top of page
mmu_circPikfyve_1878
Basic information of circular RNA
PanCircBase ID:
mmu_circPikfyve_1878
mm39_Chr. Position ID:
chr1|65277593|65291742|+
Gene name:
Pikfyve
Transcript:
ENSMUST00000081154.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
17,18,19,20,21,22,23
Exon/intron offsets:
0,5961,7275,7627,11751,13170,13977
Genomic length:
14149
Exon/intron sizes in nt:
10,81,41,12,71,15,71,00,00,000
Flanking exon/introns:
chr1:65274243-65277593|chr1:65291742-65292510
Splice length:
1878
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATGAATTCCTGTATTAAAAACCCCAAAATCCTTCTGTTGAAGTGTTCTATTGAGTATCTCTATAGAGAAGAAACTAAGTTTACCTGCATTGATCCTATTGTGCTTCAGGAAAGGGAATTCTTGAAGAATTATGTTCAACGAATAGTTGATGTTCGACCCACATTGGTTCTTGTTGAGAAAACAGTGTCTCGGATTGCTCAGGACATGTTACTGGAACATGGCATTACTCTGGTCATTAATGTAAAGTCACAAGTTTTAGAAAGAATCAGTCGAATGACCCAAGGTGATTTAGTGGTGTCCATGGACCAGCTGCTCACCAAACCCCACTTGGGCACTTGCCACAAATTTTATATGCAGATATTTCAGCTGCCTAATGAACAAACCAAAACACTGATGTTTTTTGAAGGCTGTCCACAGCATCTAGGCTGCACAATCAAGCTCAGAGGAGGCTCTGATTATGAGCTGGCTCGAGTTAAGGAGATCCTAATATTTATGATCTGTGTAGCTTATCATTCTCAGCTAGAAATCTCTTTTCTCATGGATGAGTTCGCTATGCCTCCAACATTAATGCAAAGCCCTTCATTCCATCTTCTGACGGAGGGACGAGGTGAAGAGGGAGCCTCTCAGGAGCAGGTCAGTGGCAGCTCCCTTCCTCAGGATCCTGAGTGCCCTCGTGAGGCCCTGTCTTCTGAGGATAGCACTTTGTTGGAATCAAGGACTGTGCTAGAGAAGGGTGAACTAGACAATAAAAGTATTCCACAAGCTGTTGCCTCTTTGAAGCATCAAGATTATACCACCCCCACTTGCCCAGCAGGTATTCCCTGTGCTCTTTTTGCATTGGTACCAGAGTCATTGTTGCCTCTCCATATGGATCAACAGGATGCCGTAGGAAATGAACAGCCAGAGACTTCACAGCAAACGGATGAGCAACAGGATCCCAAAAGCCAGATGAAAGCTTTTAGAGACCCTTTACAGGATGACACTGGAATGTACGTTACTGAGGAAGTCACCTCCTCTGAAGATCAACGAAAGACTTATGCCTTGACATTTAAACAGGAGTTAAAAGATGTAATCCTCTGTATCTCTCCAGTTATTACATTCCGTGAACCTTTCCTTTTAACTGAAAAGGGGATGAGATGCTCAACTCGAGATTATTTTCCAGAGCAGATTTACTGGTCTCCTCTTCTCAACAAAGAGGTGAAGGAAATGGAGAGCAGGAGGAAGAAACAGCTGCTCAGGGATCTCTCTGGACTTCAGGGCATGAATGGCAGTGTTCAGGCCAAGTCTATTCAAGTCTTACCCTCACATGAGCTAGTGAGCACCAGGATTGCTGAACATCTGGGTGACAGCCAGACCTTGGGTAGAATGCTAGCTGATTATCGAGCTAGAGGAGGAAGAATTCAGTCAAAACATTTGGACCCCTTTGTCCATTCAAAAGATGCATCATGTACTTCAGGTGGCAAATCAGGAAACAAAACTGAGAGTGATGAAGAGAGGGGATTGATTCCAAGTGATGTAATATGGCCAACAAAGGTGGACTGTCTGAACCCTGCTAACCACCAGAGGCTCTGTGTGCTCTTCAGCAGCTCTTCTGCCCAGTCCAGCAATGCTCCCAGTGCTTGTGTCAGTCCTTGGATTGTAACAATGGAGTTTTATGGAAAGAATGACCTTACACTGGGGATATTTTTAGAAAGATACTGTTTCAGGTCTTCTTACCAGTGTCCGAGCATGTTCTGTGACACCCCCATGGTTCATCACATTCGACGCTTTGTTCATGGCCAAGGCTGTGTACAGATAATTCTGAAGGAGTTGGATTCTCCAGTGCCTGGATATCAACATACAATTCTCACATATTCCTGGTGCAGAATCTGCAAACAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAAGGCTGTGTACAGATAATTCT
58.57
TCAACAGAAGGATTTTGGGGT
57.39
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAAGGCTGTGTACAGATAAT
55.38
TCAACAGAAGGATTTTGGGGT
57.39
140
PCR template sequence:
CCAAGGCTGTGTACAGATAATTCTGAAGGAGTTGGATTCTCCAGTGCCTGGATATCAACATACAATTCTCACATATTCCTGGTGCAGAATCTGCAAACAAATGAATTCCTGTATTAAAAACCCCAAAATCCTTCTGTTGAAGTGTTCTATTGAGTATCTCTATAGAGAAGAAACTAAGTTTACCTGCATTGATCCTATTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(2), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-351-5p(1), mmu-miR-22-3p(1), mmu-miR-370-3p(1), mmu-miR-297a-5p(1), mmu-miR-499-5p(1), mmu-miR-802-5p(1), mmu-miR-1187(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATCTGCAAACAAATGAATTCCTGTA
siRNA sets
GAATTCATTTGTTTGCAGA, CAGGAATTCATTTGTTTGC, AGGAATTCATTTGTTTGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPIKFYVE_1878_ORF_1
0.7947
0.057257696
1
3756
ORF sequence:
ATGAATTCCTGTATTAAAAACCCCAAAATCCTTCTGTTGAAGTGTTCTATTGAGTATCTCTATAGAGAAGAAACTAAGTTTACCTGCATTGATCCTATTGTGCTTCAGGAAAGGGAATTCTTGAAGAATTATGTTCAACGAATAGTTGATGTTCGACCCACATTGGTTCTTGTTGAGAAAACAGTGTCTCGGATTGCTCAGGACATGTTACTGGAACATGGCATTACTCTGGTCATTAATGTAAAGTCACAAGTTTTAGAAAGAATCAGTCGAATGACCCAAGGTGATTTAGTGGTGTCCATGGACCAGCTGCTCACCAAACCCCACTTGGGCACTTGCCACAAATTTTATATGCAGATATTTCAGCTGCCTAATGAACAAACCAAAACACTGATGTTTTTTGAAGGCTGTCCACAGCATCTAGGCTGCACAATCAAGCTCAGAGGAGGCTCTGATTATGAGCTGGCTCGAGTTAAGGAGATCCTAATATTTATGATCTGTGTAGCTTATCATTCTCAGCTAGAAATCTCTTTTCTCATGGATGAGTTCGCTATGCCTCCAACATTAATGCAAAGCCCTTCATTCCATCTTCTGACGGAGGGACGAGGTGAAGAGGGAGCCTCTCAGGAGCAGGTCAGTGGCAGCTCCCTTCCTCAGGATCCTGAGTGCCCTCGTGAGGCCCTGTCTTCTGAGGATAGCACTTTGTTGGAATCAAGGACTGTGCTAGAGAAGGGTGAACTAGACAATAAAAGTATTCCACAAGCTGTTGCCTCTTTGAAGCATCAAGATTATACCACCCCCACTTGCCCAGCAGGTATTCCCTGTGCTCTTTTTGCATTGGTACCAGAGTCATTGTTGCCTCTCCATATGGATCAACAGGATGCCGTAGGAAATGAACAGCCAGAGACTTCACAGCAAACGGATGAGCAACAGGATCCCAAAAGCCAGATGAAAGCTTTTAGAGACCCTTTACAGGATGACACTGGAATGTACGTTACTGAGGAAGTCACCTCCTCTGAAGATCAACGAAAGACTTATGCCTTGACATTTAAACAGGAGTTAAAAGATGTAATCCTCTGTATCTCTCCAGTTATTACATTCCGTGAACCTTTCCTTTTAACTGAAAAGGGGATGAGATGCTCAACTCGAGATTATTTTCCAGAGCAGATTTACTGGTCTCCTCTTCTCAACAAAGAGGTGAAGGAAATGGAGAGCAGGAGGAAGAAACAGCTGCTCAGGGATCTCTCTGGACTTCAGGGCATGAATGGCAGTGTTCAGGCCAAGTCTATTCAAGTCTTACCCTCACATGAGCTAGTGAGCACCAGGATTGCTGAACATCTGGGTGACAGCCAGACCTTGGGTAGAATGCTAGCTGATTATCGAGCTAGAGGAGGAAGAATTCAGTCAAAACATTTGGACCCCTTTGTCCATTCAAAAGATGCATCATGTACTTCAGGTGGCAAATCAGGAAACAAAACTGAGAGTGATGAAGAGAGGGGATTGATTCCAAGTGATGTAATATGGCCAACAAAGGTGGACTGTCTGAACCCTGCTAACCACCAGAGGCTCTGTGTGCTCTTCAGCAGCTCTTCTGCCCAGTCCAGCAATGCTCCCAGTGCTTGTGTCAGTCCTTGGATTGTAACAATGGAGTTTTATGGAAAGAATGACCTTACACTGGGGATATTTTTAGAAAGATACTGTTTCAGGTCTTCTTACCAGTGTCCGAGCATGTTCTGTGACACCCCCATGGTTCATCACATTCGACGCTTTGTTCATGGCCAAGGCTGTGTACAGATAATTCTGAAGGAGTTGGATTCTCCAGTGCCTGGATATCAACATACAATTCTCACATATTCCTGGTGCAGAATCTGCAAACAAATGAATTCCTGTATTAAAAACCCCAAAATCCTTCTGTTGAAGTGTTCTATTGAGTATCTCTATAGAGAAGAAACTAAGTTTACCTGCATTGATCCTATTGTGCTTCAGGAAAGGGAATTCTTGAAGAATTATGTTCAACGAATAGTTGATGTTCGACCCACATTGGTTCTTGTTGAGAAAACAGTGTCTCGGATTGCTCAGGACATGTTACTGGAACATGGCATTACTCTGGTCATTAATGTAAAGTCACAAGTTTTAGAAAGAATCAGTCGAATGACCCAAGGTGATTTAGTGGTGTCCATGGACCAGCTGCTCACCAAACCCCACTTGGGCACTTGCCACAAATTTTATATGCAGATATTTCAGCTGCCTAATGAACAAACCAAAACACTGATGTTTTTTGAAGGCTGTCCACAGCATCTAGGCTGCACAATCAAGCTCAGAGGAGGCTCTGATTATGAGCTGGCTCGAGTTAAGGAGATCCTAATATTTATGATCTGTGTAGCTTATCATTCTCAGCTAGAAATCTCTTTTCTCATGGATGAGTTCGCTATGCCTCCAACATTAATGCAAAGCCCTTCATTCCATCTTCTGACGGAGGGACGAGGTGAAGAGGGAGCCTCTCAGGAGCAGGTCAGTGGCAGCTCCCTTCCTCAGGATCCTGAGTGCCCTCGTGAGGCCCTGTCTTCTGAGGATAGCACTTTGTTGGAATCAAGGACTGTGCTAGAGAAGGGTGAACTAGACAATAAAAGTATTCCACAAGCTGTTGCCTCTTTGAAGCATCAAGATTATACCACCCCCACTTGCCCAGCAGGTATTCCCTGTGCTCTTTTTGCATTGGTACCAGAGTCATTGTTGCCTCTCCATATGGATCAACAGGATGCCGTAGGAAATGAACAGCCAGAGACTTCACAGCAAACGGATGAGCAACAGGATCCCAAAAGCCAGATGAAAGCTTTTAGAGACCCTTTACAGGATGACACTGGAATGTACGTTACTGAGGAAGTCACCTCCTCTGAAGATCAACGAAAGACTTATGCCTTGACATTTAAACAGGAGTTAAAAGATGTAATCCTCTGTATCTCTCCAGTTATTACATTCCGTGAACCTTTCCTTTTAACTGAAAAGGGGATGAGATGCTCAACTCGAGATTATTTTCCAGAGCAGATTTACTGGTCTCCTCTTCTCAACAAAGAGGTGAAGGAAATGGAGAGCAGGAGGAAGAAACAGCTGCTCAGGGATCTCTCTGGACTTCAGGGCATGAATGGCAGTGTTCAGGCCAAGTCTATTCAAGTCTTACCCTCACATGAGCTAGTGAGCACCAGGATTGCTGAACATCTGGGTGACAGCCAGACCTTGGGTAGAATGCTAGCTGATTATCGAGCTAGAGGAGGAAGAATTCAGTCAAAACATTTGGACCCCTTTGTCCATTCAAAAGATGCATCATGTACTTCAGGTGGCAAATCAGGAAACAAAACTGAGAGTGATGAAGAGAGGGGATTGATTCCAAGTGATGTAATATGGCCAACAAAGGTGGACTGTCTGAACCCTGCTAACCACCAGAGGCTCTGTGTGCTCTTCAGCAGCTCTTCTGCCCAGTCCAGCAATGCTCCCAGTGCTTGTGTCAGTCCTTGGATTGTAACAATGGAGTTTTATGGAAAGAATGACCTTACACTGGGGATATTTTTAGAAAGATACTGTTTCAGGTCTTCTTACCAGTGTCCGAGCATGTTCTGTGACACCCCCATGGTTCATCACATTCGACGCTTTGTTCATGGCCAAGGCTGTGTACAGATAATTCTGAAGGAGTTGGATTCTCCAGTGCCTGGATATCAACATACAATTCTCACATATTCCTGGTGCAGAATCTGCAAACAA
Peptide sequence:
MNSCIKNPKILLLKCSIEYLYREETKFTCIDPIVLQEREFLKNYVQRIVDVRPTLVLVEKTVSRIAQDMLLEHGITLVINVKSQVLERISRMTQGDLVVSMDQLLTKPHLGTCHKFYMQIFQLPNEQTKTLMFFEGCPQHLGCTIKLRGGSDYELARVKEILIFMICVAYHSQLEISFLMDEFAMPPTLMQSPSFHLLTEGRGEEGASQEQVSGSSLPQDPECPREALSSEDSTLLESRTVLEKGELDNKSIPQAVASLKHQDYTTPTCPAGIPCALFALVPESLLPLHMDQQDAVGNEQPETSQQTDEQQDPKSQMKAFRDPLQDDTGMYVTEEVTSSEDQRKTYALTFKQELKDVILCISPVITFREPFLLTEKGMRCSTRDYFPEQIYWSPLLNKEVKEMESRRKKQLLRDLSGLQGMNGSVQAKSIQVLPSHELVSTRIAEHLGDSQTLGRMLADYRARGGRIQSKHLDPFVHSKDASCTSGGKSGNKTESDEERGLIPSDVIWPTKVDCLNPANHQRLCVLFSSSSAQSSNAPSACVSPWIVTMEFYGKNDLTLGIFLERYCFRSSYQCPSMFCDTPMVHHIRRFVHGQGCVQIILKELDSPVPGYQHTILTYSWCRICKQMNSCIKNPKILLLKCSIEYLYREETKFTCIDPIVLQEREFLKNYVQRIVDVRPTLVLVEKTVSRIAQDMLLEHGITLVINVKSQVLERISRMTQGDLVVSMDQLLTKPHLGTCHKFYMQIFQLPNEQTKTLMFFEGCPQHLGCTIKLRGGSDYELARVKEILIFMICVAYHSQLEISFLMDEFAMPPTLMQSPSFHLLTEGRGEEGASQEQVSGSSLPQDPECPREALSSEDSTLLESRTVLEKGELDNKSIPQAVASLKHQDYTTPTCPAGIPCALFALVPESLLPLHMDQQDAVGNEQPETSQQTDEQQDPKSQMKAFRDPLQDDTGMYVTEEVTSSEDQRKTYALTFKQELKDVILCISPVITFREPFLLTEKGMRCSTRDYFPEQIYWSPLLNKEVKEMESRRKKQLLRDLSGLQGMNGSVQAKSIQVLPSHELVSTRIAEHLGDSQTLGRMLADYRARGGRIQSKHLDPFVHSKDASCTSGGKSGNKTESDEERGLIPSDVIWPTKVDCLNPANHQRLCVLFSSSSAQSSNAPSACVSPWIVTMEFYGKNDLTLGIFLERYCFRSSYQCPSMFCDTPMVHHIRRFVHGQGCVQIILKELDSPVPGYQHTILTYSWCRICKQ
IRESfinder result
IRESfinder score
0.699939529
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page