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mmu_circMarchf6_506
Basic information of circular RNA
PanCircBase ID:
mmu_circMarchf6_506
mm39_Chr. Position ID:
chr15|31490721|31498888|-
Gene name:
Marchf6
Transcript:
ENSMUST00000090227.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,9,8,7,6
Exon/intron offsets:
0,2163,3495,5428,7998
Genomic length:
8167
Exon/intron sizes in nt:
52,33,62,190,169
Flanking exon/introns:
chr15:31488996-31490721|chr15:31498888-31501061
Splice length:
506
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGAAAATTTGTTGGCGGATTGCTTGCAGGGCTGTTTTGTGGTGACGTGCACACTTTGTGCGTTCATCAGCCTGGTGTGGTTACGAGAGCAGATAGTCCACGGGGGAGCCCCAATTTGGCTGGAGCATGCTGCTCCACCCTTCAATGCTGCTGGACACCACCAAAATGAGGCTCCTGTAGGAGGAAATGGTGCAGAAAACCCTGCTGCTGATCAGCCAGCTAACCCAGCAGGTGAGAATGCAGTTCTGGGTGAAAACCCTGATGCCCAGGACGGTCAAGCAGAAGAGGAAGAGGAGGACAATGAGGAGGAAGATGATGCGGGTGTAGAAGATGCTGCTGATGCCAACAATGGAGCCCAAGACGACATGAACTGGAATGCTTTAGAGTGGGACCGGGCTGCAGAAGAGCTTACTTGGGAAAGAATGCTTGGACTTGATGGATCACTAGTTTTCCTGGAACACGTGTTCTGGGTGGTGTCTTTAAATACATTGTTCATTCTTGTTTTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACACGTGTTCTGGGTGGTG
60.75
TGCTCTCGTAACCACACCAG
59.68
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACACGTGTTCTGGGTGGTG
60.75
CTGCTCTCGTAACCACACCA
59.68
142
PCR template sequence:
CTTACTTGGGAAAGAATGCTTGGACTTGATGGATCACTAGTTTTCCTGGAACACGTGTTCTGGGTGGTGTCTTTAAATACATTGTTCATTCTTGTTTTTGGGAAAATTTGTTGGCGGATTGCTTGCAGGGCTGTTTTGTGGTGACGTGCACACTTTGTGCGTTCATCAGCCTGGTGTGGTTACGAGAGCAGATAGTCCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(2), mmu-miR-107-3p(2), mmu-miR-15a-5p(1), mmu-miR-7b-5p(1), mmu-miR-217-5p(1), mmu-miR-7a-5p(1), mmu-miR-370-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTCTTGTTTTTGGGAAAATTTGTTG
siRNA sets
AAATTTTCCCAAAAACAAG, ATTTTCCCAAAAACAAGAA, AACAAATTTTCCCAAAAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMARCHF6_506_ORF_1
0.4548
-0.2039795
0.019593302
186
ORF sequence:
ATGAACTGGAATGCTTTAGAGTGGGACCGGGCTGCAGAAGAGCTTACTTGGGAAAGAATGCTTGGACTTGATGGATCACTAGTTTTCCTGGAACACGTGTTCTGGGTGGTGTCTTTAAATACATTGTTCATTCTTGTTTTTGGGAAAATTTGTTGGCGGATTGCTTGCAGGGCTGTTTTGTGGTGA
Peptide sequence:
MNWNALEWDRAAEELTWERMLGLDGSLVFLEHVFWVVSLNTLFILVFGKICWRIACRAVLW
IRESfinder result
IRESfinder score
0.439217196
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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