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mmu_circStk4_577
Basic information of circular RNA
PanCircBase ID:
mmu_circStk4_577
mm39_Chr. Position ID:
chr2|163925549|163938826|+
Gene name:
Stk4
Transcript:
ENSMUST00000018353.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
3,4,5,6
Exon/intron offsets:
0,2865,5211,13109
Genomic length:
13277
Exon/intron sizes in nt:
1,29,11,51,65,168
Flanking exon/introns:
chr2:163921513-163925549|chr2:163938826-163940358
Splice length:
577
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11431, circAtlas: mmu-Stk4_0005
circBase: hsa_circ_0060523, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_133603
Human Ortholog IDs:
Mature spliced Sequence:
GTCTTATGGCAGCGTGTACAAGGCTATTCATAAAGAGACTGGCCAGATTGTTGCAATCAAGCAAGTGCCCGTGGAATCGGACCTGCAGGAGATAATCAAGGAAATCTCCATCATGCAGCAGTGTGACAGCCCTCACGTAGTCAAGTATTATGGCAGCTACTTTAAGAACACAGACCTGTGGATTGTTATGGAGTACTGTGGGGCTGGTTCTGTATCTGATATCATTCGGCTACGGAACAAGACGTTAACAGAAGATGAAATAGCTACAATATTACAATCAACTCTTAAGGGACTAGAATACCTTCATTTTATGAGAAAAATACACCGAGATATCAAGGCGGGAAATATTTTGCTAAACACAGAAGGCCATGCAAAGCTTGCAGACTTTGGAGTCGCAGGTCAACTTACAGATACCATGGCAAAGAGGAATACAGTAATAGGGACCCCGTTTTGGATGGCTCCTGAAGTTATTCAGGAAATTGGGTACAACTGTGTGGCAGACATCTGGTCTCTGGGAATAACTGCCATAGAAATGGCTGAAGGAAAGCCCCCATATGCTGATATCCATCCAATGAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGGTACAACTGTGTGGCA
59.74
TGCAACAATCTGGCCAGTCT
59.89
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGGTACAACTGTGTGGCA
59.74
CACGGGCACTTGCTTGATTG
60.39
171
PCR template sequence:
AATTGGGTACAACTGTGTGGCAGACATCTGGTCTCTGGGAATAACTGCCATAGAAATGGCTGAAGGAAAGCCCCCATATGCTGATATCCATCCAATGAGGGTCTTATGGCAGCGTGTACAAGGCTATTCATAAAGAGACTGGCCAGATTGTTGCAATCAAGCAAGTGCCCGTGGAATCGGACCTGCAGGAGATAATCAAG
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
CCATCCAATGAGGGTCTTATGGCAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTK4_577_ORF_1
0.8456
0.076474228
0.552015937
498
ORF sequence:
ATGCAGCAGTGTGACAGCCCTCACGTAGTCAAGTATTATGGCAGCTACTTTAAGAACACAGACCTGTGGATTGTTATGGAGTACTGTGGGGCTGGTTCTGTATCTGATATCATTCGGCTACGGAACAAGACGTTAACAGAAGATGAAATAGCTACAATATTACAATCAACTCTTAAGGGACTAGAATACCTTCATTTTATGAGAAAAATACACCGAGATATCAAGGCGGGAAATATTTTGCTAAACACAGAAGGCCATGCAAAGCTTGCAGACTTTGGAGTCGCAGGTCAACTTACAGATACCATGGCAAAGAGGAATACAGTAATAGGGACCCCGTTTTGGATGGCTCCTGAAGTTATTCAGGAAATTGGGTACAACTGTGTGGCAGACATCTGGTCTCTGGGAATAACTGCCATAGAAATGGCTGAAGGAAAGCCCCCATATGCTGATATCCATCCAATGAGGGTCTTATGGCAGCGTGTACAAGGCTATTCATAA
Peptide sequence:
MQQCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLTEDEIATILQSTLKGLEYLHFMRKIHRDIKAGNILLNTEGHAKLADFGVAGQLTDTMAKRNTVIGTPFWMAPEVIQEIGYNCVADIWSLGITAIEMAEGKPPYADIHPMRVLWQRVQGYS
IRESfinder result
IRESfinder score
0.461609249
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
RPF, cORF, m6A
mmu_circStk4_001
Evidence
Peptide sequence:
MQQCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLTEDEIATILQSTLKGLEYLHFMRKIHRDIKAGNILLNTEGHAKLADFGVAGQLTDTMAKRNTVIGTPFWMAPEVIQEIGYNCVADIWSLGITAIEMAEGKPPYADIHPMRVLWQRVQGYS*
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