top of page
mmu_circPdpk1_514
Basic information of circular RNA
PanCircBase ID:
mmu_circPdpk1_514
mm39_Chr. Position ID:
chr17|24310394|24319882|-
Gene name:
Pdpk1
Transcript:
ENSMUST00000102927.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,9,8,7,6
Exon/intron offsets:
0,1770,2119,6673,9390
Genomic length:
9488
Exon/intron sizes in nt:
174,97,69,76,98
Flanking exon/introns:
chr17:24307195-24310394|chr17:24319882-24320575
Splice length:
514
Other database IDs:
CIRCpedia: MMU_CIRCpedia_14043, circAtlas: mmu-Pdpk1_0006
circBase: hsa_circ_0037553, CIRCpedia: HSA_CIRCpedia_17159
Human Ortholog IDs:
Mature spliced Sequence:
AGACCTTAAACCAGAAAACATTTTGTTAAATGAAGACATGCACATCCAGATCACAGATTTTGGAACAGCAAAAGTGTTATCCCCAGAGAGCAAACAAGCCAGGGCCAACTCATTTGTAGGAACAGCACAGTATGTTTCTCCAGAGCTGCTCACAGAGAAGTCGGCGTGTAAAAGTTCAGACCTTTGGGCCCTTGGATGTATAATCTATCAGCTCGTGGCAGGACTCCCACCATTCAGAGCCGGGAATGAATATCTTATATTTCAGAAGATCATTAAGCTGGAATATCATTTCCCAGAAAAATTCTTCCCTAAGGCTAGAGATCTTGTGGAAAAACTCTTGGTTTTAGATGCCACAAAGCGTTTAGGCTGTGAAGAGATGGAAGGGTACGGGCCTCTCAAAGCTCATCCATTCTTTGAGACCATCACTTGGGAGAATTTGCACCAGCAGACACCTCCGAAGCTCACAGCTTACCTACCAGCCATGTCAGAGGATGATGAAGACTGCTATGGCAAC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACACCTCCGAAGCTCACAG
60.39
GCTTGTTTGCTCTCTGGGGA
60.25
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGACACCTCCGAAGCTCAC
60.39
GCTTGTTTGCTCTCTGGGGA
60.25
168
PCR template sequence:
TGAGACCATCACTTGGGAGAATTTGCACCAGCAGACACCTCCGAAGCTCACAGCTTACCTACCAGCCATGTCAGAGGATGATGAAGACTGCTATGGCAACAGACCTTAAACCAGAAAACATTTTGTTAAATGAAGACATGCACATCCAGATCACAGATTTTGGAACAGCAAAAGTGTTATCCCCAGAGAGCAAACAAGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-19b-3p(1), mmu-miR-19a-3p(1), mmu-miR-494-3p(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
CTGCTATGGCAACAGACCTTAAACCA
siRNA sets
TGGTTTAAGGTCTGTTGCC, TAAGGTCTGTTGCCATAGC, TTAAGGTCTGTTGCCATAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDPK1_514_ORF_1
0.8386
0.142860842
0.679528166
537
ORF sequence:
ATGATGAAGACTGCTATGGCAACAGACCTTAAACCAGAAAACATTTTGTTAAATGAAGACATGCACATCCAGATCACAGATTTTGGAACAGCAAAAGTGTTATCCCCAGAGAGCAAACAAGCCAGGGCCAACTCATTTGTAGGAACAGCACAGTATGTTTCTCCAGAGCTGCTCACAGAGAAGTCGGCGTGTAAAAGTTCAGACCTTTGGGCCCTTGGATGTATAATCTATCAGCTCGTGGCAGGACTCCCACCATTCAGAGCCGGGAATGAATATCTTATATTTCAGAAGATCATTAAGCTGGAATATCATTTCCCAGAAAAATTCTTCCCTAAGGCTAGAGATCTTGTGGAAAAACTCTTGGTTTTAGATGCCACAAAGCGTTTAGGCTGTGAAGAGATGGAAGGGTACGGGCCTCTCAAAGCTCATCCATTCTTTGAGACCATCACTTGGGAGAATTTGCACCAGCAGACACCTCCGAAGCTCACAGCTTACCTACCAGCCATGTCAGAGGATGATGAAGACTGCTATGGCAAC
Peptide sequence:
MMKTAMATDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYHFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFETITWENLHQQTPPKLTAYLPAMSEDDEDCYGN
IRESfinder result
IRESfinder score
0.612965006
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page