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mmu_circFocad_782
Basic information of circular RNA
PanCircBase ID:
mmu_circFocad_782
mm39_Chr. Position ID:
chr4|88244379|88267130|+
Gene name:
Focad
Transcript:
ENSMUST00000097992.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
22,23,24,25,26,27,28
Exon/intron offsets:
0,4826,10025,13042,16060,18436,22661
Genomic length:
22751
Exon/intron sizes in nt:
93,89,45,109,117,239,90
Flanking exon/introns:
chr4:88228150-88244379|chr4:88267130-88273604
Splice length:
782
Other database IDs:
CIRCpedia: MMU_CIRCpedia_33072, circAtlas: mmu-Focad_0030
circBase: hsa_circ_0086564, circAtlas: hsa-FOCAD_0109, CIRCpedia: HSA_CIRCpedia_63755
Human Ortholog IDs:
Mature spliced Sequence:
GTCCATGTCCAGCTTTCAGAATGGCACCGTGCAATCTTTCTTCCACAGGCCTGGCTTGCATACATGACTCGAGCTTACCATGCCATTTTACAGGGAAGGATAGCAGAGCTGGAGCTGCAGCTGCAGCACGGCAAGGAAGGCCCTGAGGAGGTGCAATACAAACGAAGCACAGCCTGGCTCTGGGTCAGAGACATGCTGACAGATGAGATCACCAAGACAGCTGCAAAAGAGAGTCCGGTGGTGAAAGCCAATGCCCTGTTAGCCTTAAGCAGCCTGGCCGTTGTGGTGTCCAAGCATGAAGCCAGCCTTTGCTCAGACTCCGATGGCGTCCTAGAGATCCAACCTAATTTCCTTCCAGTGAAAGAGTGGGTTTCCATGGTGCTTAATACTCTCCTGGTCATTGTGGATAGCCATTACCACCCCAGTGGACAACTCTTCACCTGCTTTTATCATAAGTCCTATTCTGGCGAGAACACAGCGAGCGCTATTGCGCGCTCTGCTGCCGCCACGGCTTTGTCTCTCCTAGTGCCAGTTTTCATTATCTCATGCAAAGAGAAGGTTGAGGAAATCCTGAACATGCTGACTGCCAGGTTACCTGGGAAACCAAGTGCTGATGAATCTCAGGCCGTGCAAATCCACATGGGCCTTGCGTTGGGGATGTTTCTCTCTCGCTTGTGTGAAGAGAAGCTCAGTGACATGTCTGGACAACAGATGAACCTTCTTCTGATGAAGTCCTTGGATGCCCTGGAAAGCTGCTGTTTTGACCCCAGTCTTGAATACAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAGTCCTTGGATGCCCTG
59.67
TGGCATGGTAAGCTCGAGTC
59.82
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAGTCCTTGGATGCCCTG
59.67
ATGGCATGGTAAGCTCGAGT
59.17
141
PCR template sequence:
AGAAGCTCAGTGACATGTCTGGACAACAGATGAACCTTCTTCTGATGAAGTCCTTGGATGCCCTGGAAAGCTGCTGTTTTGACCCCAGTCTTGAATACAAGTCCATGTCCAGCTTTCAGAATGGCACCGTGCAATCTTTCTTCCACAGGCCTGGCTTGCATACATGACTCGAGCTTACCATGCCATTTTACAGGGAAGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(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-490-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTTGAATACAAGTCCATGTCCAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFOCAD_782_ORF_1
1.1241
0.235447496
0.969094934
786
ORF sequence:
ATGACTCGAGCTTACCATGCCATTTTACAGGGAAGGATAGCAGAGCTGGAGCTGCAGCTGCAGCACGGCAAGGAAGGCCCTGAGGAGGTGCAATACAAACGAAGCACAGCCTGGCTCTGGGTCAGAGACATGCTGACAGATGAGATCACCAAGACAGCTGCAAAAGAGAGTCCGGTGGTGAAAGCCAATGCCCTGTTAGCCTTAAGCAGCCTGGCCGTTGTGGTGTCCAAGCATGAAGCCAGCCTTTGCTCAGACTCCGATGGCGTCCTAGAGATCCAACCTAATTTCCTTCCAGTGAAAGAGTGGGTTTCCATGGTGCTTAATACTCTCCTGGTCATTGTGGATAGCCATTACCACCCCAGTGGACAACTCTTCACCTGCTTTTATCATAAGTCCTATTCTGGCGAGAACACAGCGAGCGCTATTGCGCGCTCTGCTGCCGCCACGGCTTTGTCTCTCCTAGTGCCAGTTTTCATTATCTCATGCAAAGAGAAGGTTGAGGAAATCCTGAACATGCTGACTGCCAGGTTACCTGGGAAACCAAGTGCTGATGAATCTCAGGCCGTGCAAATCCACATGGGCCTTGCGTTGGGGATGTTTCTCTCTCGCTTGTGTGAAGAGAAGCTCAGTGACATGTCTGGACAACAGATGAACCTTCTTCTGATGAAGTCCTTGGATGCCCTGGAAAGCTGCTGTTTTGACCCCAGTCTTGAATACAAGTCCATGTCCAGCTTTCAGAATGGCACCGTGCAATCTTTCTTCCACAGGCCTGGCTTGCATACATGA
Peptide sequence:
MTRAYHAILQGRIAELELQLQHGKEGPEEVQYKRSTAWLWVRDMLTDEITKTAAKESPVVKANALLALSSLAVVVSKHEASLCSDSDGVLEIQPNFLPVKEWVSMVLNTLLVIVDSHYHPSGQLFTCFYHKSYSGENTASAIARSAAATALSLLVPVFIISCKEKVEEILNMLTARLPGKPSADESQAVQIHMGLALGMFLSRLCEEKLSDMSGQQMNLLLMKSLDALESCCFDPSLEYKSMSSFQNGTVQSFFHRPGLHT
IRESfinder result
IRESfinder score
0.408565196
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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