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mmu_circFam20b_593
Basic information of circular RNA
PanCircBase ID:
mmu_circFam20b_593
mm39_Chr. Position ID:
chr1|156533237|156544550|-
Gene name:
Fam20b
Transcript:
ENSMUST00000122424.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,11220
Genomic length:
11313
Exon/intron sizes in nt:
500,93
Flanking exon/introns:
chr1:156530055-156533237|chr1:156544550-156546435
Splice length:
593
Other database IDs:
circBase: mmu_circ_0008299, CIRCpedia: MMU_CIRCpedia_37838, circAtlas: mmu-Fam20b_0009
Human Ortholog IDs:
Mature spliced Sequence:
GATATGAATTGGCTCCCTCTGACCGCCATTTCAGTGCTTGTAAGTGTGAGGTCAGCAACTGCAGCCTACAGATTGATAACTGTCGAACCCCTGGAATTGTGGAGGCACTGCAGTGAAGAAATATGTAATCATGGAATCTCCTTGCTAATCGTCACCACCTGTTCCCTGTGATAAGCCAGCCAGGACGTGGGCTGAGGAGAAGGAAAAGAGGCCACCATGAAGCTGAAGCAGCGAGTTGTGCTGTTAGCAATACTCCTCGTCATTTTTATCTTCACCAAAGTTTTCCTGATAGACAATTTAGATACATCAGCTGCCAACCGAGAGGACCAGAGGGCTTTTCACCGAATGATGACTGGCTTGCGGGTGGAGCTGGTGCCCAAGTTGGACCATACCCTGCAGTCTCCTTGGGAGATTGCAGCCCAGTGGGTGGTGCCCCGGGAAGTGTATCCTGAAGAGACACCAGAGCTGGGAGCAATCATGCATGCCATGGCCACTAAGAAAATCATTAAAGCTGACGTGGGCTATAAAGGGACACAGCTAAAAGCTTTACTGATTCTTGAAGGAGGACAGAAAGTTGTCTTTAAGCCTAAGCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCATTAAAGCTGACGTGGGCT
60
CTGTAGGCTGCAGTTGCTGA
60.32
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCATTAAAGCTGACGTGGGCT
60
TCTGTAGGCTGCAGTTGCTG
60.32
163
PCR template sequence:
CTAAGAAAATCATTAAAGCTGACGTGGGCTATAAAGGGACACAGCTAAAAGCTTTACTGATTCTTGAAGGAGGACAGAAAGTTGTCTTTAAGCCTAAGCGGATATGAATTGGCTCCCTCTGACCGCCATTTCAGTGCTTGTAAGTGTGAGGTCAGCAACTGCAGCCTACAGATTGATAACTGTCGAACCCCTGGAATTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-207(1), mmu-miR-540-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTAAGCCTAAGCGGATATGAATTGGC
siRNA sets
ATTCATATCCGCTTAGGCT, AATTCATATCCGCTTAGGC, TTCATATCCGCTTAGGCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFAM20B_593_ORF_1
1.0236
0.289356932
0.642634122
384
ORF sequence:
ATGAAGCTGAAGCAGCGAGTTGTGCTGTTAGCAATACTCCTCGTCATTTTTATCTTCACCAAAGTTTTCCTGATAGACAATTTAGATACATCAGCTGCCAACCGAGAGGACCAGAGGGCTTTTCACCGAATGATGACTGGCTTGCGGGTGGAGCTGGTGCCCAAGTTGGACCATACCCTGCAGTCTCCTTGGGAGATTGCAGCCCAGTGGGTGGTGCCCCGGGAAGTGTATCCTGAAGAGACACCAGAGCTGGGAGCAATCATGCATGCCATGGCCACTAAGAAAATCATTAAAGCTGACGTGGGCTATAAAGGGACACAGCTAAAAGCTTTACTGATTCTTGAAGGAGGACAGAAAGTTGTCTTTAAGCCTAAGCGGATATGA
Peptide sequence:
MKLKQRVVLLAILLVIFIFTKVFLIDNLDTSAANREDQRAFHRMMTGLRVELVPKLDHTLQSPWEIAAQWVVPREVYPEETPELGAIMHAMATKKIIKADVGYKGTQLKALLILEGGQKVVFKPKRI
IRESfinder result
IRESfinder score
0.52281152
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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