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mmu_circArhgef28_868
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgef28_868
mm39_Chr. Position ID:
chr13|98065918|98073369|-
Gene name:
Arhgef28
Transcript:
ENSMUST00000238746.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
27,26,25,24
Exon/intron offsets:
0,1367,7264,7412
Genomic length:
7451
Exon/intron sizes in nt:
295,486,48,39
Flanking exon/introns:
chr13:98036324-98065918|chr13:98073369-98075967
Splice length:
868
Other database IDs:
circBase: mmu_circ_0004930, CIRCpedia: MMU_CIRCpedia_35691, circAtlas: mmu-Arhgef28_0001
circAtlas: hsa-ARHGEF28_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTGGAATATAGAAGTTTCTCCGGTTCTTCACAGTCAGAGATTATACAAGCAATACAGAATTTAACGCGTCTCCTCTACAGCCTTCAGGCTGCCTTGACCATCCAGGACAGTCACATTGAGATCCACAAACTGGTTCTACAGCAGCGGGAGAGCTTGGCCCCTAGCCACTCCTTCCGAGGTGGCCCCTTGCAAGACCAGGAGAAATCCCGCTACCTGGAAAAGCAGCGTGAAGAGCTGGCCAACATCCACAAGCTTCAACACCAGTTCCAGCAGGAGCAGCGGCGCTGGCACCGCACGTGCGACCAGCAACAGCGCGAGCAGGAAGCCCAAGAGAGCTGGCTGCAGGCGCGGGAACGTGAGTGCCAGTCCCAGGAGGAATTGTTGCTGCGCCACCGTAGCGAGCTGGACCACCAACTCCAGGAGTACCAGCAGAGCCTTGAGCGGCTACGGGAGGGCCAGCGGATGGTGGAGAGGGAGAGACAGAAGATGCGTGTCCAGCAGGGTCTGCTGGGCCACTGCAAGCATAGTCGCCAGCGGAGCCTCCCAGCCGTCTTCTCTCCAGGGAGCAAGGAGGTAACAGAACTTAACCGAGCTGAGAGTTTGTGTCATGAAAATTCATTTTTCATCAATGAAGCTTTTGGACACATGTCACTTAACACGTCCAATAAACCAAACCCATCAGGGGTCCCCTGGGATGCTCACCCCCTGGAGGGGTCTCATTTTGATTTGGCAAGGACTAGTGAGAGTCCAACAGAACTGAAGATAGACATTTCTCAGCCTCCTGATGTCAACTCTGAACTCTGGACAACGGGGCCGGGCCATCAGAGACCTGCTCTCCAAGAAAACAGCAAGGAGTCTTATAAAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAACTCTGGACAACGGGG
60.32
GAAGGCTGTAGAGGAGACGC
59.9
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGAACTCTGGACAACGGG
59.32
GAAGGCTGTAGAGGAGACGC
59.9
161
PCR template sequence:
ATTTCTCAGCCTCCTGATGTCAACTCTGAACTCTGGACAACGGGGCCGGGCCATCAGAGACCTGCTCTCCAAGAAAACAGCAAGGAGTCTTATAAAAATGGTGGAATATAGAAGTTTCTCCGGTTCTTCACAGTCAGAGATTATACAAGCAATACAGAATTTAACGCGTCTCCTCTACAGCCTTCAGGCTGCCTTGACCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-370-3p(3), mmu-miR-137-3p(1), mmu-miR-328-3p(1), mmu-miR-324-5p(1), mmu-miR-185-5p(1), mmu-miR-431-5p(1), mmu-miR-425-5p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTTATAAAAATGGTGGAATATAGAA
siRNA sets
TTCCACCATTTTTATAAGA, ATTCCACCATTTTTATAAG, ATATTCCACCATTTTTATA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGEF28_868_ORF_1
1.0949
0.29721721
0.992079588
951
ORF sequence:
ATGTCAACTCTGAACTCTGGACAACGGGGCCGGGCCATCAGAGACCTGCTCTCCAAGAAAACAGCAAGGAGTCTTATAAAAATGGTGGAATATAGAAGTTTCTCCGGTTCTTCACAGTCAGAGATTATACAAGCAATACAGAATTTAACGCGTCTCCTCTACAGCCTTCAGGCTGCCTTGACCATCCAGGACAGTCACATTGAGATCCACAAACTGGTTCTACAGCAGCGGGAGAGCTTGGCCCCTAGCCACTCCTTCCGAGGTGGCCCCTTGCAAGACCAGGAGAAATCCCGCTACCTGGAAAAGCAGCGTGAAGAGCTGGCCAACATCCACAAGCTTCAACACCAGTTCCAGCAGGAGCAGCGGCGCTGGCACCGCACGTGCGACCAGCAACAGCGCGAGCAGGAAGCCCAAGAGAGCTGGCTGCAGGCGCGGGAACGTGAGTGCCAGTCCCAGGAGGAATTGTTGCTGCGCCACCGTAGCGAGCTGGACCACCAACTCCAGGAGTACCAGCAGAGCCTTGAGCGGCTACGGGAGGGCCAGCGGATGGTGGAGAGGGAGAGACAGAAGATGCGTGTCCAGCAGGGTCTGCTGGGCCACTGCAAGCATAGTCGCCAGCGGAGCCTCCCAGCCGTCTTCTCTCCAGGGAGCAAGGAGGTAACAGAACTTAACCGAGCTGAGAGTTTGTGTCATGAAAATTCATTTTTCATCAATGAAGCTTTTGGACACATGTCACTTAACACGTCCAATAAACCAAACCCATCAGGGGTCCCCTGGGATGCTCACCCCCTGGAGGGGTCTCATTTTGATTTGGCAAGGACTAGTGAGAGTCCAACAGAACTGAAGATAGACATTTCTCAGCCTCCTGATGTCAACTCTGAACTCTGGACAACGGGGCCGGGCCATCAGAGACCTGCTCTCCAAGAAAACAGCAAGGAGTCTTATAAAAAT
Peptide sequence:
MSTLNSGQRGRAIRDLLSKKTARSLIKMVEYRSFSGSSQSEIIQAIQNLTRLLYSLQAALTIQDSHIEIHKLVLQQRESLAPSHSFRGGPLQDQEKSRYLEKQREELANIHKLQHQFQQEQRRWHRTCDQQQREQEAQESWLQARERECQSQEELLLRHRSELDHQLQEYQQSLERLREGQRMVERERQKMRVQQGLLGHCKHSRQRSLPAVFSPGSKEVTELNRAESLCHENSFFINEAFGHMSLNTSNKPNPSGVPWDAHPLEGSHFDLARTSESPTELKIDISQPPDVNSELWTTGPGHQRPALQENSKESYKN
IRESfinder result
IRESfinder score
0.468927623
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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