top of page
mmu_circPkhd1_1680
Basic information of circular RNA
PanCircBase ID:
mmu_circPkhd1_1680
mm39_Chr. Position ID:
chr1|20358419|20451818|-
Gene name:
Pkhd1
Transcript:
ENSMUST00000088448.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
51,50,49,48,47,46,45,44,43,42,41,40
Exon/intron offsets:
0,22329,23837,59015,62217,70644,72790,75923,85660,86516,89179,93207
Genomic length:
93399
Exon/intron sizes in nt:
6,61,96,17,82,47,13,31,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:20345871-20358419|chr1:20451818-20461688
Splice length:
1680
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAACTTGAAGCACTGTTTGTATTCTAAGAGTGAGAAGATGCTGGGAGCCAGGGATCTGGGGGCCAGAGTCATCATTCAGTCCTTCCCAGAGGAACCCAGCTTCGTCAAGCTGAAGGGAGTGCAGTTCAGAGACCTGGGACAGGCCTTCCATAAGCACCTGAGCTCACTCGCACTGGTGGGAGCTATGAGAGGCTCTTATATCCAAAGCTGTTCAGTGTGGAACTCCTTCAGCAGAGGCCTTAGCATGCACAGGACCTGGGGTCTGAAGGTGGACAGCAATGTATTCTATAAGATTGTAGGGCATGCCCTGCTGCTGGGGTCCTACCTGGACGGAAGGTTTAGCACTAGTGAGACTGTTACTGGAAGAAAAAATGGTTGGTGGGAACAGGGAAGTACAATAAGAAACAATGTGATCATCAGTGTTTCTGCAGCTGAGGGACTGTCCGGTTCTGAAATGTTGGCACCAGCTGGCATCTACACTTTCAGTCCCACCAATGTGATGGAGGGCAACAGAGTGTGTGCAGCTGGCTATGGATATGTCTTCCACCTTGTGACCAGCCAAACATTACAAGCTCCACTCCTCTCATTCAATTGGAATACTGCTCATTCTTGTACAAGATATGGTCTCCTTGTATATCCTAAATTTCAACCACCTTGGAATAATGACACTGGCTTCACTCTGTTCCAAAACTTCATGGTTTGGGGAAGTGCTGGTGGTGCCCAGATTTTTAGAAGTAACAATCTACACCTGAAAAACTTCCAAGTTTATGCATGCAGAGATTTTGGAATTGACATTTTGGAAAGTGATGCGAACACTTTGATTACCGACAGCTTTTTACTTGGTCATTTCACCCACAAGGGAAGTCTATGTATGTCAGCTGGGATCAAAACTCCCCAAAGATGGGAACTGACCATTTCGAACACAACTTTTGTTAATTTTGATGGCAACTGTGTGGCCATCAGAACCTGTTCTGGCTGTTTCCAAGGACAGGGTGGCTATACTGTGAAGACCAGGCAATTGAAGTTTGTAAACTCTTCAAATTTAGTAGCATTTCCATTTCCTCATGCAGCAGTTCTGGAAGACTTAGACGGGTCCCTGTCTGGGAAAAATGGGTCTCATGTTCTTGCATCTATGGAAACCCTCTCAGACACATGCTTGACCAATGCAAGCTTCAGTCAGATTGTCCCTGGCAGCGTCTGTGGCGAAGCTGTTCTCTTCCATCGTATGTCTATTGCTCTAGCCAATAGCCTTGATGTTCCTAAGAATTTAACCATTACTGACATCAGTAATAAGACAATCACTGTCAATTATGTGGAAGACACCCTGTCTAACTACTACGGCTGGATGGCTCTGCTCTTGGATCAAGAGACCTACTCGCTGCAGTTTGAGAGCCCTTGGATGAACAGATCTCTGCAGTACTCAGCAACGTTTGACAGCTTTGCTCCTGGAAATTACCTCCTGATAATGCACAGGGACCTACCACCTTATCCTGACATCCTCCTCAGATGTGGGAGTCAGGTGGGCCATTCACTTCCATTTCATCCTTTGCCTAGTCAAGACAGAGCCTGTGATTGGTTCTTCAATAGGCAATTGAGGCAGCTCACCTACCTGGTTTCAGGTGAAGGTCAAGTTAAGGTATTTCTCCAACTGAAGCCTGGTGTACCTCCAAGTGTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATTGAGGCAGCTCACCTACC
59.46
GAATGATGACTCTGGCCCCC
60.18
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTGAGGCAGCTCACCTACC
59.46
CTGGCTCCCAGCATCTTCTC
60.18
141
PCR template sequence:
TTCAATAGGCAATTGAGGCAGCTCACCTACCTGGTTTCAGGTGAAGGTCAAGTTAAGGTATTTCTCCAACTGAAGCCTGGTGTACCTCCAAGTGTTTCAGGTAACTTGAAGCACTGTTTGTATTCTAAGAGTGAGAAGATGCTGGGAGCCAGGGATCTGGGGGCCAGAGTCATCATTCAGTCCTTCCCAGAGGAACCCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-200a-3p(1), mmu-miR-223-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-203-3p(1), mmu-miR-23a-3p(1), mmu-miR-138-5p(1), mmu-miR-339-5p(1), mmu-miR-381-3p(1), mmu-miR-149-5p(1), mmu-miR-212-3p(1), mmu-miR-382-5p(1), mmu-miR-802-5p(1), mmu-miR-300-3p(1), mmu-miR-539-5p(1), mmu-miR-484(1), mmu-miR-452-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
CCAAGTGTTTCAGGTAACTTGAAGCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKHD1_1680_ORF_1
0.7227
0.039957156
0.999999998
3321
ORF sequence:
ATGCTGGGAGCCAGGGATCTGGGGGCCAGAGTCATCATTCAGTCCTTCCCAGAGGAACCCAGCTTCGTCAAGCTGAAGGGAGTGCAGTTCAGAGACCTGGGACAGGCCTTCCATAAGCACCTGAGCTCACTCGCACTGGTGGGAGCTATGAGAGGCTCTTATATCCAAAGCTGTTCAGTGTGGAACTCCTTCAGCAGAGGCCTTAGCATGCACAGGACCTGGGGTCTGAAGGTGGACAGCAATGTATTCTATAAGATTGTAGGGCATGCCCTGCTGCTGGGGTCCTACCTGGACGGAAGGTTTAGCACTAGTGAGACTGTTACTGGAAGAAAAAATGGTTGGTGGGAACAGGGAAGTACAATAAGAAACAATGTGATCATCAGTGTTTCTGCAGCTGAGGGACTGTCCGGTTCTGAAATGTTGGCACCAGCTGGCATCTACACTTTCAGTCCCACCAATGTGATGGAGGGCAACAGAGTGTGTGCAGCTGGCTATGGATATGTCTTCCACCTTGTGACCAGCCAAACATTACAAGCTCCACTCCTCTCATTCAATTGGAATACTGCTCATTCTTGTACAAGATATGGTCTCCTTGTATATCCTAAATTTCAACCACCTTGGAATAATGACACTGGCTTCACTCTGTTCCAAAACTTCATGGTTTGGGGAAGTGCTGGTGGTGCCCAGATTTTTAGAAGTAACAATCTACACCTGAAAAACTTCCAAGTTTATGCATGCAGAGATTTTGGAATTGACATTTTGGAAAGTGATGCGAACACTTTGATTACCGACAGCTTTTTACTTGGTCATTTCACCCACAAGGGAAGTCTATGTATGTCAGCTGGGATCAAAACTCCCCAAAGATGGGAACTGACCATTTCGAACACAACTTTTGTTAATTTTGATGGCAACTGTGTGGCCATCAGAACCTGTTCTGGCTGTTTCCAAGGACAGGGTGGCTATACTGTGAAGACCAGGCAATTGAAGTTTGTAAACTCTTCAAATTTAGTAGCATTTCCATTTCCTCATGCAGCAGTTCTGGAAGACTTAGACGGGTCCCTGTCTGGGAAAAATGGGTCTCATGTTCTTGCATCTATGGAAACCCTCTCAGACACATGCTTGACCAATGCAAGCTTCAGTCAGATTGTCCCTGGCAGCGTCTGTGGCGAAGCTGTTCTCTTCCATCGTATGTCTATTGCTCTAGCCAATAGCCTTGATGTTCCTAAGAATTTAACCATTACTGACATCAGTAATAAGACAATCACTGTCAATTATGTGGAAGACACCCTGTCTAACTACTACGGCTGGATGGCTCTGCTCTTGGATCAAGAGACCTACTCGCTGCAGTTTGAGAGCCCTTGGATGAACAGATCTCTGCAGTACTCAGCAACGTTTGACAGCTTTGCTCCTGGAAATTACCTCCTGATAATGCACAGGGACCTACCACCTTATCCTGACATCCTCCTCAGATGTGGGAGTCAGGTGGGCCATTCACTTCCATTTCATCCTTTGCCTAGTCAAGACAGAGCCTGTGATTGGTTCTTCAATAGGCAATTGAGGCAGCTCACCTACCTGGTTTCAGGTGAAGGTCAAGTTAAGGTATTTCTCCAACTGAAGCCTGGTGTACCTCCAAGTGTTTCAGGTAACTTGAAGCACTGTTTGTATTCTAAGAGTGAGAAGATGCTGGGAGCCAGGGATCTGGGGGCCAGAGTCATCATTCAGTCCTTCCCAGAGGAACCCAGCTTCGTCAAGCTGAAGGGAGTGCAGTTCAGAGACCTGGGACAGGCCTTCCATAAGCACCTGAGCTCACTCGCACTGGTGGGAGCTATGAGAGGCTCTTATATCCAAAGCTGTTCAGTGTGGAACTCCTTCAGCAGAGGCCTTAGCATGCACAGGACCTGGGGTCTGAAGGTGGACAGCAATGTATTCTATAAGATTGTAGGGCATGCCCTGCTGCTGGGGTCCTACCTGGACGGAAGGTTTAGCACTAGTGAGACTGTTACTGGAAGAAAAAATGGTTGGTGGGAACAGGGAAGTACAATAAGAAACAATGTGATCATCAGTGTTTCTGCAGCTGAGGGACTGTCCGGTTCTGAAATGTTGGCACCAGCTGGCATCTACACTTTCAGTCCCACCAATGTGATGGAGGGCAACAGAGTGTGTGCAGCTGGCTATGGATATGTCTTCCACCTTGTGACCAGCCAAACATTACAAGCTCCACTCCTCTCATTCAATTGGAATACTGCTCATTCTTGTACAAGATATGGTCTCCTTGTATATCCTAAATTTCAACCACCTTGGAATAATGACACTGGCTTCACTCTGTTCCAAAACTTCATGGTTTGGGGAAGTGCTGGTGGTGCCCAGATTTTTAGAAGTAACAATCTACACCTGAAAAACTTCCAAGTTTATGCATGCAGAGATTTTGGAATTGACATTTTGGAAAGTGATGCGAACACTTTGATTACCGACAGCTTTTTACTTGGTCATTTCACCCACAAGGGAAGTCTATGTATGTCAGCTGGGATCAAAACTCCCCAAAGATGGGAACTGACCATTTCGAACACAACTTTTGTTAATTTTGATGGCAACTGTGTGGCCATCAGAACCTGTTCTGGCTGTTTCCAAGGACAGGGTGGCTATACTGTGAAGACCAGGCAATTGAAGTTTGTAAACTCTTCAAATTTAGTAGCATTTCCATTTCCTCATGCAGCAGTTCTGGAAGACTTAGACGGGTCCCTGTCTGGGAAAAATGGGTCTCATGTTCTTGCATCTATGGAAACCCTCTCAGACACATGCTTGACCAATGCAAGCTTCAGTCAGATTGTCCCTGGCAGCGTCTGTGGCGAAGCTGTTCTCTTCCATCGTATGTCTATTGCTCTAGCCAATAGCCTTGATGTTCCTAAGAATTTAACCATTACTGACATCAGTAATAAGACAATCACTGTCAATTATGTGGAAGACACCCTGTCTAACTACTACGGCTGGATGGCTCTGCTCTTGGATCAAGAGACCTACTCGCTGCAGTTTGAGAGCCCTTGGATGAACAGATCTCTGCAGTACTCAGCAACGTTTGACAGCTTTGCTCCTGGAAATTACCTCCTGATAATGCACAGGGACCTACCACCTTATCCTGACATCCTCCTCAGATGTGGGAGTCAGGTGGGCCATTCACTTCCATTTCATCCTTTGCCTAGTCAAGACAGAGCCTGTGATTGGTTCTTCAATAGGCAATTGAGGCAGCTCACCTACCTGGTTTCAGGTGAAGGTCAAGTTAAGGTATTTCTCCAACTGAAGCCTGGTGTACCTCCAAGTGTTTCA
Peptide sequence:
MLGARDLGARVIIQSFPEEPSFVKLKGVQFRDLGQAFHKHLSSLALVGAMRGSYIQSCSVWNSFSRGLSMHRTWGLKVDSNVFYKIVGHALLLGSYLDGRFSTSETVTGRKNGWWEQGSTIRNNVIISVSAAEGLSGSEMLAPAGIYTFSPTNVMEGNRVCAAGYGYVFHLVTSQTLQAPLLSFNWNTAHSCTRYGLLVYPKFQPPWNNDTGFTLFQNFMVWGSAGGAQIFRSNNLHLKNFQVYACRDFGIDILESDANTLITDSFLLGHFTHKGSLCMSAGIKTPQRWELTISNTTFVNFDGNCVAIRTCSGCFQGQGGYTVKTRQLKFVNSSNLVAFPFPHAAVLEDLDGSLSGKNGSHVLASMETLSDTCLTNASFSQIVPGSVCGEAVLFHRMSIALANSLDVPKNLTITDISNKTITVNYVEDTLSNYYGWMALLLDQETYSLQFESPWMNRSLQYSATFDSFAPGNYLLIMHRDLPPYPDILLRCGSQVGHSLPFHPLPSQDRACDWFFNRQLRQLTYLVSGEGQVKVFLQLKPGVPPSVSGNLKHCLYSKSEKMLGARDLGARVIIQSFPEEPSFVKLKGVQFRDLGQAFHKHLSSLALVGAMRGSYIQSCSVWNSFSRGLSMHRTWGLKVDSNVFYKIVGHALLLGSYLDGRFSTSETVTGRKNGWWEQGSTIRNNVIISVSAAEGLSGSEMLAPAGIYTFSPTNVMEGNRVCAAGYGYVFHLVTSQTLQAPLLSFNWNTAHSCTRYGLLVYPKFQPPWNNDTGFTLFQNFMVWGSAGGAQIFRSNNLHLKNFQVYACRDFGIDILESDANTLITDSFLLGHFTHKGSLCMSAGIKTPQRWELTISNTTFVNFDGNCVAIRTCSGCFQGQGGYTVKTRQLKFVNSSNLVAFPFPHAAVLEDLDGSLSGKNGSHVLASMETLSDTCLTNASFSQIVPGSVCGEAVLFHRMSIALANSLDVPKNLTITDISNKTITVNYVEDTLSNYYGWMALLLDQETYSLQFESPWMNRSLQYSATFDSFAPGNYLLIMHRDLPPYPDILLRCGSQVGHSLPFHPLPSQDRACDWFFNRQLRQLTYLVSGEGQVKVFLQLKPGVPPSVS
IRESfinder result
IRESfinder score
0.704341402
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page