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mmu_circRrn3_414
Basic information of circular RNA
PanCircBase ID:
mmu_circRrn3_414
mm39_Chr. Position ID:
chr16|13606641|13609853|+
Gene name:
Rrn3
Transcript:
ENSMUST00000023363.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
4,5,6,7,8
Exon/intron offsets:
0,182,755,1843,3142
Genomic length:
3212
Exon/intron sizes in nt:
90,130,60,64,70
Flanking exon/introns:
chr16:13601993-13606641|chr16:13609853-13610811
Splice length:
414
Other database IDs:
circBase: mmu_circ_0006075, CIRCpedia: MMU_CIRCpedia_8566, circAtlas: mmu-Rrn3_0012
Human Ortholog IDs:
Mature spliced Sequence:
GATGACCAGATCATTAACTGGCTACTAGAATTTCGTTCCTCTGTCATGTACTTGACAAAAGACTTTGAGCAACTTATAAACATCATATTGAGATTGCCCTGGTTGAATAGAAGTCAGAGAGTGGTGGAGGAGTATTTGGCTTTTCTTGGTAATCTTGTGTCTGCACAGACTGTCTTCCTTAGACCATGTCTCAGCATGATTGCGTCTCATTTTGTACCTCCCCGAGTAATTGTCAAGGAAGGTGGCATAGATGTTTCAGATTCTGATGACGAAGATGACAATCTTCCTGCAATTTTTGACACATGTCACAGAGCCTTGCAAATAATAACAAGATATGTCCCATCGACACCATGGTTTCTAATGCCAATACTGGTGGAGAAATTCCCGTTTGTGAGGAAGTCCGAGAGAACATTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCCATCGACACCATGGTT
60.04
AGTTGCTCAAAGTCTTTTGTCAAGT
59.82
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCCATCGACACCATGGTT
60.04
TGCTCAAAGTCTTTTGTCAAGT
56.68
149
PCR template sequence:
CTTGCAAATAATAACAAGATATGTCCCATCGACACCATGGTTTCTAATGCCAATACTGGTGGAGAAATTCCCGTTTGTGAGGAAGTCCGAGAGAACATTGGATGACCAGATCATTAACTGGCTACTAGAATTTCGTTCCTCTGTCATGTACTTGACAAAAGACTTTGAGCAACTTATAAACATCATATTGAGATTGCCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-26a-5p(1), mmu-miR-26b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGAGAGAACATTGGATGACCAGATCA
siRNA sets
GTCATCCAATGTTCTCTCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRRN3_414_ORF_1
0.8326
-0.019381451
0.864947708
783
ORF sequence:
ATGTACTTGACAAAAGACTTTGAGCAACTTATAAACATCATATTGAGATTGCCCTGGTTGAATAGAAGTCAGAGAGTGGTGGAGGAGTATTTGGCTTTTCTTGGTAATCTTGTGTCTGCACAGACTGTCTTCCTTAGACCATGTCTCAGCATGATTGCGTCTCATTTTGTACCTCCCCGAGTAATTGTCAAGGAAGGTGGCATAGATGTTTCAGATTCTGATGACGAAGATGACAATCTTCCTGCAATTTTTGACACATGTCACAGAGCCTTGCAAATAATAACAAGATATGTCCCATCGACACCATGGTTTCTAATGCCAATACTGGTGGAGAAATTCCCGTTTGTGAGGAAGTCCGAGAGAACATTGGATGACCAGATCATTAACTGGCTACTAGAATTTCGTTCCTCTGTCATGTACTTGACAAAAGACTTTGAGCAACTTATAAACATCATATTGAGATTGCCCTGGTTGAATAGAAGTCAGAGAGTGGTGGAGGAGTATTTGGCTTTTCTTGGTAATCTTGTGTCTGCACAGACTGTCTTCCTTAGACCATGTCTCAGCATGATTGCGTCTCATTTTGTACCTCCCCGAGTAATTGTCAAGGAAGGTGGCATAGATGTTTCAGATTCTGATGACGAAGATGACAATCTTCCTGCAATTTTTGACACATGTCACAGAGCCTTGCAAATAATAACAAGATATGTCCCATCGACACCATGGTTTCTAATGCCAATACTGGTGGAGAAATTCCCGTTTGTGAGGAAGTCCGAGAGAACATTG
Peptide sequence:
MYLTKDFEQLINIILRLPWLNRSQRVVEEYLAFLGNLVSAQTVFLRPCLSMIASHFVPPRVIVKEGGIDVSDSDDEDDNLPAIFDTCHRALQIITRYVPSTPWFLMPILVEKFPFVRKSERTLDDQIINWLLEFRSSVMYLTKDFEQLINIILRLPWLNRSQRVVEEYLAFLGNLVSAQTVFLRPCLSMIASHFVPPRVIVKEGGIDVSDSDDEDDNLPAIFDTCHRALQIITRYVPSTPWFLMPILVEKFPFVRKSERTL
IRESfinder result
IRESfinder score
0.599689714
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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