top of page
mmu_circPkhd1_3095
Basic information of circular RNA
PanCircBase ID:
mmu_circPkhd1_3095
mm39_Chr. Position ID:
chr1|20590377|20623820|-
Gene name:
Pkhd1
Transcript:
ENSMUST00000088448.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
33,32,31,30,29,28,27,26,25,24,23
Exon/intron offsets:
0,2510,13689,14382,17119,20160,27115,27937,29532,30693,33315
Genomic length:
33443
Exon/intron sizes in nt:
14,41,60,26,81,96,13,60,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:20579336-20590377|chr1:20623820-20625301
Splice length:
3095
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTCTGTGTCCACGGAGGGAACAGGAGATGGATCTGAATTGATTGAGGTGACAGCTCAAAGACTCCAGAGGACAAGCCCACCTTTGGGAGGACACTTCTTCCTTTACCTCTCTGACACAGTGATACCTGATGTTCCGGTGCGCATGTCTGCCCGACAGCTGCATAAGCTACTGCAGGACAGTGCTGATGAGTCCACATCTGGATATCTCAATGCCGGTGACTTCACTGTGACAGAGGATCTGAATTCCTGCTATGAACATGTGTGGACTCTTTCTTGGACCACTCAGACTGGGGATTTGCCCAATTTTATCAGGGTCTCTGATCAAAATCTTACTGGGGTGAATCCCACTGTAACTGCTCGCGTGGTATATGATGGTGGAGTTTTCCTTGGACCCATCTTTGGAGACATGTTGGCTACTGCCAACCAGCAAACTCAGGTGGCTGTACAGGTGAATGACATACCAGCCTATTGTTCAGGCTCCTGTTCTTTCCAATACCAGCAAGAGTCAACTCCCAGTGTGGATCATGTGTGGTACTCCCTTGGAAGCGATGTCAACTTGCTGGTTCATTTTACTGGAACTGGTTTCCCTAGAGACACCCAGTTCTTACAGGTCACGGTGAACAAAACTAGCTGTGAAGTTCTTTTCTCAAATGAAACCAATGTGGCCTGTGAGCTGGCTCTGCTACCAGTTGGAGTGCACCAGATTTTTATGCTGGTGATACCGTCAGGCCTTGCTGTTCATGCCAGTGGAGAAGACCTCCTCCTGCATGTGGAACCCAGGCTGGATGCTGTGGAGCCTTCTACAGCTGCAGAGATTGGAGGACGGTGGGTTACTCTCCGAGGCTCTAGTTTGGAAGGTGTTAGCCTGGTGTTATTTGGAACTCAGTCATGTGTCATTGATGCCATTAGAAGCAATTCACAACAAATTCAATGCAAAGTCCCACCTAGGGGGAAAGATGGATACACTGTGAATGTGACTGTGATCAGTGGCGACCACTCTACAGTTCTTGCCAGAGCATTTACATATGTCTCCTCTTTAAATCCAGTGATTGTGTCATTGAGCAGAAACAGAAGCAGCATAGCAGGAGGTGAGATTCTGTTCCTTGGGATGTCACTGCTGGTGAACTACACAGATCTGGATGTGCAAATCCATGTGCAGGATACTTCTGCTCAGGTCCTTTCACAGACAGCGTGGGGACTGGAGGTAGTGTTGCCTCCACTAGTACCTGGCATCCATGTGATTTCAGCATTCATCAATGGAGTCAGTATTCGTTCACAAGGGGTTGATCTCTATATCCAGTACCTCACTGAAGTTTTCAGCGTGGAACCTTGCTCTGGGTCTCTCTTGGGTGGAACTCTCCTCAGTCTCTTAGGAACAGGACTGGGCAGAGACCCAGCTCTGATTCGGGTGCTTGTGGACAATCATCCTTGTGATATTGTGAACTTAACGGAAGTGAACATTTGGTGTGAGACTCCTCCAGCTGTACTACCACCCAGGGCAGATGTTCTCACTGTCCTAGCCTCTGTGGAGATCTGGGCTGGCAACACTTCCTTCTTCCATGGACCAAGCTTGGTGGGGAAGGGCTTTACCTTCACATATGAAGCAGCAGCAACACCAGTGGTCACTGCTATGTGGGGAGAATTCAGGAACAACAGTGTGAGGTTTTATGTGGAAGGAAGTAACATCTCTGACTCAGTCATTCTTTTGGGGTCCTTGAAATGTGAACTTGAAGTACAATTTTTTGGTGATAGCATGAACTTGTCTGGGTGCTTTTTTCCTCTCCATAGTTTGGAAGCCGGGGTCTATACTCTCCAAGTTCGTCACAAGAGGATGGGGTTTGCCAATATGTCTGTGGTGCCTCAGAAATTTGAGTTGTCACCTCAGATTATTGCCATCTTCCCAACACATGGGTCTAAATGTGGTGGGACAGTACTTACTGTGAAGGGCATGGCCTTCAGTTCCAGAAAGAGGTCAGTTCATGTTGACATTTCAGGCCCTTTTGCTTGCATGATTTTGAGTTTGGAAGACCACACAGTCCTATGCCAGACCAGATTTGTGGGTGACCAATTTTCTGAAGCATCACTGGCTCTAAACATCACAGTTCTGGTCAATGGGCTGACCAGCAAGTGTAAGGGGAACTGTACACTCTTCATAGAGGAAGCAGCAACTCCTATTGTGGATGCTTTGACTATAAGCATCAGTGGGTCTCTAACCATGGTGCTGATGAGAGGCCGGAGGTTAGCTACCACTGCTGATGAGCCAATAGCATTTGTGGATGATCAACTTCCCTGCCACACAACATTCTTCAATACCAGCCATGTGGCATGCCAGATAAGAGATTTGGCCCCAGGCTTCCACTATCTGTCAGCTGTTCATACAAGTGCTGGATATGCTTGCCTCAATAGTGTTTCTAGAAACTTCTTCATCGTGCCTCAGGTGCTTGATTATTTTCCTAAGGACTTTAGCATCCATGGTGGAAGTCTCTTGACGATAAAAGGCACAGCCCTGCGAGGATGGAAAGCTACAGTTGTCTATGTTGGCCGGCAGGCTTGTCTAACAGTGAACTTCAGCTCTGACTTCATCCAGTGCATTGTTCCTGCAGGAAATGGCTCTGCTGCTCTGGAAATTGATGTGAATGGAGTTTTATACCACATAGGACTTGTTGATTACAGCAGTATCTTCACCCCAGAATTGCTTTCTGTTTCACGGAGCCAAGACATCTTAACCTTTACAGTGGCCCGGATCTCAGGGGCTGCAAATGTTGACATTTTTATTGGGACATCACCGTGTCTAGGTGTTGCTGGCAACCGTACAGTTCTCCAGTGCATGGTCCCTCTGCTTCCTGCTGGGGAGTATCTTGTCACAGGTTATGATCACAGCCGAGGGTGGGCCTCATCCACTCTCATTCTTGTGCTGAGAGCCACTGTGACCTCAGTGACCAAGAACTATGGTTGCCTGGGTGGAAGGCTTTTGCATGTGCTCGGAGCAGGATTTTCTCCAGGGAACATCTCAGCTGCCGTATGTGGTGCTCCATGCCAAGTCTTGGCTAATGCGACAGTGTCTGCCTTCAGCTGCTTGGTTCTGCCCCTGCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATCTCAGCTGCCGTATGTGG
59.89
AAAGGTGGGCTTGTCCTCTG
59.89
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCTCAGCTGCCGTATGTGG
59.89
CAAAGGTGGGCTTGTCCTCT
59.89
173
PCR template sequence:
TCTCCAGGGAACATCTCAGCTGCCGTATGTGGTGCTCCATGCCAAGTCTTGGCTAATGCGACAGTGTCTGCCTTCAGCTGCTTGGTTCTGCCCCTGCATGCTCTGTGTCCACGGAGGGAACAGGAGATGGATCTGAATTGATTGAGGTGACAGCTCAAAGACTCCAGAGGACAAGCCCACCTTTGGGAGGACACTTCTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
30
Interacting miRNAs (#binding sites)
mmu-miR-27a-3p(3), mmu-miR-23b-3p(2), mmu-miR-27b-3p(2), mmu-miR-23a-3p(2), mmu-miR-128-3p(2), mmu-miR-136-5p(2), mmu-miR-382-3p(2), mmu-miR-425-5p(2), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-29b-3p(1), mmu-miR-29c-3p(1), mmu-miR-33-5p(1), mmu-miR-216a-5p(1), mmu-miR-203-3p(1), mmu-miR-125b-5p(1), mmu-miR-138-5p(1), mmu-miR-181b-5p(1), mmu-miR-214-3p(1), mmu-miR-125a-5p(1), mmu-miR-541-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-342-3p(1), mmu-miR-300-3p(1), mmu-miR-338-3p(1), mmu-miR-181d-5p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGCCCCTGCATGCTCTGTGTCCACG
