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mmu_circPkhd1_370
Basic information of circular RNA
PanCircBase ID:
mmu_circPkhd1_370
mm39_Chr. Position ID:
chr1|20484444|20520601|-
Gene name:
Pkhd1
Transcript:
ENSMUST00000088448.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
37,36
Exon/intron offsets:
0,36000
Genomic length:
36157
Exon/intron sizes in nt:
2,13,157
Flanking exon/introns:
chr1:20462443-20484444|chr1:20520601-20573165
Splice length:
370
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_146607
Human Ortholog IDs:
Mature spliced Sequence:
GGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCGGTCACCTGCTACTGCTTGATGCGAACACTAGCTTCCTGAACTCCCTGCACATTAAAGGTGGCAAGCTGATCTTCATGGATCCAGGACCCATTGAGCTCAGAGCCCACTCCATCCTTATTACAGATGGTGGAGAGCTCCATATTGGATCTGAGGAAAAGCCTTTCCAAGGCAAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGTGTCCATTCCACTCCC
60.34
CGTGTGGCACTCTTTGAGGA
60.25
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGTGTCCATTCCACTCCC
60.34
TCGTGTGGCACTCTTTGAGG
60.25
153
PCR template sequence:
AAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCATGGGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCG
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-138-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTTCCCTGCATGGGCAACTTTTCCT
siRNA sets
GAAAAGTTGCCCATGCAGG, AGGAAAAGTTGCCCATGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKHD1_370_ORF_1
0.8398
0.151869589
0.434527296
390
ORF sequence:
ATGGAACTCTTTCCCTGCATGGGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCGGTCACCTGCTACTGCTTGATGCGAACACTAGCTTCCTGAACTCCCTGCACATTAAAGGTGGCAAGCTGATCTTCATGGATCCAGGACCCATTGAGCTCAGAGCCCACTCCATCCTTATTACAGATGGTGGAGAGCTCCATATTGGATCTGAGGAAAAGCCTTTCCAAGGCAAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCAT
Peptide sequence:
MELFPCMGNFSFQFCRRWSRPHSWFPQRVPHDGDSVTVETGHLLLLDANTSFLNSLHIKGGKLIFMDPGPIELRAHSILITDGGELHIGSEEKPFQGKARIKIYGSVHSTPFFPYGVKFLAVRNGTLSLH
IRESfinder result
IRESfinder score
0.657419386
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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