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mmu_circPkhd1_1355
Basic information of circular RNA
PanCircBase ID:
mmu_circPkhd1_1355
mm39_Chr. Position ID:
chr1|20434342|20520601|-
Gene name:
Pkhd1
Transcript:
ENSMUST00000088448.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
44,43,42,41,40,39,38,37,36
Exon/intron offsets:
0,9737,10593,13256,17284,27346,27893,50102,86102
Genomic length:
86259
Exon/intron sizes in nt:
1,13,13,15,71,26,19,21,00,00,00,00,000
Flanking exon/introns:
chr1:20431315-20434342|chr1:20520601-20573165
Splice length:
1355
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCGGTCACCTGCTACTGCTTGATGCGAACACTAGCTTCCTGAACTCCCTGCACATTAAAGGTGGCAAGCTGATCTTCATGGATCCAGGACCCATTGAGCTCAGAGCCCACTCCATCCTTATTACAGATGGTGGAGAGCTCCATATTGGATCTGAGGAAAAGCCTTTCCAAGGCAAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCATGGTTCAGTTCCAGAGGTTACTGTCACCTATCTTCAAGCAGCTGCACATGCAGGAGACAAAGTGTTGACTCTGGGGGAAGCTGTGGACTGGAAGCCTGGGGATGAGGCTGTCATTACCAGTGGGATGACTGTAGCAGGAGCTGAAGCAACAGAAGTTGTTGTTGTAGAAACTGTCCACAATGCAGACCTCCATCTCAGGAACCCCCTGAGATATTCCTATGATTTCAGAGAGAACTGGGTAGCTGGAGAGAATCCTATTTTGAAGCCAACAGTTGCTCTCCTCAGCAGGAACATTATCATCCAAGGAAACTTCACACTTGAGAGGGTAAAGCTTCTCAATTCATGCCAGGAGGCCAACACTGCTAAAGGTAACTTGAAGCACTGTTTGTATTCTAAGAGTGAGAAGATGCTGGGAGCCAGGGATCTGGGGGCCAGAGTCATCATTCAGTCCTTCCCAGAGGAACCCAGCTTCGTCAAGCTGAAGGGAGTGCAGTTCAGAGACCTGGGACAGGCCTTCCATAAGCACCTGAGCTCACTCGCACTGGTGGGAGCTATGAGAGGCTCTTATATCCAAAGCTGTTCAGTGTGGAACTCCTTCAGCAGAGGCCTTAGCATGCACAGGACCTGGGGTCTGAAGGTGGACAGCAATGTATTCTATAAGATTGTAGGGCATGCCCTGCTGCTGGGGTCCTACCTGGACGGAAGGTTTAGCACTAGTGAGACTGTTACTGGAAGAAAAAATGGTTGGTGGGAACAGGGAAGTACAATAAGAAACAATGTGATCATCAGTGTTTCTGCAGCTGAGGGACTGTCCGGTTCTGAAATGTTGGCACCAGCTGGCATCTACACTTTCAGTCCCACCAATGTGATGGAGGGCAACAGAGTGTGTGCAGCTGGCTATGGATATGTCTTCCACCTTGTGACCAGCCAAACATTACAAGCTCCACTCCTCTCATTCAATTGGAATACTGCTCATTCTTGTACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTTGTGACCAGCCAAACA
60.03
CGTGTGGCACTCTTTGAGGA
60.25
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTTGTGACCAGCCAAACA
60.03
TCGTGTGGCACTCTTTGAGG
60.25
147
PCR template sequence:
