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mmu_circPrex2_400
Basic information of circular RNA
PanCircBase ID:
mmu_circPrex2_400
mm39_Chr. Position ID:
chr1|11159940|11171391|+
Gene name:
Prex2
Transcript:
ENSMUST00000027056.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,7,8
Exon/intron offsets:
0,8746,11347
Genomic length:
11451
Exon/intron sizes in nt:
16,21,34,104
Flanking exon/introns:
chr1:11150348-11159940|chr1:11171391-11177826
Splice length:
400
Other database IDs:
CIRCpedia: MMU_CIRCpedia_219448, circAtlas: mmu-Prex2_0038
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GAATTACTGAAGCGGACTCCACGGAGACATAGTGACTACACAGCAGTGATGGAAGCACTCCAAGCCATGAAAGCCGTGTGTTCCAACATTAATGAGGCCAAGAGACAGATGGAGAAACTGGAAGTTTTAGAAGAGTGGCAGGCACACATTGAAGGCTGGGAGGGGTCCAACATTACTGACACCTGTACTGAGATGCTGATGTGTGGAGTCCTAATGAAAATTTCTTCCGGAAATATTCAAGAACGAGTGTTTTTTCTTTTTGATAATCTTTTAGTATACTGCAAAAGAAAACACAGACGGCTGAAGAATAGTAAGGCATCCACAGATGGGTATCGGTATGTCTTTCGAGGGCGGATCAATACTGAGGTGATGGAAGTGGAAAATGTGGATGACGGCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGTCTTTCGAGGGCGGATC
59.89
GGAACACACGGCTTTCATGG
59.76
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCTTTCGAGGGCGGATCAA
60.11
GGAACACACGGCTTTCATGG
59.76
145
PCR template sequence:
CTGAAGAATAGTAAGGCATCCACAGATGGGTATCGGTATGTCTTTCGAGGGCGGATCAATACTGAGGTGATGGAAGTGGAAAATGTGGATGACGGCACAGGAATTACTGAAGCGGACTCCACGGAGACATAGTGACTACACAGCAGTGATGGAAGCACTCCAAGCCATGAAAGCCGTGTGTTCCAACATTAATGAGGCCA
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-342-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGACGGCACAGGAATTACTGAAGC
siRNA sets
CTTCAGTAATTCCTGTGCC, TTCAGTAATTCCTGTGCCG, TCAGTAATTCCTGTGCCGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPREX2_400_ORF_1
0.8603
0.201376193
0.542539053
417
ORF sequence:
ATGTGGATGACGGCACAGGAATTACTGAAGCGGACTCCACGGAGACATAGTGACTACACAGCAGTGATGGAAGCACTCCAAGCCATGAAAGCCGTGTGTTCCAACATTAATGAGGCCAAGAGACAGATGGAGAAACTGGAAGTTTTAGAAGAGTGGCAGGCACACATTGAAGGCTGGGAGGGGTCCAACATTACTGACACCTGTACTGAGATGCTGATGTGTGGAGTCCTAATGAAAATTTCTTCCGGAAATATTCAAGAACGAGTGTTTTTTCTTTTTGATAATCTTTTAGTATACTGCAAAAGAAAACACAGACGGCTGAAGAATAGTAAGGCATCCACAGATGGGTATCGGTATGTCTTTCGAGGGCGGATCAATACTGAGGTGATGGAAGTGGAAAATGTGGATGACGGCACA
Peptide sequence:
MWMTAQELLKRTPRRHSDYTAVMEALQAMKAVCSNINEAKRQMEKLEVLEEWQAHIEGWEGSNITDTCTEMLMCGVLMKISSGNIQERVFFLFDNLLVYCKRKHRRLKNSKASTDGYRYVFRGRINTEVMEVENVDDGT
IRESfinder result
IRESfinder score
0.405363983
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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