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mmu_circPknox1_670
Basic information of circular RNA
PanCircBase ID:
mmu_circPknox1_670
mm39_Chr. Position ID:
chr17|31809576|31818617|+
Gene name:
Pknox1
Transcript:
ENSMUST00000097352.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
4,5,6,7,8
Exon/intron offsets:
0,1502,4622,6193,8912
Genomic length:
9041
Exon/intron sizes in nt:
1,72,17,11,00,98,129
Flanking exon/introns:
chr17:31807561-31809576|chr17:31818617-31821759
Splice length:
670
Other database IDs:
circAtlas: mmu-Pknox1_0015
Human Ortholog IDs:
Mature spliced Sequence:
GCATCCACTATTTCCGTTGCTAGCTTTGTTGTTTGAGAAGTGTGAGCAGTCCACACAGGGCTCAGAAGGCACGACGTCTGCCAGCTTCGATGTGGACATTGAGAACTTTGTCAGGAAGCAAGAAAAGGATGGGAAACCCTTCTTCTGTGAAGATCCGGAAACTGACAACCTAATGGTGAAAGCAATCCAGGTCCTGCGCATTCATCTTCTTGAACTGGAGAAGGTTAATGAGCTCTGTAAAGATTTCTGTAGTCGGTACATTGCTTGTCTGAAGACAAAAATGAACAGCGAGACCTTGTTGAGTGGGGAGCCTGGAAGTCCGTACTCCCCTGTGCAATCCCAGCAGATTCAGAGTGCCATCACAGGCACGCTCAGCCCCCAGGGAATCGTGGTGCCAGCATCAGCCCTACAACAGGGAAATGTAACCATGGCAACAGTGGCAGGTGGCACAGTGTACCAGCCTGTCACCGTCGTCACTCCGCAAGGCCAAGTGGTCACGCAGGCATTATCTCCTGGGACAATTAGGATCCAGAACTCACAGCTGCAGTTGCAGTTGAACCAAGACCTCAGCATCTTGCATCAAGAGGATGGCTCCTCCAAGAACAAGAGGGGTGTCCTGCCGAAGCACGCCACCAACGTGATGCGGTCCTGGCTCTTTCAGCACATAGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCCAAGAACAAGAGGGGT
58.93
CTTCTGAGCCCTGTGTGGAC
60.32
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCCAAGAACAAGAGGGGTG
60.27
CTTCTGAGCCCTGTGTGGAC
60.32
145
PCR template sequence:
CATCTTGCATCAAGAGGATGGCTCCTCCAAGAACAAGAGGGGTGTCCTGCCGAAGCACGCCACCAACGTGATGCGGTCCTGGCTCTTTCAGCACATAGGGGCATCCACTATTTCCGTTGCTAGCTTTGTTGTTTGAGAAGTGTGAGCAGTCCACACAGGGCTCAGAAGGCACGACGTCTGCCAGCTTCGATGTGGACATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-503-5p(1), mmu-miR-183-5p(1), mmu-miR-27a-5p(1), mmu-miR-300-3p(1), mmu-miR-484(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGCACATAGGGGCATCCACTATTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKNOX1_670_ORF_1
1.2021
0.233482915
0.854356638
534
ORF sequence:
ATGGTGAAAGCAATCCAGGTCCTGCGCATTCATCTTCTTGAACTGGAGAAGGTTAATGAGCTCTGTAAAGATTTCTGTAGTCGGTACATTGCTTGTCTGAAGACAAAAATGAACAGCGAGACCTTGTTGAGTGGGGAGCCTGGAAGTCCGTACTCCCCTGTGCAATCCCAGCAGATTCAGAGTGCCATCACAGGCACGCTCAGCCCCCAGGGAATCGTGGTGCCAGCATCAGCCCTACAACAGGGAAATGTAACCATGGCAACAGTGGCAGGTGGCACAGTGTACCAGCCTGTCACCGTCGTCACTCCGCAAGGCCAAGTGGTCACGCAGGCATTATCTCCTGGGACAATTAGGATCCAGAACTCACAGCTGCAGTTGCAGTTGAACCAAGACCTCAGCATCTTGCATCAAGAGGATGGCTCCTCCAAGAACAAGAGGGGTGTCCTGCCGAAGCACGCCACCAACGTGATGCGGTCCTGGCTCTTTCAGCACATAGGGGCATCCACTATTTCCGTTGCTAGCTTTGTTGTTTGA
Peptide sequence:
MVKAIQVLRIHLLELEKVNELCKDFCSRYIACLKTKMNSETLLSGEPGSPYSPVQSQQIQSAITGTLSPQGIVVPASALQQGNVTMATVAGGTVYQPVTVVTPQGQVVTQALSPGTIRIQNSQLQLQLNQDLSILHQEDGSSKNKRGVLPKHATNVMRSWLFQHIGASTISVASFVV
IRESfinder result
IRESfinder score
0.500385277
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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