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mmu_circPcx_1022
Basic information of circular RNA
PanCircBase ID:
mmu_circPcx_1022
mm39_Chr. Position ID:
chr19|4651627|4654611|+
Gene name:
Pcx
Transcript:
ENSMUST00000068004.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
3,4,5,6,7,8,9
Exon/intron offsets:
0,265,610,874,1158,1460,2865
Genomic length:
2984
Exon/intron sizes in nt:
13,61,85,16,61,46,11,80,00,000
Flanking exon/introns:
chr19:4565718-4651627|chr19:4654611-4657559
Splice length:
1022
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATGCTGAAGTTCCAAACAGTTCGAGGGGGCCTGAGGCTCCTGGGTGTCCGCCGATCCTCCTCGGCCCCTGTTGCCTCCCCAAATGTCCGGCGTCTGGAGTATAAGCCTATCAAGAAAGTAATGGTGGCCAACAGAGGTGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAGGAAAATGGTGTAGATGCGGTGCATCCTGGCTATGGGTTCCTCTCAGAGCGAGCAGACTTTGCCCAGGCCTGCCAAGATGCTGGAGTCCGGTTCATTGGTCCAAGCCCAGAGGTGGTCCGCAAGATGGGAGACAAGGTGGAAGCCCGGGCCATTGCCATCGCTGCAGGCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAGGAGTTGGAAGAGAATTACACCCGGGCCTACTCCGAGGCCTTGGCAGCCTTTGGGAATGGAGCGTTGTTTGTGGAGAAGTTCATTGAGAAGCCAAGGCACATTGAGGTGCAGATCCTAGGGGACCAGTATGGGAACATCCTGCACCTGTACGAGCGAGACTGCTCCATCCAGCGTCGGCACCAGAAGGTGGTAGAGATCGCCCCTGCTACCCACCTGGATCCCCAACTTCGCTCACGTCTCACCAGTGACTCTGTCAAACTTGCCAAGCAGGTAGGCTATGAGAACGCCGGCACTGTGGAGTTCCTGGTGGACAAGCACGGCAAGCACTACTTCATCGAGGTCAATTCCCGCCTGCAGGTGGAGCACACGGTCACCGAGGAGATCACAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTTCCTGGTGGACAAGCA
59.89
GGACATTTGGGGAGGCAACA
60.54
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTTCCTGGTGGACAAGCA
59.89
ACATTTGGGGAGGCAACAGG
60.54
178
PCR template sequence:
GCACTGTGGAGTTCCTGGTGGACAAGCACGGCAAGCACTACTTCATCGAGGTCAATTCCCGCCTGCAGGTGGAGCACACGGTCACCGAGGAGATCACAGAATGCTGAAGTTCCAAACAGTTCGAGGGGGCCTGAGGCTCCTGGGTGTCCGCCGATCCTCCTCGGCCCCTGTTGCCTCCCCAAATGTCCGGCGTCTGGAGT
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-206-3p(1), mmu-miR-216a-5p(1), mmu-miR-139-5p(1), mmu-miR-128-3p(1), mmu-miR-182-5p(1), mmu-miR-452-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGGAGATCACAGAATGCTGAAGTTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPCX_1022_ORF_1
1.2871
0.548159807
0.998853002
1029
ORF sequence:
ATGCTGAAGTTCCAAACAGTTCGAGGGGGCCTGAGGCTCCTGGGTGTCCGCCGATCCTCCTCGGCCCCTGTTGCCTCCCCAAATGTCCGGCGTCTGGAGTATAAGCCTATCAAGAAAGTAATGGTGGCCAACAGAGGTGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAGGAAAATGGTGTAGATGCGGTGCATCCTGGCTATGGGTTCCTCTCAGAGCGAGCAGACTTTGCCCAGGCCTGCCAAGATGCTGGAGTCCGGTTCATTGGTCCAAGCCCAGAGGTGGTCCGCAAGATGGGAGACAAGGTGGAAGCCCGGGCCATTGCCATCGCTGCAGGCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAGGAGTTGGAAGAGAATTACACCCGGGCCTACTCCGAGGCCTTGGCAGCCTTTGGGAATGGAGCGTTGTTTGTGGAGAAGTTCATTGAGAAGCCAAGGCACATTGAGGTGCAGATCCTAGGGGACCAGTATGGGAACATCCTGCACCTGTACGAGCGAGACTGCTCCATCCAGCGTCGGCACCAGAAGGTGGTAGAGATCGCCCCTGCTACCCACCTGGATCCCCAACTTCGCTCACGTCTCACCAGTGACTCTGTCAAACTTGCCAAGCAGGTAGGCTATGAGAACGCCGGCACTGTGGAGTTCCTGGTGGACAAGCACGGCAAGCACTACTTCATCGAGGTCAATTCCCGCCTGCAGGTGGAGCACACGGTCACCGAGGAGATCACAGAATGCTGA
Peptide sequence:
MLKFQTVRGGLRLLGVRRSSSAPVASPNVRRLEYKPIKKVMVANRGEIAIRVFRACTELGIRTVAVYSEQDTGQMHRQKADEAYLIGRGLAPVQAYLHIPDIIKVAKENGVDAVHPGYGFLSERADFAQACQDAGVRFIGPSPEVVRKMGDKVEARAIAIAAGVPVVPGTDSPISSLHEAHEFSNTYGFPIIFKAAYGGGGRGMRVVHSYEELEENYTRAYSEALAAFGNGALFVEKFIEKPRHIEVQILGDQYGNILHLYERDCSIQRRHQKVVEIAPATHLDPQLRSRLTSDSVKLAKQVGYENAGTVEFLVDKHGKHYFIEVNSRLQVEHTVTEEITEC
IRESfinder result
IRESfinder score
0.282439384
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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