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mmu_circRufy3_1159
Basic information of circular RNA
PanCircBase ID:
mmu_circRufy3_1159
mm39_Chr. Position ID:
chr5|88762799|88786937|+
Gene name:
Rufy3
Transcript:
ENSMUST00000196894.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,1521,2394,6360,12280,13084,15596,17498,20251,22251,24040
Genomic length:
24138
Exon/intron sizes in nt:
174,118,102,124,62,66,70,93,84,168,98
Flanking exon/introns:
chr5:88713335-88762799|chr5:88786937-88788447
Splice length:
1159
Other database IDs:
CIRCpedia: MMU_CIRCpedia_229427, circAtlas: mmu-Rufy3_0001
circBase: hsa_circ_0069912, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_49020
Human Ortholog IDs:
Mature spliced Sequence:
ATCCCAATTATCTCATGGCTAACGAACGCATGAACCTGATGAACATGGCAAAGCTGAGCATCAAGGGCTTGATTGAATCGGCTCTGAATCTGGGGCGGACCCTGGACTCTGACTACGCACCTCTCCAGCAGTTTTTCGTGGTGATGGAACACTGCCTGAAACACGGCTTGAAAGCCAAGAAAACTTTTCTTGGACAAAATAAATCCTTCTGGGGGCCTCTAGAGCTGGTGGAGAAGCTTGTTCCAGAAGCTGCAGAAATAACAGCGAGTGTAAAAGACCTCCCAGGACTCAAGACACCAGTTGGCAGAGGAAGAGCCTGGCTTCGGTTGGCATTGATGCAAAAGAAGCTTTCTGAGTATATGAAAGCCTTGATCAATAAGAAGGAACTTCTCAGTGAGTTCTATGAAGTCAATGCCCTCATGATGGAAGAAGAAGGAGCTATTATCGCTGGTCTCCTGGTGGGTCTGAATGTCATCGATGCCAATTTCTGCATGAAAGGAGAAGACCTGGACTCTCAGGTTGGAGTTATAGATTTTTCGATGTATCTCAAAGATGGAAACAGTAGTAAAGGTAGTGAAGGGGATGGACAGATTACTGCGATCCTAGACCAGAAGAACTATGTAGAAGAACTCAACAGACATCTGAATGCAACTGTAAACAACCTTCAGACAAAAGTAGATCTGTTAGAAAAATCCAACACTAAATTGACAGAAGAACTTGCCGTTGCCAACAACAGAATTATTACCTTACAAGAAGAAATGGAACGAGTTAAAGAAGAAAGCTCCTATCTACTGGAATCCAATCGGAAGGGTCCTAAACAAGACAGAACTGCAGAAGGGCAAGCGCTGAGCGAAGCCAGAAAGCATCTAAAGGAGGAGACACAGTTAAGATTGGATGTCGAGAAGGAGCTGGAGCTGCAGATCAGCATGAGGCAGGAGATGGAACTGGCTATGAAGATGCTGGAGAAGGATGTCTGTGAGAAGCAGGATGCCCTGGTGTCTCTGCGGCAGCAGCTGGACGATCTCCGGGCTCTTAAGCATGAGCTCGCCTTTAAACTGCAGAGTTCAGACCTAGGAGTGAAACAGAAAAGTGAATTAAACAGTCGCTTGGAAGAAAAGACCAATCAGATGGCTGCCACCATTAAACAGCTGGAGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGACCAATCAGATGGCTGCC
60.11
GTCCGCCCCAGATTCAGAG
59.86
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACCAATCAGATGGCTGCCA
60.39
GTCCGCCCCAGATTCAGAG
59.86
142
PCR template sequence:
