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mmu_circIpo9_608
Basic information of circular RNA
PanCircBase ID:
mmu_circIpo9_608
mm39_Chr. Position ID:
chr1|135333558|135337219|-
Gene name:
Ipo9
Transcript:
ENSMUST00000041023.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
10,9,8,7,6,5
Exon/intron offsets:
0,696,938,1131,2167,3572
Genomic length:
3661
Exon/intron sizes in nt:
152,59,101,120,87,89
Flanking exon/introns:
chr1:135332060-135333558|chr1:135337219-135346974
Splice length:
608
Other database IDs:
circAtlas: mmu-Ipo9_0007
circAtlas: hsa-IPO9_0019
Human Ortholog IDs:
Mature spliced Sequence:
AGTTTACTCGAGAAGTGACAGACACACAGATGCCACTTGTTGCTCCTGTCATTCTGCCAGAGATGTATAAGATATTCACCATGGCCGAGGTGTATGGTATTCGAACTCGTTCCCGAGCAGTGGAGATTTTTACTACTTGTGCGCATATGATCTGTAACATGGAGGAACTGGAAAAGGGTGCAGCCAAAGTCCTGATCTTCCCCGTGGTGCAGCAGTTCACAGAGGCCTTTGTTCAGGCACTCCAGATGCCCGATGGCCCCACATCTGACAGTGGCTTTAAGATGGAGGTCCTGAAGGCAGTGACAGCCTTGGTGAAAAACTTCCCAAAGCACATGGTGTCCTCCATGCAACAGATCCTGCCCATTGTTTGGAACACTCTAACTGAAAGTGCTGCCTTTTATGTGAGGACGGAAGTGAATTACACAGAGGAAGTGGAAGATCCTGTGGATTCGGATGGAGAAGTCCTGGGCTTTGAGAACCTCGTCTTTAGCATTTTTGAGTTTGTCCATGCCCTACTGGAGAACAGCAAGTTCAAAAGCACCGTTAAGAAGGCTCTGCCCGAGCTCATTTACTACATCATCCTGTACATGCAGATCACCGAGGAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACCGTTAAGAAGGCTCT
59.02
TACCATACACCTCGGCCATG
59.24
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACCGTTAAGAAGGCTCTGC
58.92
TACCATACACCTCGGCCATG
59.24
169
PCR template sequence:
TGCCCTACTGGAGAACAGCAAGTTCAAAAGCACCGTTAAGAAGGCTCTGCCCGAGCTCATTTACTACATCATCCTGTACATGCAGATCACCGAGGAGCAGAGTTTACTCGAGAAGTGACAGACACACAGATGCCACTTGTTGCTCCTGTCATTCTGCCAGAGATGTATAAGATATTCACCATGGCCGAGGTGTATGGTAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-106a-5p(1), mmu-miR-324-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CACCGAGGAGCAGAGTTTACTCGAGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCIPO9_608_ORF_1
1.2281
0.365140169
0.943392925
597
ORF sequence:
ATGCCACTTGTTGCTCCTGTCATTCTGCCAGAGATGTATAAGATATTCACCATGGCCGAGGTGTATGGTATTCGAACTCGTTCCCGAGCAGTGGAGATTTTTACTACTTGTGCGCATATGATCTGTAACATGGAGGAACTGGAAAAGGGTGCAGCCAAAGTCCTGATCTTCCCCGTGGTGCAGCAGTTCACAGAGGCCTTTGTTCAGGCACTCCAGATGCCCGATGGCCCCACATCTGACAGTGGCTTTAAGATGGAGGTCCTGAAGGCAGTGACAGCCTTGGTGAAAAACTTCCCAAAGCACATGGTGTCCTCCATGCAACAGATCCTGCCCATTGTTTGGAACACTCTAACTGAAAGTGCTGCCTTTTATGTGAGGACGGAAGTGAATTACACAGAGGAAGTGGAAGATCCTGTGGATTCGGATGGAGAAGTCCTGGGCTTTGAGAACCTCGTCTTTAGCATTTTTGAGTTTGTCCATGCCCTACTGGAGAACAGCAAGTTCAAAAGCACCGTTAAGAAGGCTCTGCCCGAGCTCATTTACTACATCATCCTGTACATGCAGATCACCGAGGAGCAGAGTTTACTCGAGAAGTGA
Peptide sequence:
MPLVAPVILPEMYKIFTMAEVYGIRTRSRAVEIFTTCAHMICNMEELEKGAAKVLIFPVVQQFTEAFVQALQMPDGPTSDSGFKMEVLKAVTALVKNFPKHMVSSMQQILPIVWNTLTESAAFYVRTEVNYTEEVEDPVDSDGEVLGFENLVFSIFEFVHALLENSKFKSTVKKALPELIYYIILYMQITEEQSLLEK
IRESfinder result
IRESfinder score
0.580567859
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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