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mmu_circPapola_603
Basic information of circular RNA
PanCircBase ID:
mmu_circPapola_603
mm39_Chr. Position ID:
chr12|105793202|105801043|+
Gene name:
Papola
Transcript:
ENSMUST00000109901.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
17,18,19,20,21
Exon/intron offsets:
0,1337,2113,6156,7766
Genomic length:
7841
Exon/intron sizes in nt:
143,101,221,63,75
Flanking exon/introns:
chr12:105789936-105793202|chr12:105801043-105803023
Splice length:
603
Other database IDs:
circAtlas: mmu-Papola_0041
Human Ortholog IDs:
Mature spliced Sequence:
CATTCAACAGAAGGAGTCAAGTTAACAGCTCTGAATGACAGCAGCCTTGACTTGTCTATGGACAGTGATAACAGCATGTCTGTGCCTTCACCCACCAGTGCTATGAAGACCAGTCCATTGAATAGTTCTGGCAGCTCCCAGGGCAGAAACAGTCCTGCTCCAGCTGTGACCGCAGCATCTGTGACCAGCATCCAGGCTTCTGAGGTTTCTGTACCGCAAGCAAATTCCAGTGAAAGCCCAGGGGGTCCATCGAGCGAAAGCATTCCTCAAACTGCCACACAGCCAGCCATTTCTCCACCACCAAAGCCTACAGTCTCCAGAGTTGTCTCCTCAACACGACTGGTAAACCCATCGCCTAGACCTTCAGGAAACACAGCAACAAAAGTCCCTAATCCTATAGTAGGAGTCAAGAGAACGTCCTCACCCAATAAAGAAGAAAGTCCTAAGAAAACCAAAACAGAAGAGGATGAAACAAGTGAAGATGCTAACTGTCTTGCTTTGAGTGGACATGATAAAACAGAGACAAAGGAACAAGTTGATCTGGAGACAAGTGCGGTTCAATCAGAAACTGTTCCGGCATCGGCTTCTCTGTTGGCCTCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGGAGACAAGTGCGGTTC
59.97
TGGGTGAAGGCACAGACATG
60.25
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGGAGACAAGTGCGGTTC
59.97
GTGGGTGAAGGCACAGACAT
60.25
159
PCR template sequence:
TGGACATGATAAAACAGAGACAAAGGAACAAGTTGATCTGGAGACAAGTGCGGTTCAATCAGAAACTGTTCCGGCATCGGCTTCTCTGTTGGCCTCTCAGCATTCAACAGAAGGAGTCAAGTTAACAGCTCTGAATGACAGCAGCCTTGACTTGTCTATGGACAGTGATAACAGCATGTCTGTGCCTTCACCCACCAGTG
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-434-3p(1), mmu-miR-22-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTGGCCTCTCAGCATTCAACAGAAG
siRNA sets
TGTTGAATGCTGAGAGGCC, CTGTTGAATGCTGAGAGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPAPOLA_603_ORF_1
1.1429
0.116805379
0.996400049
1149
ORF sequence:
ATGGACAGTGATAACAGCATGTCTGTGCCTTCACCCACCAGTGCTATGAAGACCAGTCCATTGAATAGTTCTGGCAGCTCCCAGGGCAGAAACAGTCCTGCTCCAGCTGTGACCGCAGCATCTGTGACCAGCATCCAGGCTTCTGAGGTTTCTGTACCGCAAGCAAATTCCAGTGAAAGCCCAGGGGGTCCATCGAGCGAAAGCATTCCTCAAACTGCCACACAGCCAGCCATTTCTCCACCACCAAAGCCTACAGTCTCCAGAGTTGTCTCCTCAACACGACTGGTAAACCCATCGCCTAGACCTTCAGGAAACACAGCAACAAAAGTCCCTAATCCTATAGTAGGAGTCAAGAGAACGTCCTCACCCAATAAAGAAGAAAGTCCTAAGAAAACCAAAACAGAAGAGGATGAAACAAGTGAAGATGCTAACTGTCTTGCTTTGAGTGGACATGATAAAACAGAGACAAAGGAACAAGTTGATCTGGAGACAAGTGCGGTTCAATCAGAAACTGTTCCGGCATCGGCTTCTCTGTTGGCCTCTCAGCATTCAACAGAAGGAGTCAAGTTAACAGCTCTGAATGACAGCAGCCTTGACTTGTCTATGGACAGTGATAACAGCATGTCTGTGCCTTCACCCACCAGTGCTATGAAGACCAGTCCATTGAATAGTTCTGGCAGCTCCCAGGGCAGAAACAGTCCTGCTCCAGCTGTGACCGCAGCATCTGTGACCAGCATCCAGGCTTCTGAGGTTTCTGTACCGCAAGCAAATTCCAGTGAAAGCCCAGGGGGTCCATCGAGCGAAAGCATTCCTCAAACTGCCACACAGCCAGCCATTTCTCCACCACCAAAGCCTACAGTCTCCAGAGTTGTCTCCTCAACACGACTGGTAAACCCATCGCCTAGACCTTCAGGAAACACAGCAACAAAAGTCCCTAATCCTATAGTAGGAGTCAAGAGAACGTCCTCACCCAATAAAGAAGAAAGTCCTAAGAAAACCAAAACAGAAGAGGATGAAACAAGTGAAGATGCTAACTGTCTTGCTTTGAGTGGACATGATAAAACAGAGACAAAGGAACAAGTTGATCTGGAGACAAGTGCGGTTCAATCAGAAACTGTTCCGGCATCGGCTTCTCTGTTGGCCTCTCAG
Peptide sequence:
MDSDNSMSVPSPTSAMKTSPLNSSGSSQGRNSPAPAVTAASVTSIQASEVSVPQANSSESPGGPSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPSPRPSGNTATKVPNPIVGVKRTSSPNKEESPKKTKTEEDETSEDANCLALSGHDKTETKEQVDLETSAVQSETVPASASLLASQHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGRNSPAPAVTAASVTSIQASEVSVPQANSSESPGGPSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPSPRPSGNTATKVPNPIVGVKRTSSPNKEESPKKTKTEEDETSEDANCLALSGHDKTETKEQVDLETSAVQSETVPASASLLASQ
IRESfinder result
IRESfinder score
0.551620441
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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