GTGCAGCTGGCTATGGATATGTCTTCCACCTTGTGACCAGCCAAACATTACAAGCTCCACTCCTCTCATTCAATTGGAATACTGCTCATTCTTGTACAAGGGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-138-5p(2), mmu-miR-23b-3p(1), mmu-miR-200a-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-33-5p(1), mmu-miR-23a-3p(1), mmu-miR-149-5p(1), mmu-miR-212-3p(1), mmu-miR-370-3p(1), mmu-miR-802-5p(1), mmu-miR-673-5p(1), mmu-miR-452-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
ATTCTTGTACAAGGGCAACTTTTCCT
siRNA sets
AAAGTTGCCCTTGTACAAG, AAAAGTTGCCCTTGTACAA, AAGTTGCCCTTGTACAAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKHD1_1355_ORF_1
0.9354
0.104162559
0.998315324
1320
ORF sequence:
ATGGATCCAGGACCCATTGAGCTCAGAGCCCACTCCATCCTTATTACAGATGGTGGAGAGCTCCATATTGGATCTGAGGAAAAGCCTTTCCAAGGCAAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCATGGTTCAGTTCCAGAGGTTACTGTCACCTATCTTCAAGCAGCTGCACATGCAGGAGACAAAGTGTTGACTCTGGGGGAAGCTGTGGACTGGAAGCCTGGGGATGAGGCTGTCATTACCAGTGGGATGACTGTAGCAGGAGCTGAAGCAACAGAAGTTGTTGTTGTAGAAACTGTCCACAATGCAGACCTCCATCTCAGGAACCCCCTGAGATATTCCTATGATTTCAGAGAGAACTGGGTAGCTGGAGAGAATCCTATTTTGAAGCCAACAGTTGCTCTCCTCAGCAGGAACATTATCATCCAAGGAAACTTCACACTTGAGAGGGTAAAGCTTCTCAATTCATGCCAGGAGGCCAACACTGCTAAAGGTAACTTGAAGCACTGTTTGTATTCTAAGAGTGAGAAGATGCTGGGAGCCAGGGATCTGGGGGCCAGAGTCATCATTCAGTCCTTCCCAGAGGAACCCAGCTTCGTCAAGCTGAAGGGAGTGCAGTTCAGAGACCTGGGACAGGCCTTCCATAAGCACCTGAGCTCACTCGCACTGGTGGGAGCTATGAGAGGCTCTTATATCCAAAGCTGTTCAGTGTGGAACTCCTTCAGCAGAGGCCTTAGCATGCACAGGACCTGGGGTCTGAAGGTGGACAGCAATGTATTCTATAAGATTGTAGGGCATGCCCTGCTGCTGGGGTCCTACCTGGACGGAAGGTTTAGCACTAGTGAGACTGTTACTGGAAGAAAAAATGGTTGGTGGGAACAGGGAAGTACAATAAGAAACAATGTGATCATCAGTGTTTCTGCAGCTGAGGGACTGTCCGGTTCTGAAATGTTGGCACCAGCTGGCATCTACACTTTCAGTCCCACCAATGTGATGGAGGGCAACAGAGTGTGTGCAGCTGGCTATGGATATGTCTTCCACCTTGTGACCAGCCAAACATTACAAGCTCCACTCCTCTCATTCAATTGGAATACTGCTCATTCTTGTACAAGGGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCGGTCACCTGCTACTGCTTGATGCGAACACTAGCTTCCTGA
Peptide sequence:
MDPGPIELRAHSILITDGGELHIGSEEKPFQGKARIKIYGSVHSTPFFPYGVKFLAVRNGTLSLHGSVPEVTVTYLQAAAHAGDKVLTLGEAVDWKPGDEAVITSGMTVAGAEATEVVVVETVHNADLHLRNPLRYSYDFRENWVAGENPILKPTVALLSRNIIIQGNFTLERVKLLNSCQEANTAKGNLKHCLYSKSEKMLGARDLGARVIIQSFPEEPSFVKLKGVQFRDLGQAFHKHLSSLALVGAMRGSYIQSCSVWNSFSRGLSMHRTWGLKVDSNVFYKIVGHALLLGSYLDGRFSTSETVTGRKNGWWEQGSTIRNNVIISVSAAEGLSGSEMLAPAGIYTFSPTNVMEGNRVCAAGYGYVFHLVTSQTLQAPLLSFNWNTAHSCTRATFPSNSAEGGPGLTVGFLKECHTMATVSQWRPVTCYCLMRTLAS
IRESfinder result
IRESfinder score
0.598500602
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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