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mmu_circPkhd1_2127
Basic information of circular RNA
PanCircBase ID:
mmu_circPkhd1_2127
mm39_Chr. Position ID:
chr1|20417434|20573316|-
Gene name:
Pkhd1
Transcript:
ENSMUST00000088448.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
14
Exon/intron indexes:
48,47,46,45,44,43,42,41,40,39,38,37,36,35
Exon/intron offsets:
0,3202,11629,13775,16908,26645,27501,30164,34192,44254,44801,67010,103010,155731
Genomic length:
155882
Exon/intron sizes in nt:
24,71,33,13,51,06,11,30,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:20382434-20417434|chr1:20573316-20579116
Splice length:
2127
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CCCTAAAGTGGAAAGAGATGAAGTTCTCATCTATAATAGCTCCTGTAACATTACCATGGAAACTGAGGCAGAGATGGAGTGTGAGATGCCTAATCAGCCAATTACCGCCAAGATTACTGAAATACAGAAAAGCTGGGGCCAGAACACTCAGGGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCGGTCACCTGCTACTGCTTGATGCGAACACTAGCTTCCTGAACTCCCTGCACATTAAAGGTGGCAAGCTGATCTTCATGGATCCAGGACCCATTGAGCTCAGAGCCCACTCCATCCTTATTACAGATGGTGGAGAGCTCCATATTGGATCTGAGGAAAAGCCTTTCCAAGGCAAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCATGGTTCAGTTCCAGAGGTTACTGTCACCTATCTTCAAGCAGCTGCACATGCAGGAGACAAAGTGTTGACTCTGGGGGAAGCTGTGGACTGGAAGCCTGGGGATGAGGCTGTCATTACCAGTGGGATGACTGTAGCAGGAGCTGAAGCAACAGAAGTTGTTGTTGTAGAAACTGTCCACAATGCAGACCTCCATCTCAGGAACCCCCTGAGATATTCCTATGATTTCAGAGAGAACTGGGTAGCTGGAGAGAATCCTATTTTGAAGCCAACAGTTGCTCTCCTCAGCAGGAACATTATCATCCAAGGAAACTTCACACTTGAGAGGGTAAAGCTTCTCAATTCATGCCAGGAGGCCAACACTGCTAAAGGTAACTTGAAGCACTGTTTGTATTCTAAGAGTGAGAAGATGCTGGGAGCCAGGGATCTGGGGGCCAGAGTCATCATTCAGTCCTTCCCAGAGGAACCCAGCTTCGTCAAGCTGAAGGGAGTGCAGTTCAGAGACCTGGGACAGGCCTTCCATAAGCACCTGAGCTCACTCGCACTGGTGGGAGCTATGAGAGGCTCTTATATCCAAAGCTGTTCAGTGTGGAACTCCTTCAGCAGAGGCCTTAGCATGCACAGGACCTGGGGTCTGAAGGTGGACAGCAATGTATTCTATAAGATTGTAGGGCATGCCCTGCTGCTGGGGTCCTACCTGGACGGAAGGTTTAGCACTAGTGAGACTGTTACTGGAAGAAAAAATGGTTGGTGGGAACAGGGAAGTACAATAAGAAACAATGTGATCATCAGTGTTTCTGCAGCTGAGGGACTGTCCGGTTCTGAAATGTTGGCACCAGCTGGCATCTACACTTTCAGTCCCACCAATGTGATGGAGGGCAACAGAGTGTGTGCAGCTGGCTATGGATATGTCTTCCACCTTGTGACCAGCCAAACATTACAAGCTCCACTCCTCTCATTCAATTGGAATACTGCTCATTCTTGTACAAGATATGGTCTCCTTGTATATCCTAAATTTCAACCACCTTGGAATAATGACACTGGCTTCACTCTGTTCCAAAACTTCATGGTTTGGGGAAGTGCTGGTGGTGCCCAGATTTTTAGAAGTAACAATCTACACCTGAAAAACTTCCAAGTTTATGCATGCAGAGATTTTGGAATTGACATTTTGGAAAGTGATGCGAACACTTTGATTACCGACAGCTTTTTACTTGGTCATTTCACCCACAAGGGAAGTCTATGTATGTCAGCTGGGATCAAAACTCCCCAAAGATGGGAACTGACCATTTCGAACACAACTTTTGTTAATTTTGATGGCAACTGTGTGGCCATCAGAACCTGTTCTGGCTGTTTCCAAGGACAGGGTGGCTATACTGTGAAGACCAGGCAATTGAAGTTTGTAAACTCTTCAAATTTAGTAGCATTTCCATTTCCTCATGCAGCAGTTCTGGAAGACTTAGACGGGTCCCTGTCTGGGAAAAATGGGTCTCATGTTCTTGCATCTATGGAAACCCTCTCAGACACATGCTTGACCAATGCAAGCTTCAGTCAGATTGTCCCTGGCAGCGTCTGTGGCGAAGCTGTTCTCTTCCATCGTATGTCTATTGCTCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTCAGATTGTCCCTGGCA
59.67
CACACTCCATCTCTGCCTCA
59.1
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTCAGATTGTCCCTGGCA
59.67
CACACTCCATCTCTGCCTCAG
60.13
149
PCR template sequence:
CCCTCTCAGACACATGCTTGACCAATGCAAGCTTCAGTCAGATTGTCCCTGGCAGCGTCTGTGGCGAAGCTGTTCTCTTCCATCGTATGTCTATTGCTCTCCCTAAAGTGGAAAGAGATGAAGTTCTCATCTATAATAGCTCCTGTAACATTACCATGGAAACTGAGGCAGAGATGGAGTGTGAGATGCCTAATCAGCCA
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-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-203-3p(1), mmu-miR-23a-3p(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-370-3p(1), mmu-miR-802-5p(1), mmu-miR-300-3p(1), mmu-miR-673-5p(1), mmu-miR-452-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
TGTCTATTGCTCTCCCTAAAGTGGAA
siRNA sets
TTTAGGGAGAGCAATAGAC, CTTTAGGGAGAGCAATAGA, TTAGGGAGAGCAATAGACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKHD1_2127_ORF_1
0.9427
0.074010041
1
4197
ORF sequence:
ATGGAAACTGAGGCAGAGATGGAGTGTGAGATGCCTAATCAGCCAATTACCGCCAAGATTACTGAAATACAGAAAAGCTGGGGCCAGAACACTCAGGGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCGGTCACCTGCTACTGCTTGATGCGAACACTAGCTTCCTGAACTCCCTGCACATTAAAGGTGGCAAGCTGATCTTCATGGATCCAGGACCCATTGAGCTCAGAGCCCACTCCATCCTTATTACAGATGGTGGAGAGCTCCATATTGGATCTGAGGAAAAGCCTTTCCAAGGCAAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCATGGTTCAGTTCCAGAGGTTACTGTCACCTATCTTCAAGCAGCTGCACATGCAGGAGACAAAGTGTTGACTCTGGGGGAAGCTGTGGACTGGAAGCCTGGGGATGAGGCTGTCATTACCAGTGGGATGACTGTAGCAGGAGCTGAAGCAACAGAAGTTGTTGTTGTAGAAACTGTCCACAATGCAGACCTCCATCTCAGGAACCCCCTGAGATATTCCTATGATTTCAGAGAGAACTGGGTAGCTGGAGAGAATCCTATTTTGAAGCCAACAGTTGCTCTCCTCAGCAGGAACATTATCATCCAAGGAAACTTCACACTTGAGAGGGTAAAGCTTCTCAATTCATGCCAGGAGGCCAACACTGCTAAAGGTAACTTGAAGCACTGTTTGTATTCTAAGAGTGAGAAGATGCTGGGAGCCAGGGATCTGGGGGCCAGAGTCATCATTCAGTCCTTCCCAGAGGAACCCAGCTTCGTCAAGCTGAAGGGAGTGCAGTTCAGAGACCTGGGACAGGCCTTCCATAAGCACCTGAGCTCACTCGCACTGGTGGGAGCTATGAGAGGCTCTTATATCCAAAGCTGTTCAGTGTGGAACTCCTTCAGCAGAGGCCTTAGCATGCACAGGACCTGGGGTCTGAAGGTGGACAGCAATGTATTCTATAAGATTGTAGGGCATGCCCTGCTGCTGGGGTCCTACCTGGACGGAAGGTTTAGCACTAGTGAGACTGTTACTGGAAGAAAAAATGGTTGGTGGGAACAGGGAAGTACAATAAGAAACAATGTGATCATCAGTGTTTCTGCAGCTGAGGGACTGTCCGGTTCTGAAATGTTGGCACCAGCTGGCATCTACACTTTCAGTCCCACCAATGTGATGGAGGGCAACAGAGTGTGTGCAGCTGGCTATGGATATGTCTTCCACCTTGTGACCAGCCAAACATTACAAGCTCCACTCCTCTCATTCAATTGGAATACTGCTCATTCTTGTACAAGATATGGTCTCCTTGTATATCCTAAATTTCAACCACCTTGGAATAATGACACTGGCTTCACTCTGTTCCAAAACTTCATGGTTTGGGGAAGTGCTGGTGGTGCCCAGATTTTTAGAAGTAACAATCTACACCTGAAAAACTTCCAAGTTTATGCATGCAGAGATTTTGGAATTGACATTTTGGAAAGTGATGCGAACACTTTGATTACCGACAGCTTTTTACTTGGTCATTTCACCCACAAGGGAAGTCTATGTATGTCAGCTGGGATCAAAACTCCCCAAAGATGGGAACTGACCATTTCGAACACAACTTTTGTTAATTTTGATGGCAACTGTGTGGCCATCAGAACCTGTTCTGGCTGTTTCCAAGGACAGGGTGGCTATACTGTGAAGACCAGGCAATTGAAGTTTGTAAACTCTTCAAATTTAGTAGCATTTCCATTTCCTCATGCAGCAGTTCTGGAAGACTTAGACGGGTCCCTGTCTGGGAAAAATGGGTCTCATGTTCTTGCATCTATGGAAACCCTCTCAGACACATGCTTGACCAATGCAAGCTTCAGTCAGATTGTCCCTGGCAGCGTCTGTGGCGAAGCTGTTCTCTTCCATCGTATGTCTATTGCTCTCCCTAAAGTGGAAAGAGATGAAGTTCTCATCTATAATAGCTCCTGTAACATTACCATGGAAACTGAGGCAGAGATGGAGTGTGAGATGCCTAATCAGCCAATTACCGCCAAGATTACTGAAATACAGAAAAGCTGGGGCCAGAACACTCAGGGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCGGTCACCTGCTACTGCTTGATGCGAACACTAGCTTCCTGAACTCCCTGCACATTAAAGGTGGCAAGCTGATCTTCATGGATCCAGGACCCATTGAGCTCAGAGCCCACTCCATCCTTATTACAGATGGTGGAGAGCTCCATATTGGATCTGAGGAAAAGCCTTTCCAAGGCAAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCATGGTTCAGTTCCAGAGGTTACTGTCACCTATCTTCAAGCAGCTGCACATGCAGGAGACAAAGTGTTGACTCTGGGGGAAGCTGTGGACTGGAAGCCTGGGGATGAGGCTGTCATTACCAGTGGGATGACTGTAGCAGGAGCTGAAGCAACAGAAGTTGTTGTTGTAGAAACTGTCCACAATGCAGACCTCCATCTCAGGAACCCCCTGAGATATTCCTATGATTTCAGAGAGAACTGGGTAGCTGGAGAGAATCCTATTTTGAAGCCAACAGTTGCTCTCCTCAGCAGGAACATTATCATCCAAGGAAACTTCACACTTGAGAGGGTAAAGCTTCTCAATTCATGCCAGGAGGCCAACACTGCTAAAGGTAACTTGAAGCACTGTTTGTATTCTAAGAGTGAGAAGATGCTGGGAGCCAGGGATCTGGGGGCCAGAGTCATCATTCAGTCCTTCCCAGAGGAACCCAGCTTCGTCAAGCTGAAGGGAGTGCAGTTCAGAGACCTGGGACAGGCCTTCCATAAGCACCTGAGCTCACTCGCACTGGTGGGAGCTATGAGAGGCTCTTATATCCAAAGCTGTTCAGTGTGGAACTCCTTCAGCAGAGGCCTTAGCATGCACAGGACCTGGGGTCTGAAGGTGGACAGCAATGTATTCTATAAGATTGTAGGGCATGCCCTGCTGCTGGGGTCCTACCTGGACGGAAGGTTTAGCACTAGTGAGACTGTTACTGGAAGAAAAAATGGTTGGTGGGAACAGGGAAGTACAATAAGAAACAATGTGATCATCAGTGTTTCTGCAGCTGAGGGACTGTCCGGTTCTGAAATGTTGGCACCAGCTGGCATCTACACTTTCAGTCCCACCAATGTGATGGAGGGCAACAGAGTGTGTGCAGCTGGCTATGGATATGTCTTCCACCTTGTGACCAGCCAAACATTACAAGCTCCACTCCTCTCATTCAATTGGAATACTGCTCATTCTTGTACAAGATATGGTCTCCTTGTATATCCTAAATTTCAACCACCTTGGAATAATGACACTGGCTTCACTCTGTTCCAAAACTTCATGGTTTGGGGAAGTGCTGGTGGTGCCCAGATTTTTAGAAGTAACAATCTACACCTGAAAAACTTCCAAGTTTATGCATGCAGAGATTTTGGAATTGACATTTTGGAAAGTGATGCGAACACTTTGATTACCGACAGCTTTTTACTTGGTCATTTCACCCACAAGGGAAGTCTATGTATGTCAGCTGGGATCAAAACTCCCCAAAGATGGGAACTGACCATTTCGAACACAACTTTTGTTAATTTTGATGGCAACTGTGTGGCCATCAGAACCTGTTCTGGCTGTTTCCAAGGACAGGGTGGCTATACTGTGAAGACCAGGCAATTGAAGTTTGTAAACTCTTCAAATTTAGTAGCATTTCCATTTCCTCATGCAGCAGTTCTGGAAGACTTAGACGGGTCCCTGTCTGGGAAAAATGGGTCTCATGTTCTTGCATCTATGGAAACCCTCTCAGACACATGCTTGACCAATGCAAGCTTCAGTCAGATTGTCCCTGGCAGCGTCTGTGGCGAAGCTGTTCTCTTCCATCGTATGTCTATTGCT
Peptide sequence:
METEAEMECEMPNQPITAKITEIQKSWGQNTQGNFSFQFCRRWSRPHSWFPQRVPHDGDSVTVETGHLLLLDANTSFLNSLHIKGGKLIFMDPGPIELRAHSILITDGGELHIGSEEKPFQGKARIKIYGSVHSTPFFPYGVKFLAVRNGTLSLHGSVPEVTVTYLQAAAHAGDKVLTLGEAVDWKPGDEAVITSGMTVAGAEATEVVVVETVHNADLHLRNPLRYSYDFRENWVAGENPILKPTVALLSRNIIIQGNFTLERVKLLNSCQEANTAKGNLKHCLYSKSEKMLGARDLGARVIIQSFPEEPSFVKLKGVQFRDLGQAFHKHLSSLALVGAMRGSYIQSCSVWNSFSRGLSMHRTWGLKVDSNVFYKIVGHALLLGSYLDGRFSTSETVTGRKNGWWEQGSTIRNNVIISVSAAEGLSGSEMLAPAGIYTFSPTNVMEGNRVCAAGYGYVFHLVTSQTLQAPLLSFNWNTAHSCTRYGLLVYPKFQPPWNNDTGFTLFQNFMVWGSAGGAQIFRSNNLHLKNFQVYACRDFGIDILESDANTLITDSFLLGHFTHKGSLCMSAGIKTPQRWELTISNTTFVNFDGNCVAIRTCSGCFQGQGGYTVKTRQLKFVNSSNLVAFPFPHAAVLEDLDGSLSGKNGSHVLASMETLSDTCLTNASFSQIVPGSVCGEAVLFHRMSIALPKVERDEVLIYNSSCNITMETEAEMECEMPNQPITAKITEIQKSWGQNTQGNFSFQFCRRWSRPHSWFPQRVPHDGDSVTVETGHLLLLDANTSFLNSLHIKGGKLIFMDPGPIELRAHSILITDGGELHIGSEEKPFQGKARIKIYGSVHSTPFFPYGVKFLAVRNGTLSLHGSVPEVTVTYLQAAAHAGDKVLTLGEAVDWKPGDEAVITSGMTVAGAEATEVVVVETVHNADLHLRNPLRYSYDFRENWVAGENPILKPTVALLSRNIIIQGNFTLERVKLLNSCQEANTAKGNLKHCLYSKSEKMLGARDLGARVIIQSFPEEPSFVKLKGVQFRDLGQAFHKHLSSLALVGAMRGSYIQSCSVWNSFSRGLSMHRTWGLKVDSNVFYKIVGHALLLGSYLDGRFSTSETVTGRKNGWWEQGSTIRNNVIISVSAAEGLSGSEMLAPAGIYTFSPTNVMEGNRVCAAGYGYVFHLVTSQTLQAPLLSFNWNTAHSCTRYGLLVYPKFQPPWNNDTGFTLFQNFMVWGSAGGAQIFRSNNLHLKNFQVYACRDFGIDILESDANTLITDSFLLGHFTHKGSLCMSAGIKTPQRWELTISNTTFVNFDGNCVAIRTCSGCFQGQGGYTVKTRQLKFVNSSNLVAFPFPHAAVLEDLDGSLSGKNGSHVLASMETLSDTCLTNASFSQIVPGSVCGEAVLFHRMSIA
IRESfinder result
IRESfinder score
0.637107009
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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