siRNA sets
ACACAGAGCATGCAGGGGC, TGGACACAGAGCATGCAGG, GGACACAGAGCATGCAGGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKHD1_3095_ORF_1
0.8537
0.066502782
0.999999986
2994
ORF sequence:
ATGTCTGCCCGACAGCTGCATAAGCTACTGCAGGACAGTGCTGATGAGTCCACATCTGGATATCTCAATGCCGGTGACTTCACTGTGACAGAGGATCTGAATTCCTGCTATGAACATGTGTGGACTCTTTCTTGGACCACTCAGACTGGGGATTTGCCCAATTTTATCAGGGTCTCTGATCAAAATCTTACTGGGGTGAATCCCACTGTAACTGCTCGCGTGGTATATGATGGTGGAGTTTTCCTTGGACCCATCTTTGGAGACATGTTGGCTACTGCCAACCAGCAAACTCAGGTGGCTGTACAGGTGAATGACATACCAGCCTATTGTTCAGGCTCCTGTTCTTTCCAATACCAGCAAGAGTCAACTCCCAGTGTGGATCATGTGTGGTACTCCCTTGGAAGCGATGTCAACTTGCTGGTTCATTTTACTGGAACTGGTTTCCCTAGAGACACCCAGTTCTTACAGGTCACGGTGAACAAAACTAGCTGTGAAGTTCTTTTCTCAAATGAAACCAATGTGGCCTGTGAGCTGGCTCTGCTACCAGTTGGAGTGCACCAGATTTTTATGCTGGTGATACCGTCAGGCCTTGCTGTTCATGCCAGTGGAGAAGACCTCCTCCTGCATGTGGAACCCAGGCTGGATGCTGTGGAGCCTTCTACAGCTGCAGAGATTGGAGGACGGTGGGTTACTCTCCGAGGCTCTAGTTTGGAAGGTGTTAGCCTGGTGTTATTTGGAACTCAGTCATGTGTCATTGATGCCATTAGAAGCAATTCACAACAAATTCAATGCAAAGTCCCACCTAGGGGGAAAGATGGATACACTGTGAATGTGACTGTGATCAGTGGCGACCACTCTACAGTTCTTGCCAGAGCATTTACATATGTCTCCTCTTTAAATCCAGTGATTGTGTCATTGAGCAGAAACAGAAGCAGCATAGCAGGAGGTGAGATTCTGTTCCTTGGGATGTCACTGCTGGTGAACTACACAGATCTGGATGTGCAAATCCATGTGCAGGATACTTCTGCTCAGGTCCTTTCACAGACAGCGTGGGGACTGGAGGTAGTGTTGCCTCCACTAGTACCTGGCATCCATGTGATTTCAGCATTCATCAATGGAGTCAGTATTCGTTCACAAGGGGTTGATCTCTATATCCAGTACCTCACTGAAGTTTTCAGCGTGGAACCTTGCTCTGGGTCTCTCTTGGGTGGAACTCTCCTCAGTCTCTTAGGAACAGGACTGGGCAGAGACCCAGCTCTGATTCGGGTGCTTGTGGACAATCATCCTTGTGATATTGTGAACTTAACGGAAGTGAACATTTGGTGTGAGACTCCTCCAGCTGTACTACCACCCAGGGCAGATGTTCTCACTGTCCTAGCCTCTGTGGAGATCTGGGCTGGCAACACTTCCTTCTTCCATGGACCAAGCTTGGTGGGGAAGGGCTTTACCTTCACATATGAAGCAGCAGCAACACCAGTGGTCACTGCTATGTGGGGAGAATTCAGGAACAACAGTGTGAGGTTTTATGTGGAAGGAAGTAACATCTCTGACTCAGTCATTCTTTTGGGGTCCTTGAAATGTGAACTTGAAGTACAATTTTTTGGTGATAGCATGAACTTGTCTGGGTGCTTTTTTCCTCTCCATAGTTTGGAAGCCGGGGTCTATACTCTCCAAGTTCGTCACAAGAGGATGGGGTTTGCCAATATGTCTGTGGTGCCTCAGAAATTTGAGTTGTCACCTCAGATTATTGCCATCTTCCCAACACATGGGTCTAAATGTGGTGGGACAGTACTTACTGTGAAGGGCATGGCCTTCAGTTCCAGAAAGAGGTCAGTTCATGTTGACATTTCAGGCCCTTTTGCTTGCATGATTTTGAGTTTGGAAGACCACACAGTCCTATGCCAGACCAGATTTGTGGGTGACCAATTTTCTGAAGCATCACTGGCTCTAAACATCACAGTTCTGGTCAATGGGCTGACCAGCAAGTGTAAGGGGAACTGTACACTCTTCATAGAGGAAGCAGCAACTCCTATTGTGGATGCTTTGACTATAAGCATCAGTGGGTCTCTAACCATGGTGCTGATGAGAGGCCGGAGGTTAGCTACCACTGCTGATGAGCCAATAGCATTTGTGGATGATCAACTTCCCTGCCACACAACATTCTTCAATACCAGCCATGTGGCATGCCAGATAAGAGATTTGGCCCCAGGCTTCCACTATCTGTCAGCTGTTCATACAAGTGCTGGATATGCTTGCCTCAATAGTGTTTCTAGAAACTTCTTCATCGTGCCTCAGGTGCTTGATTATTTTCCTAAGGACTTTAGCATCCATGGTGGAAGTCTCTTGACGATAAAAGGCACAGCCCTGCGAGGATGGAAAGCTACAGTTGTCTATGTTGGCCGGCAGGCTTGTCTAACAGTGAACTTCAGCTCTGACTTCATCCAGTGCATTGTTCCTGCAGGAAATGGCTCTGCTGCTCTGGAAATTGATGTGAATGGAGTTTTATACCACATAGGACTTGTTGATTACAGCAGTATCTTCACCCCAGAATTGCTTTCTGTTTCACGGAGCCAAGACATCTTAACCTTTACAGTGGCCCGGATCTCAGGGGCTGCAAATGTTGACATTTTTATTGGGACATCACCGTGTCTAGGTGTTGCTGGCAACCGTACAGTTCTCCAGTGCATGGTCCCTCTGCTTCCTGCTGGGGAGTATCTTGTCACAGGTTATGATCACAGCCGAGGGTGGGCCTCATCCACTCTCATTCTTGTGCTGAGAGCCACTGTGACCTCAGTGACCAAGAACTATGGTTGCCTGGGTGGAAGGCTTTTGCATGTGCTCGGAGCAGGATTTTCTCCAGGGAACATCTCAGCTGCCGTATGTGGTGCTCCATGCCAAGTCTTGGCTAATGCGACAGTGTCTGCCTTCAGCTGCTTGGTTCTGCCCCTGCATGCTCTGTGTCCACGGAGGGAACAGGAGATGGATCTGAATTGA
Peptide sequence:
MSARQLHKLLQDSADESTSGYLNAGDFTVTEDLNSCYEHVWTLSWTTQTGDLPNFIRVSDQNLTGVNPTVTARVVYDGGVFLGPIFGDMLATANQQTQVAVQVNDIPAYCSGSCSFQYQQESTPSVDHVWYSLGSDVNLLVHFTGTGFPRDTQFLQVTVNKTSCEVLFSNETNVACELALLPVGVHQIFMLVIPSGLAVHASGEDLLLHVEPRLDAVEPSTAAEIGGRWVTLRGSSLEGVSLVLFGTQSCVIDAIRSNSQQIQCKVPPRGKDGYTVNVTVISGDHSTVLARAFTYVSSLNPVIVSLSRNRSSIAGGEILFLGMSLLVNYTDLDVQIHVQDTSAQVLSQTAWGLEVVLPPLVPGIHVISAFINGVSIRSQGVDLYIQYLTEVFSVEPCSGSLLGGTLLSLLGTGLGRDPALIRVLVDNHPCDIVNLTEVNIWCETPPAVLPPRADVLTVLASVEIWAGNTSFFHGPSLVGKGFTFTYEAAATPVVTAMWGEFRNNSVRFYVEGSNISDSVILLGSLKCELEVQFFGDSMNLSGCFFPLHSLEAGVYTLQVRHKRMGFANMSVVPQKFELSPQIIAIFPTHGSKCGGTVLTVKGMAFSSRKRSVHVDISGPFACMILSLEDHTVLCQTRFVGDQFSEASLALNITVLVNGLTSKCKGNCTLFIEEAATPIVDALTISISGSLTMVLMRGRRLATTADEPIAFVDDQLPCHTTFFNTSHVACQIRDLAPGFHYLSAVHTSAGYACLNSVSRNFFIVPQVLDYFPKDFSIHGGSLLTIKGTALRGWKATVVYVGRQACLTVNFSSDFIQCIVPAGNGSAALEIDVNGVLYHIGLVDYSSIFTPELLSVSRSQDILTFTVARISGAANVDIFIGTSPCLGVAGNRTVLQCMVPLLPAGEYLVTGYDHSRGWASSTLILVLRATVTSVTKNYGCLGGRLLHVLGAGFSPGNISAAVCGAPCQVLANATVSAFSCLVLPLHALCPRREQEMDLN
IRESfinder result
IRESfinder score
0.70435282
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page