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mmu_circStk4_409
Basic information of circular RNA
PanCircBase ID:
mmu_circStk4_409
mm39_Chr. Position ID:
chr2|163925549|163930925|+
Gene name:
Stk4
Transcript:
ENSMUST00000018353.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,2865,5211
Genomic length:
5376
Exon/intron sizes in nt:
12,91,15,165
Flanking exon/introns:
chr2:163921513-163925549|chr2:163930925-163938658
Splice length:
409
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11430, circAtlas: mmu-Stk4_0011
circBase: hsa_circ_0060522, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_34336
Human Ortholog IDs:
Mature spliced Sequence:
GTCTTATGGCAGCGTGTACAAGGCTATTCATAAAGAGACTGGCCAGATTGTTGCAATCAAGCAAGTGCCCGTGGAATCGGACCTGCAGGAGATAATCAAGGAAATCTCCATCATGCAGCAGTGTGACAGCCCTCACGTAGTCAAGTATTATGGCAGCTACTTTAAGAACACAGACCTGTGGATTGTTATGGAGTACTGTGGGGCTGGTTCTGTATCTGATATCATTCGGCTACGGAACAAGACGTTAACAGAAGATGAAATAGCTACAATATTACAATCAACTCTTAAGGGACTAGAATACCTTCATTTTATGAGAAAAATACACCGAGATATCAAGGCGGGAAATATTTTGCTAAACACAGAAGGCCATGCAAAGCTTGCAGACTTTGGAGTCGCAGGTCAACTTACA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACCGAGATATCAAGGCGGG
60.32
TGCAACAATCTGGCCAGTCT
59.89
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACCGAGATATCAAGGCGG
59.61
TGCAACAATCTGGCCAGTCT
59.89
143
PCR template sequence:
TATGAGAAAAATACACCGAGATATCAAGGCGGGAAATATTTTGCTAAACACAGAAGGCCATGCAAAGCTTGCAGACTTTGGAGTCGCAGGTCAACTTACAGTCTTATGGCAGCGTGTACAAGGCTATTCATAAAGAGACTGGCCAGATTGTTGCAATCAAGCAAGTGCCCGTGGAATCGGACCTGCAGGAGATAATCAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-101a-3p(1), mmu-miR-369-3p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGGTCAACTTACAGTCTTATGGCAGC
siRNA sets
ATAAGACTGTAAGTTGACC, CATAAGACTGTAAGTTGAC, TAAGACTGTAAGTTGACCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTK4_409_ORF_1
1.1367
0.212077655
0.724335518
450
ORF sequence:
ATGCAAAGCTTGCAGACTTTGGAGTCGCAGGTCAACTTACAGTCTTATGGCAGCGTGTACAAGGCTATTCATAAAGAGACTGGCCAGATTGTTGCAATCAAGCAAGTGCCCGTGGAATCGGACCTGCAGGAGATAATCAAGGAAATCTCCATCATGCAGCAGTGTGACAGCCCTCACGTAGTCAAGTATTATGGCAGCTACTTTAAGAACACAGACCTGTGGATTGTTATGGAGTACTGTGGGGCTGGTTCTGTATCTGATATCATTCGGCTACGGAACAAGACGTTAACAGAAGATGAAATAGCTACAATATTACAATCAACTCTTAAGGGACTAGAATACCTTCATTTTATGAGAAAAATACACCGAGATATCAAGGCGGGAAATATTTTGCTAAACACAGAAGGCCATGCAAAGCTTGCAGACTTTGGAGTCGCAGGTCAACTTACA
Peptide sequence:
MQSLQTLESQVNLQSYGSVYKAIHKETGQIVAIKQVPVESDLQEIIKEISIMQQCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLTEDEIATILQSTLKGLEYLHFMRKIHRDIKAGNILLNTEGHAKLADFGVAGQLT
IRESfinder result
IRESfinder score
0.524104196
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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