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mmu_circPkd2_402
Basic information of circular RNA
PanCircBase ID:
mmu_circPkd2_402
mm39_Chr. Position ID:
chr5|104637098|104642857|+
Gene name:
Pkd2
Transcript:
ENSMUST00000086831.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
8,9,10
Exon/intron offsets:
0,1411,5660
Genomic length:
5759
Exon/intron sizes in nt:
182,121,99
Flanking exon/introns:
chr5:104634680-104637098|chr5:104642857-104646306
Splice length:
402
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_124042
Human Ortholog IDs:
Mature spliced Sequence:
CTCTTCAAATTCATCAATTTTAATAGGACCATGAGCCAGCTCTCCACAACCATGTCTCGATGTGCCAAAGACCTCTTCGGCTTCACCATAATGTTCTCCATCATCTTCTTGGCATACGCACAGCTGGCATACCTTGTCTTCGGCACCCAGGTCGATGACTTCAGCACTTTCCAAGAATGTATCTTCACCCAGTTCCGCATCATTTTGGGTGATATCAACTTCGCAGAGATCGAGGAAGCTAACCGAGTTTTGGGGCCACTTTATTTTACTACATTTGTGTTCTTTATGTTCTTCATTCTTTTGAATATGTTCCTGGCGATCATCAATGATTCGTACTCTGAAGTGAAATCCGATCTGGCCCAGCAGAAAGCAGAAATGGAACTCTCAGACCTTATCAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGAAATCCGATCTGGCCCA
60.11
ATGGTGAAGCCGAAGAGGTC
59.75
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGAAATCCGATCTGGCCCA
60.11
GGTGAAGCCGAAGAGGTCTT
59.68
147
PCR template sequence:
GAATATGTTCCTGGCGATCATCAATGATTCGTACTCTGAAGTGAAATCCGATCTGGCCCAGCAGAAAGCAGAAATGGAACTCTCAGACCTTATCAGAAAGCTCTTCAAATTCATCAATTTTAATAGGACCATGAGCCAGCTCTCCACAACCATGTCTCGATGTGCCAAAGACCTCTTCGGCTTCACCATAATGTTCTCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-210-3p(1), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-149-5p(1), mmu-miR-127-5p(1), mmu-miR-96-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CCTTATCAGAAAGCTCTTCAAATTCA
siRNA sets
AATTTGAAGAGCTTTCTGA, ATTTGAAGAGCTTTCTGAT, GAATTTGAAGAGCTTTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKD2_402_ORF_1
1.2166
0.345284036
0.981973063
774
ORF sequence:
ATGAGCCAGCTCTCCACAACCATGTCTCGATGTGCCAAAGACCTCTTCGGCTTCACCATAATGTTCTCCATCATCTTCTTGGCATACGCACAGCTGGCATACCTTGTCTTCGGCACCCAGGTCGATGACTTCAGCACTTTCCAAGAATGTATCTTCACCCAGTTCCGCATCATTTTGGGTGATATCAACTTCGCAGAGATCGAGGAAGCTAACCGAGTTTTGGGGCCACTTTATTTTACTACATTTGTGTTCTTTATGTTCTTCATTCTTTTGAATATGTTCCTGGCGATCATCAATGATTCGTACTCTGAAGTGAAATCCGATCTGGCCCAGCAGAAAGCAGAAATGGAACTCTCAGACCTTATCAGAAAGCTCTTCAAATTCATCAATTTTAATAGGACCATGAGCCAGCTCTCCACAACCATGTCTCGATGTGCCAAAGACCTCTTCGGCTTCACCATAATGTTCTCCATCATCTTCTTGGCATACGCACAGCTGGCATACCTTGTCTTCGGCACCCAGGTCGATGACTTCAGCACTTTCCAAGAATGTATCTTCACCCAGTTCCGCATCATTTTGGGTGATATCAACTTCGCAGAGATCGAGGAAGCTAACCGAGTTTTGGGGCCACTTTATTTTACTACATTTGTGTTCTTTATGTTCTTCATTCTTTTGAATATGTTCCTGGCGATCATCAATGATTCGTACTCTGAAGTGAAATCCGATCTGGCCCAGCAGAAAGCAGAAATGGAACTCTCAGACCTTATCAGAAAG
Peptide sequence:
MSQLSTTMSRCAKDLFGFTIMFSIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPLYFTTFVFFMFFILLNMFLAIINDSYSEVKSDLAQQKAEMELSDLIRKLFKFINFNRTMSQLSTTMSRCAKDLFGFTIMFSIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPLYFTTFVFFMFFILLNMFLAIINDSYSEVKSDLAQQKAEMELSDLIRK
IRESfinder result
IRESfinder score
0.736163776
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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