACTCCGATGGCGTCCTAGAGATCCAACCTAATTTCCTTCCAGTGAAAGAGTGGGTTTCCATGGTGCTTAATACTCTCCTGGTCATTGTGGATAGCCATTACCACCCCAGTGGACAACTCTTCACCTGCTTTTATCATAAGTCCTATTCTGGCGAGAACACAGCGAGCGCTATTGCGCGCTCTGCTGCCGCCACGGCTTTGTCTCTCCTAGTGCCAGTTTTCATTATCTCATGCAAAGAGAAGGTTGAGGAAATCCTGAACATGCTGACTGCCAGGTTACCTGGGAAACCAAGTGCTGATGAATCTCAGGCCGTGCAAATCCACATGGGCCTTGCGTTGGGGATGTTTCTCTCTCGCTTGTGTGAAGAGAAGCTCAGTGACATGTCTGGACAACAGATGAACCTTCTTCTGATGAAGTCCTTGGATGCCCTGGAAAGCTGCTGTTTTGACCCCAGTCTTGAATACAACATTGGAAGAATTCTTTACATCTCTTGTGAGACAAGAGATGGTGAATATGCCCCGTGGGATATATCACTCTGCATTGAAAGGAGGCGTGCGCTCAGACCAAGGGAAGACAGTAGCAGGAATCCCGAACTTCATATTGAAGACATACGAAACAAACAAGCAACCAGGATTGAAACCTGGCCTGGCAGGTGGCATGCTGTTTTGCTATGA
Peptide sequence:
MVNMPRGIYHSALKGGVRSDQGKTVAGIPNFILKTYETNKQPGLKPGLAGGMLFCYDLAMYQSKDGKPLNRLMASRGRSFKQTTLALIHEVHVQLSEWHRAIFLPQAWLAYMTRAYHAILQGRIAELELQLQHGKEGPEEVQYKRSTAWLWVRDMLTDEITKTAAKESPVVKANALLALSSLAVVVSKHEASLCSDSDGVLEIQPNFLPVKEWVSMVLNTLLVIVDSHYHPSGQLFTCFYHKSYSGENTASAIARSAAATALSLLVPVFIISCKEKVEEILNMLTARLPGKPSADESQAVQIHMGLALGMFLSRLCEEKLSDMSGQQMNLLLMKSLDALESCCFDPSLEYNIGRILYISCETRDGEYAPWDISLCIERRRALRPREDSSRNPELHIEDIRNKQATRIETWPGRWHAVLL
IRESfinder result
IRESfinder score
0.409534064
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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