top of page
mmu_circPikfyve_399
Basic information of circular RNA
PanCircBase ID:
mmu_circPikfyve_399
mm39_Chr. Position ID:
chr1|65299157|65304505|+
Gene name:
Pikfyve
Transcript:
ENSMUST00000081154.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
31,32,33,34
Exon/intron offsets:
0,2881,4348,5250
Genomic length:
5348
Exon/intron sizes in nt:
121,96,84,98
Flanking exon/introns:
chr1:65298079-65299157|chr1:65304505-65304920
Splice length:
399
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_146457
Human Ortholog IDs:
Mature spliced Sequence:
ATGTATTTGATGGTCATTTGCTGGGATCCACAGACAGCCAGGTGAAGGAAAAGTCAACCATGAAAGCCATCTTTGCTAATTTGCTTCCAGGAAACAGCTACAATCCCATTCCATTTCCTTTTGATCCAGATAAACACTACTTAATGTATGAACATGAACGGGTGCCCATTGCTGTCTGTGAGAAAGAGCCCAGCTCCATCATTGCTTTTGCACTCAGTTGTAAAGAATACCGCAATGCCTTAGAGGAATTGTCCAAAGCAACTCTGCGGAACAGTGCTGAAGAAGGGCTCCCAGCCAATAGTGCTTTAGATAACAGACCTAAGAGTAGCAGCCCTATTAGACTACCTGAAATCAGTGGAGGACAGACAAACCGCACAGTAGAAGCAGAACCTCAGCCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGGAGGACAGACAAACCG
59.61
AGCTGTTTCCTGGAAGCAAA
57.93
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGACAGACAAACCGCACA
60.53
AGCTGTTTCCTGGAAGCAAA
57.93
141
PCR template sequence:
AGTGCTTTAGATAACAGACCTAAGAGTAGCAGCCCTATTAGACTACCTGAAATCAGTGGAGGACAGACAAACCGCACAGTAGAAGCAGAACCTCAGCCAAATGTATTTGATGGTCATTTGCTGGGATCCACAGACAGCCAGGTGAAGGAAAAGTCAACCATGAAAGCCATCTTTGCTAATTTGCTTCCAGGAAACAGCTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-196a-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-301a-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GAACCTCAGCCAAATGTATTTGATGG
siRNA sets
AAATACATTTGGCTGAGGT, CAAATACATTTGGCTGAGG, TCAAATACATTTGGCTGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPIKFYVE_399_ORF_1
0.9963
0.198644068
0.938705453
738
ORF sequence:
ATGAAAGCCATCTTTGCTAATTTGCTTCCAGGAAACAGCTACAATCCCATTCCATTTCCTTTTGATCCAGATAAACACTACTTAATGTATGAACATGAACGGGTGCCCATTGCTGTCTGTGAGAAAGAGCCCAGCTCCATCATTGCTTTTGCACTCAGTTGTAAAGAATACCGCAATGCCTTAGAGGAATTGTCCAAAGCAACTCTGCGGAACAGTGCTGAAGAAGGGCTCCCAGCCAATAGTGCTTTAGATAACAGACCTAAGAGTAGCAGCCCTATTAGACTACCTGAAATCAGTGGAGGACAGACAAACCGCACAGTAGAAGCAGAACCTCAGCCAAATGTATTTGATGGTCATTTGCTGGGATCCACAGACAGCCAGGTGAAGGAAAAGTCAACCATGAAAGCCATCTTTGCTAATTTGCTTCCAGGAAACAGCTACAATCCCATTCCATTTCCTTTTGATCCAGATAAACACTACTTAATGTATGAACATGAACGGGTGCCCATTGCTGTCTGTGAGAAAGAGCCCAGCTCCATCATTGCTTTTGCACTCAGTTGTAAAGAATACCGCAATGCCTTAGAGGAATTGTCCAAAGCAACTCTGCGGAACAGTGCTGAAGAAGGGCTCCCAGCCAATAGTGCTTTAGATAACAGACCTAAGAGTAGCAGCCCTATTAGACTACCTGAAATCAGTGGAGGACAGACAAACCGCACAGTAGAAGCAGAACCTCAGCCA
Peptide sequence:
MKAIFANLLPGNSYNPIPFPFDPDKHYLMYEHERVPIAVCEKEPSSIIAFALSCKEYRNALEELSKATLRNSAEEGLPANSALDNRPKSSSPIRLPEISGGQTNRTVEAEPQPNVFDGHLLGSTDSQVKEKSTMKAIFANLLPGNSYNPIPFPFDPDKHYLMYEHERVPIAVCEKEPSSIIAFALSCKEYRNALEELSKATLRNSAEEGLPANSALDNRPKSSSPIRLPEISGGQTNRTVEAEPQP
IRESfinder result
IRESfinder score
0.582838574
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page