AGAGTTCAGACCTAGGAGTGAAACAGAAAAGTGAATTAAACAGTCGCTTGGAAGAAAAGACCAATCAGATGGCTGCCACCATTAAACAGCTGGAGCAAAGATCCCAATTATCTCATGGCTAACGAACGCATGAACCTGATGAACATGGCAAAGCTGAGCATCAAGGGCTTGATTGAATCGGCTCTGAATCTGGGGCGGAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-181a-5p(1), mmu-miR-34a-5p(1), mmu-miR-196a-5p(1), mmu-miR-181b-5p(1), mmu-miR-182-5p(1), mmu-miR-3087-3p(1), mmu-miR-484(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
AGCTGGAGCAAAGATCCCAATTATCT
siRNA sets
TAATTGGGATCTTTGCTCC, GATAATTGGGATCTTTGCT, ATAATTGGGATCTTTGCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRUFY3_1159_ORF_1
1.1434
0.294157346
0.998426968
1167
ORF sequence:
ATGGCTAACGAACGCATGAACCTGATGAACATGGCAAAGCTGAGCATCAAGGGCTTGATTGAATCGGCTCTGAATCTGGGGCGGACCCTGGACTCTGACTACGCACCTCTCCAGCAGTTTTTCGTGGTGATGGAACACTGCCTGAAACACGGCTTGAAAGCCAAGAAAACTTTTCTTGGACAAAATAAATCCTTCTGGGGGCCTCTAGAGCTGGTGGAGAAGCTTGTTCCAGAAGCTGCAGAAATAACAGCGAGTGTAAAAGACCTCCCAGGACTCAAGACACCAGTTGGCAGAGGAAGAGCCTGGCTTCGGTTGGCATTGATGCAAAAGAAGCTTTCTGAGTATATGAAAGCCTTGATCAATAAGAAGGAACTTCTCAGTGAGTTCTATGAAGTCAATGCCCTCATGATGGAAGAAGAAGGAGCTATTATCGCTGGTCTCCTGGTGGGTCTGAATGTCATCGATGCCAATTTCTGCATGAAAGGAGAAGACCTGGACTCTCAGGTTGGAGTTATAGATTTTTCGATGTATCTCAAAGATGGAAACAGTAGTAAAGGTAGTGAAGGGGATGGACAGATTACTGCGATCCTAGACCAGAAGAACTATGTAGAAGAACTCAACAGACATCTGAATGCAACTGTAAACAACCTTCAGACAAAAGTAGATCTGTTAGAAAAATCCAACACTAAATTGACAGAAGAACTTGCCGTTGCCAACAACAGAATTATTACCTTACAAGAAGAAATGGAACGAGTTAAAGAAGAAAGCTCCTATCTACTGGAATCCAATCGGAAGGGTCCTAAACAAGACAGAACTGCAGAAGGGCAAGCGCTGAGCGAAGCCAGAAAGCATCTAAAGGAGGAGACACAGTTAAGATTGGATGTCGAGAAGGAGCTGGAGCTGCAGATCAGCATGAGGCAGGAGATGGAACTGGCTATGAAGATGCTGGAGAAGGATGTCTGTGAGAAGCAGGATGCCCTGGTGTCTCTGCGGCAGCAGCTGGACGATCTCCGGGCTCTTAAGCATGAGCTCGCCTTTAAACTGCAGAGTTCAGACCTAGGAGTGAAACAGAAAAGTGAATTAAACAGTCGCTTGGAAGAAAAGACCAATCAGATGGCTGCCACCATTAAACAGCTGGAGCAAAGATCCCAATTATCTCATGGCTAA
Peptide sequence:
MANERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEVNALMMEEEGAIIAGLLVGLNVIDANFCMKGEDLDSQVGVIDFSMYLKDGNSSKGSEGDGQITAILDQKNYVEELNRHLNATVNNLQTKVDLLEKSNTKLTEELAVANNRIITLQEEMERVKEESSYLLESNRKGPKQDRTAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKLQSSDLGVKQKSELNSRLEEKTNQMAATIKQLEQRSQLSHG
IRESfinder result
IRESfinder score
0.317220819
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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