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mmu_circArhgef28_781
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgef28_781
mm39_Chr. Position ID:
chr13|98065918|98067771|-
Gene name:
Arhgef28
Transcript:
ENSMUST00000238746.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
27,26
Exon/intron offsets:
0,1367
Genomic length:
1853
Exon/intron sizes in nt:
295,486
Flanking exon/introns:
chr13:98036324-98065918|chr13:98067771-98073182
Splice length:
781
Other database IDs:
circBase: mmu_circ_0004929, CIRCpedia: MMU_CIRCpedia_35690, circAtlas: mmu-Arhgef28_0007
Human Ortholog IDs:
Mature spliced Sequence:
GCTGCCTTGACCATCCAGGACAGTCACATTGAGATCCACAAACTGGTTCTACAGCAGCGGGAGAGCTTGGCCCCTAGCCACTCCTTCCGAGGTGGCCCCTTGCAAGACCAGGAGAAATCCCGCTACCTGGAAAAGCAGCGTGAAGAGCTGGCCAACATCCACAAGCTTCAACACCAGTTCCAGCAGGAGCAGCGGCGCTGGCACCGCACGTGCGACCAGCAACAGCGCGAGCAGGAAGCCCAAGAGAGCTGGCTGCAGGCGCGGGAACGTGAGTGCCAGTCCCAGGAGGAATTGTTGCTGCGCCACCGTAGCGAGCTGGACCACCAACTCCAGGAGTACCAGCAGAGCCTTGAGCGGCTACGGGAGGGCCAGCGGATGGTGGAGAGGGAGAGACAGAAGATGCGTGTCCAGCAGGGTCTGCTGGGCCACTGCAAGCATAGTCGCCAGCGGAGCCTCCCAGCCGTCTTCTCTCCAGGGAGCAAGGAGGTAACAGAACTTAACCGAGCTGAGAGTTTGTGTCATGAAAATTCATTTTTCATCAATGAAGCTTTTGGACACATGTCACTTAACACGTCCAATAAACCAAACCCATCAGGGGTCCCCTGGGATGCTCACCCCCTGGAGGGGTCTCATTTTGATTTGGCAAGGACTAGTGAGAGTCCAACAGAACTGAAGATAGACATTTCTCAGCCTCCTGATGTCAACTCTGAACTCTGGACAACGGGGCCGGGCCATCAGAGACCTGCTCTCCAAGAAAACAGCAAGGAGTCTTATAAAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAACTCTGGACAACGGGG
60.32
CTCTCCCGCTGCTGTAGAAC
60.18
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGAACTCTGGACAACGGG
59.32
CTCTCCCGCTGCTGTAGAAC
60.18
141
PCR template sequence:
ATTTCTCAGCCTCCTGATGTCAACTCTGAACTCTGGACAACGGGGCCGGGCCATCAGAGACCTGCTCTCCAAGAAAACAGCAAGGAGTCTTATAAAAATGGCTGCCTTGACCATCCAGGACAGTCACATTGAGATCCACAAACTGGTTCTACAGCAGCGGGAGAGCTTGGCCCCTAGCCACTCCTTCCGAGGTGGCCCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-370-3p(3), 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
TCTTATAAAAATGGCTGCCTTGACCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGEF28_781_ORF_1
1.0619
0.333927493
0.986551182
864
ORF sequence:
ATGTCAACTCTGAACTCTGGACAACGGGGCCGGGCCATCAGAGACCTGCTCTCCAAGAAAACAGCAAGGAGTCTTATAAAAATGGCTGCCTTGACCATCCAGGACAGTCACATTGAGATCCACAAACTGGTTCTACAGCAGCGGGAGAGCTTGGCCCCTAGCCACTCCTTCCGAGGTGGCCCCTTGCAAGACCAGGAGAAATCCCGCTACCTGGAAAAGCAGCGTGAAGAGCTGGCCAACATCCACAAGCTTCAACACCAGTTCCAGCAGGAGCAGCGGCGCTGGCACCGCACGTGCGACCAGCAACAGCGCGAGCAGGAAGCCCAAGAGAGCTGGCTGCAGGCGCGGGAACGTGAGTGCCAGTCCCAGGAGGAATTGTTGCTGCGCCACCGTAGCGAGCTGGACCACCAACTCCAGGAGTACCAGCAGAGCCTTGAGCGGCTACGGGAGGGCCAGCGGATGGTGGAGAGGGAGAGACAGAAGATGCGTGTCCAGCAGGGTCTGCTGGGCCACTGCAAGCATAGTCGCCAGCGGAGCCTCCCAGCCGTCTTCTCTCCAGGGAGCAAGGAGGTAACAGAACTTAACCGAGCTGAGAGTTTGTGTCATGAAAATTCATTTTTCATCAATGAAGCTTTTGGACACATGTCACTTAACACGTCCAATAAACCAAACCCATCAGGGGTCCCCTGGGATGCTCACCCCCTGGAGGGGTCTCATTTTGATTTGGCAAGGACTAGTGAGAGTCCAACAGAACTGAAGATAGACATTTCTCAGCCTCCTGATGTCAACTCTGAACTCTGGACAACGGGGCCGGGCCATCAGAGACCTGCTCTCCAAGAAAACAGCAAGGAGTCTTATAAAAAT
Peptide sequence:
MSTLNSGQRGRAIRDLLSKKTARSLIKMAALTIQDSHIEIHKLVLQQRESLAPSHSFRGGPLQDQEKSRYLEKQREELANIHKLQHQFQQEQRRWHRTCDQQQREQEAQESWLQARERECQSQEELLLRHRSELDHQLQEYQQSLERLREGQRMVERERQKMRVQQGLLGHCKHSRQRSLPAVFSPGSKEVTELNRAESLCHENSFFINEAFGHMSLNTSNKPNPSGVPWDAHPLEGSHFDLARTSESPTELKIDISQPPDVNSELWTTGPGHQRPALQENSKESYKN
IRESfinder result
IRESfinder score
0.448580295
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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