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mmu_circArhgef28_1035
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgef28_1035
mm39_Chr. Position ID:
chr13|98165884|98282103|-
Gene name:
Arhgef28
Transcript:
ENSMUST00000109426.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
9,8,7,6,5,4,3,2
Exon/intron offsets:
0,499,14423,21569,24414,45622,47796,116175
Genomic length:
116219
Exon/intron sizes in nt:
61,56,67,181,184,294,148,44
Flanking exon/introns:
chr13:98133441-98165884|chr13:98282103-98342580
Splice length:
1035
Other database IDs:
circAtlas: mmu-Arhgef28_0018
circAtlas: hsa-ARHGEF28_0033, CIRCpedia: HSA_CIRCpedia_158606
Human Ortholog IDs:
Mature spliced Sequence:
ATGCAGGAGCCATGGAGTTGAGCTGCAGTGAAGTGCCTCTTTATGGACAGAAGACGGTCTATGCAAAGTTTGGCAAAAACGTGTATCTACCCGAAGATGCGGAGTTTTACTTTGTTTATGGCGGGTCGCATCAGAGGCACGTGGTGATTGCTGACCGTGTCCAGGACAATGTCCTCCAATCTAGCATTCCAGGCCACTGGCTTCAGGAGACGGTGACGGTATCTGTGTGCCTCTGCTCGGAAGGGTACTCCCCAGTGACCATGGGCTCTGGCTCAGTGACCTACGTGGACAACATGGCCTGCAGGCTGGCTCGTCTGCTGGTCACTCAGGCTGACCGACTCACGGCCTGCAGTCACCAGACGCTGCTGACCCCGTTTGCCCTGACAGTGGAAGCGCTGCCTGCCTTGGATGAGGAGCTCGTGCTGGCTCTGACCCAACTGGAGCTGCCTTTGGGTTGGACAGTCCTGGGAAATTCCTCACTTGAAGTATCTCTACACAGAGAGTCTCTCCTGCATCTGGCTGTGAGATGGGCCCTCCCTAAGCTATTCCACTTCCTCTTGTGTCTCCCTGGAGGAGTCAAGGCCTTGAAGCTACCTAATGAAGAGGCCACCACACCATTAGACTTAGCTTTGCAAGGTGGACACTCCACACTGGTAGAAGACATCACAAATTTTCAGGGTAGCCATTCCCCAGGCTTCTCCCGACTGCGTCTTAACGAAGAGGCCACTCTGCAGTTTGTTCATTCATCGGAAACATTGACCCTGACCGTTAACCACACAGCTGAGCATCTCTTGGAAGCAGACATCAAACTCTTCCGGAAATATTTCTGGGACAGAGCCTTTCTTGTCAAGGCTCTTGAGCAAGAAGCCAAGACTGAGAAAGCAACCATGCCTTCTGGAGCTGCAGAAACTGAAGAAGAGGTTAGGAATTTGGAGTCTGGCAGATCACCATCGGAGGAGGAGGAGGATGCAAAGAGCATCAAAAGCCAGGTGGATGGGCCGAGTGAACACGAAGACCAGGACCGCCTACCTCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGCAGATCACCATCGGAG
60.25
AAGAGGCACTTCACTGCAGC
60.89
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGATCACCATCGGAGGAG
59.97
GCATAGACCGTCTTCTGTCCA
59.52
160
PCR template sequence:
TCTGGCAGATCACCATCGGAGGAGGAGGAGGATGCAAAGAGCATCAAAAGCCAGGTGGATGGGCCGAGTGAACACGAAGACCAGGACCGCCTACCTCTGGATGCAGGAGCCATGGAGTTGAGCTGCAGTGAAGTGCCTCTTTATGGACAGAAGACGGTCTATGCAAAGTTTGGCAAAAACGTGTATCTACCCGAAGATGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-miR-199a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-335-5p(1), mmu-miR-298-5p(1), mmu-miR-196a-5p(1), mmu-miR-495-3p(1), mmu-let-7d-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGCCTACCTCTGGATGCAGGAGCCAT
siRNA sets
ATGGCTCCTGCATCCAGAG,TGGCTCCTGCATCCAGAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGEF28_1035_ORF_1
0.9947
0.26294124
0.999996215
2058
ORF sequence:
ATGGAGTTGAGCTGCAGTGAAGTGCCTCTTTATGGACAGAAGACGGTCTATGCAAAGTTTGGCAAAAACGTGTATCTACCCGAAGATGCGGAGTTTTACTTTGTTTATGGCGGGTCGCATCAGAGGCACGTGGTGATTGCTGACCGTGTCCAGGACAATGTCCTCCAATCTAGCATTCCAGGCCACTGGCTTCAGGAGACGGTGACGGTATCTGTGTGCCTCTGCTCGGAAGGGTACTCCCCAGTGACCATGGGCTCTGGCTCAGTGACCTACGTGGACAACATGGCCTGCAGGCTGGCTCGTCTGCTGGTCACTCAGGCTGACCGACTCACGGCCTGCAGTCACCAGACGCTGCTGACCCCGTTTGCCCTGACAGTGGAAGCGCTGCCTGCCTTGGATGAGGAGCTCGTGCTGGCTCTGACCCAACTGGAGCTGCCTTTGGGTTGGACAGTCCTGGGAAATTCCTCACTTGAAGTATCTCTACACAGAGAGTCTCTCCTGCATCTGGCTGTGAGATGGGCCCTCCCTAAGCTATTCCACTTCCTCTTGTGTCTCCCTGGAGGAGTCAAGGCCTTGAAGCTACCTAATGAAGAGGCCACCACACCATTAGACTTAGCTTTGCAAGGTGGACACTCCACACTGGTAGAAGACATCACAAATTTTCAGGGTAGCCATTCCCCAGGCTTCTCCCGACTGCGTCTTAACGAAGAGGCCACTCTGCAGTTTGTTCATTCATCGGAAACATTGACCCTGACCGTTAACCACACAGCTGAGCATCTCTTGGAAGCAGACATCAAACTCTTCCGGAAATATTTCTGGGACAGAGCCTTTCTTGTCAAGGCTCTTGAGCAAGAAGCCAAGACTGAGAAAGCAACCATGCCTTCTGGAGCTGCAGAAACTGAAGAAGAGGTTAGGAATTTGGAGTCTGGCAGATCACCATCGGAGGAGGAGGAGGATGCAAAGAGCATCAAAAGCCAGGTGGATGGGCCGAGTGAACACGAAGACCAGGACCGCCTACCTCTGGATGCAGGAGCCATGGAGTTGAGCTGCAGTGAAGTGCCTCTTTATGGACAGAAGACGGTCTATGCAAAGTTTGGCAAAAACGTGTATCTACCCGAAGATGCGGAGTTTTACTTTGTTTATGGCGGGTCGCATCAGAGGCACGTGGTGATTGCTGACCGTGTCCAGGACAATGTCCTCCAATCTAGCATTCCAGGCCACTGGCTTCAGGAGACGGTGACGGTATCTGTGTGCCTCTGCTCGGAAGGGTACTCCCCAGTGACCATGGGCTCTGGCTCAGTGACCTACGTGGACAACATGGCCTGCAGGCTGGCTCGTCTGCTGGTCACTCAGGCTGACCGACTCACGGCCTGCAGTCACCAGACGCTGCTGACCCCGTTTGCCCTGACAGTGGAAGCGCTGCCTGCCTTGGATGAGGAGCTCGTGCTGGCTCTGACCCAACTGGAGCTGCCTTTGGGTTGGACAGTCCTGGGAAATTCCTCACTTGAAGTATCTCTACACAGAGAGTCTCTCCTGCATCTGGCTGTGAGATGGGCCCTCCCTAAGCTATTCCACTTCCTCTTGTGTCTCCCTGGAGGAGTCAAGGCCTTGAAGCTACCTAATGAAGAGGCCACCACACCATTAGACTTAGCTTTGCAAGGTGGACACTCCACACTGGTAGAAGACATCACAAATTTTCAGGGTAGCCATTCCCCAGGCTTCTCCCGACTGCGTCTTAACGAAGAGGCCACTCTGCAGTTTGTTCATTCATCGGAAACATTGACCCTGACCGTTAACCACACAGCTGAGCATCTCTTGGAAGCAGACATCAAACTCTTCCGGAAATATTTCTGGGACAGAGCCTTTCTTGTCAAGGCTCTTGAGCAAGAAGCCAAGACTGAGAAAGCAACCATGCCTTCTGGAGCTGCAGAAACTGAAGAAGAGGTTAGGAATTTGGAGTCTGGCAGATCACCATCGGAGGAGGAGGAGGATGCAAAGAGCATCAAAAGCCAGGTGGATGGGCCGAGTGAACACGAAGACCAGGACCGCCTACCTCTG
Peptide sequence:
MELSCSEVPLYGQKTVYAKFGKNVYLPEDAEFYFVYGGSHQRHVVIADRVQDNVLQSSIPGHWLQETVTVSVCLCSEGYSPVTMGSGSVTYVDNMACRLARLLVTQADRLTACSHQTLLTPFALTVEALPALDEELVLALTQLELPLGWTVLGNSSLEVSLHRESLLHLAVRWALPKLFHFLLCLPGGVKALKLPNEEATTPLDLALQGGHSTLVEDITNFQGSHSPGFSRLRLNEEATLQFVHSSETLTLTVNHTAEHLLEADIKLFRKYFWDRAFLVKALEQEAKTEKATMPSGAAETEEEVRNLESGRSPSEEEEDAKSIKSQVDGPSEHEDQDRLPLDAGAMELSCSEVPLYGQKTVYAKFGKNVYLPEDAEFYFVYGGSHQRHVVIADRVQDNVLQSSIPGHWLQETVTVSVCLCSEGYSPVTMGSGSVTYVDNMACRLARLLVTQADRLTACSHQTLLTPFALTVEALPALDEELVLALTQLELPLGWTVLGNSSLEVSLHRESLLHLAVRWALPKLFHFLLCLPGGVKALKLPNEEATTPLDLALQGGHSTLVEDITNFQGSHSPGFSRLRLNEEATLQFVHSSETLTLTVNHTAEHLLEADIKLFRKYFWDRAFLVKALEQEAKTEKATMPSGAAETEEEVRNLESGRSPSEEEEDAKSIKSQVDGPSEHEDQDRLPL
IRESfinder result
IRESfinder score
0.481874898
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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