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mmu_circPikfyve_646
Basic information of circular RNA
PanCircBase ID:
mmu_circPikfyve_646
mm39_Chr. Position ID:
chr1|65258912|65270012|+
Gene name:
Pikfyve
Transcript:
ENSMUST00000190058.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,9,10,11,12
Exon/intron offsets:
0,2516,3751,4408,11040
Genomic length:
11100
Exon/intron sizes in nt:
158,112,148,168,60
Flanking exon/introns:
chr1:65255231-65258912|chr1:65270012-65272888
Splice length:
646
Other database IDs:
circAtlas: mmu-Pikfyve_0041
Human Ortholog IDs:
Mature spliced Sequence:
GACAGTGCTCAGTTAAAGGATCTGTGGAAGAAAATCTGCCATCACACCAGTGGGATGGAATTTCAAGATCACCGTTACTGGTTGAGAACACATCCCAACTGCATTGTAGGGAAGGAATTAGTCAACTGGCTAATCAGAAATGGACACATCGCTACAAGGGCACAAGCTATAGCAATTGGACAAGCAATGGTTGATGGACGTTGGTTGGATTGTGTTAGTCATCATGATCAGCTTTTCAGGGACGAATATGCGTTGTATAGACCACTTCAGAGTACAGAATTTTCTGAGACACCTTCTCCAGACAGTGACTCTGTGAACTCTGTGGAAGGACACTCCGAGCCATCCTGGTTTAAAGACATAAAATTTGATGACAGTGACACAGAACAGATTGCTGAAGAAGGTGACGATAATTTGGCTAATTCTGCCAGTCCTAGCAAGCGCACCTCAGTCAGCAGTTTCCAGTCCACAGTGGACAGTGACTCAGCCGCTTCTATCAGCCTGAACGTGGAGCTGGACAACGTGAACTTCCATATCAAGAAGCCCTCCAAGTACCCACATGTGCCCCCTCACCCTGCTGACCAGAAAGAGTATTTGGTTTCTGACACTGGAGGACAGCAGCTCTCAATAAGTGATGCCTTCATCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCACCCTGCTGACCAGAAA
59.6
TCCATCCCACTGGTGTGATG
59.38
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCACCCTGCTGACCAGAAAG
59.6
TTCCATCCCACTGGTGTGATG
60
140
PCR template sequence:
AAGTACCCACATGTGCCCCCTCACCCTGCTGACCAGAAAGAGTATTTGGTTTCTGACACTGGAGGACAGCAGCTCTCAATAAGTGATGCCTTCATCAAAGGACAGTGCTCAGTTAAAGGATCTGTGGAAGAAAATCTGCCATCACACCAGTGGGATGGAATTTCAAGATCACCGTTACTGGTTGAGAACACATCCCAACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-320-3p(1), mmu-miR-433-5p(1), mmu-miR-325-3p(1), mmu-miR-1198-5p(1), mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCTTCATCAAAGGACAGTGCTCAGT
siRNA sets
ACTGAGCACTGTCCTTTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPIKFYVE_646_ORF_1
0.7795
0.129334877
0.91506362
786
ORF sequence:
ATGGAATTTCAAGATCACCGTTACTGGTTGAGAACACATCCCAACTGCATTGTAGGGAAGGAATTAGTCAACTGGCTAATCAGAAATGGACACATCGCTACAAGGGCACAAGCTATAGCAATTGGACAAGCAATGGTTGATGGACGTTGGTTGGATTGTGTTAGTCATCATGATCAGCTTTTCAGGGACGAATATGCGTTGTATAGACCACTTCAGAGTACAGAATTTTCTGAGACACCTTCTCCAGACAGTGACTCTGTGAACTCTGTGGAAGGACACTCCGAGCCATCCTGGTTTAAAGACATAAAATTTGATGACAGTGACACAGAACAGATTGCTGAAGAAGGTGACGATAATTTGGCTAATTCTGCCAGTCCTAGCAAGCGCACCTCAGTCAGCAGTTTCCAGTCCACAGTGGACAGTGACTCAGCCGCTTCTATCAGCCTGAACGTGGAGCTGGACAACGTGAACTTCCATATCAAGAAGCCCTCCAAGTACCCACATGTGCCCCCTCACCCTGCTGACCAGAAAGAGTATTTGGTTTCTGACACTGGAGGACAGCAGCTCTCAATAAGTGATGCCTTCATCAAAGGACAGTGCTCAGTTAAAGGATCTGTGGAAGAAAATCTGCCATCACACCAGTGGGATGGAATTTCAAGATCACCGTTACTGGTTGAGAACACATCCCAACTGCATTGTAGGGAAGGAATTAGTCAACTGGCTAATCAGAAATGGACACATCGCTACAAGGGCACAAGCTATAGCAATTGGACAAGCAATGGTTGA
Peptide sequence:
MEFQDHRYWLRTHPNCIVGKELVNWLIRNGHIATRAQAIAIGQAMVDGRWLDCVSHHDQLFRDEYALYRPLQSTEFSETPSPDSDSVNSVEGHSEPSWFKDIKFDDSDTEQIAEEGDDNLANSASPSKRTSVSSFQSTVDSDSAASISLNVELDNVNFHIKKPSKYPHVPPHPADQKEYLVSDTGGQQLSISDAFIKGQCSVKGSVEENLPSHQWDGISRSPLLVENTSQLHCREGISQLANQKWTHRYKGTSYSNWTSNG
IRESfinder result
IRESfinder score
0.610128702
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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