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mmu_circPkd1l1_682
Basic information of circular RNA
PanCircBase ID:
mmu_circPkd1l1_682
mm39_Chr. Position ID:
chr11|8851141|8859999|-
Gene name:
Pkd1l1
Transcript:
ENSMUST00000154153.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
21,20,19,18
Exon/intron offsets:
0,1267,7527,8659
Genomic length:
8858
Exon/intron sizes in nt:
216,210,57,199
Flanking exon/introns:
chr11:8840767-8851141|chr11:8859999-8866246
Splice length:
682
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATATAACTCCACTCTGGAAAGCCTGTCTACTCTCCGGCTGGCAGGAAGTTACATGGAAACCAGGAACTACATTACCATGATCACTGGGATCCTGAGCCGCTTGTATGTGGAGAGCAGAAACACTTCTTCGTGTGGTCAGTGGTCACAAATACAGGATGTATTAATTTCTTCAGCATGCAAAGTACCTTATACAGATCAGGAAGGAATGATGGATTCTATTCATATATTGAGAGACCTCATAAGCTTCCCTAATAAGTTGAGCTTGACGAGTGCCATGTGCATCTTCAAATACACCAAGATGTTCCTTGCTCAAGGCCAGTTCTCCAGGAGGTTGCTAGTCGACAAAAAACTAAGAGTTGAATTTGTCCTTCTCATCTCTGGAGTCTGGGAAGCTGCCAAAGAGGATGCGAGGGATGGGGACTATCTGCAGGAAGAAGGCATGAAGATCATCTCTGACATGTTACTAATTCACGTAAGCACTGGGCAGATGGAGTTCCAGACCCTTCTCCATCGTAGCCCTCAGAGCTCTATCCAGAACCTAGGCTTCGTCCAGGTACATTTCCCCAGTGACCTGGCCTCCTTGCACAGTACTACTCAAGAGGCAACACAAAGCTCATGCTATATCAGCCAGCTCATGTTCTTCATGAAGAGTCCTTATCTAGGGGGACAAGTTCCTGGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCAACACAAAGCTCATGC
59.68
TCCATGTAACTTCCTGCCAGC
60.34
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGAGGCAACACAAAGCTCA
59.32
ATGTAACTTCCTGCCAGCCG
60.39
141
PCR template sequence:
GCACAGTACTACTCAAGAGGCAACACAAAGCTCATGCTATATCAGCCAGCTCATGTTCTTCATGAAGAGTCCTTATCTAGGGGGACAAGTTCCTGGGCAGATATAACTCCACTCTGGAAAGCCTGTCTACTCTCCGGCTGGCAGGAAGTTACATGGAAACCAGGAACTACATTACCATGATCACTGGGATCCTGAGCCGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-381-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-183-5p(1), mmu-miR-758-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-697(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGTTCCTGGGCAGATATAACTCCACT
siRNA sets
TTATATCTGCCCAGGAACT, GAGTTATATCTGCCCAGGA, GTTATATCTGCCCAGGAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKD1L1_682_ORF_1
0.8586
0.091178107
0.783140052
636
ORF sequence:
ATGGAAACCAGGAACTACATTACCATGATCACTGGGATCCTGAGCCGCTTGTATGTGGAGAGCAGAAACACTTCTTCGTGTGGTCAGTGGTCACAAATACAGGATGTATTAATTTCTTCAGCATGCAAAGTACCTTATACAGATCAGGAAGGAATGATGGATTCTATTCATATATTGAGAGACCTCATAAGCTTCCCTAATAAGTTGAGCTTGACGAGTGCCATGTGCATCTTCAAATACACCAAGATGTTCCTTGCTCAAGGCCAGTTCTCCAGGAGGTTGCTAGTCGACAAAAAACTAAGAGTTGAATTTGTCCTTCTCATCTCTGGAGTCTGGGAAGCTGCCAAAGAGGATGCGAGGGATGGGGACTATCTGCAGGAAGAAGGCATGAAGATCATCTCTGACATGTTACTAATTCACGTAAGCACTGGGCAGATGGAGTTCCAGACCCTTCTCCATCGTAGCCCTCAGAGCTCTATCCAGAACCTAGGCTTCGTCCAGGTACATTTCCCCAGTGACCTGGCCTCCTTGCACAGTACTACTCAAGAGGCAACACAAAGCTCATGCTATATCAGCCAGCTCATGTTCTTCATGAAGAGTCCTTATCTAGGGGGACAAGTTCCTGGGCAGATATAA
Peptide sequence:
METRNYITMITGILSRLYVESRNTSSCGQWSQIQDVLISSACKVPYTDQEGMMDSIHILRDLISFPNKLSLTSAMCIFKYTKMFLAQGQFSRRLLVDKKLRVEFVLLISGVWEAAKEDARDGDYLQEEGMKIISDMLLIHVSTGQMEFQTLLHRSPQSSIQNLGFVQVHFPSDLASLHSTTQEATQSSCYISQLMFFMKSPYLGGQVPGQI
IRESfinder result
IRESfinder score
0.675853406
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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