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mmu_circArhgef28_549
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgef28_549
mm39_Chr. Position ID:
chr13|98165884|98190482|-
Gene name:
Arhgef28
Transcript:
ENSMUST00000109426.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,8,7,6,5
Exon/intron offsets:
0,499,14423,21569,24414
Genomic length:
24598
Exon/intron sizes in nt:
61,56,67,181,184
Flanking exon/introns:
chr13:98133441-98165884|chr13:98190482-98211506
Splice length:
549
Other database IDs:
circBase: mmu_circ_0004931, CIRCpedia: MMU_CIRCpedia_35713, circAtlas: mmu-Arhgef28_0006
circBase: hsa_circ_0006874, circAtlas: hsa-ARHGEF28_0024, CIRCpedia: HSA_CIRCpedia_52531
Human Ortholog IDs:
Mature spliced Sequence:
TATCTCTACACAGAGAGTCTCTCCTGCATCTGGCTGTGAGATGGGCCCTCCCTAAGCTATTCCACTTCCTCTTGTGTCTCCCTGGAGGAGTCAAGGCCTTGAAGCTACCTAATGAAGAGGCCACCACACCATTAGACTTAGCTTTGCAAGGTGGACACTCCACACTGGTAGAAGACATCACAAATTTTCAGGGTAGCCATTCCCCAGGCTTCTCCCGACTGCGTCTTAACGAAGAGGCCACTCTGCAGTTTGTTCATTCATCGGAAACATTGACCCTGACCGTTAACCACACAGCTGAGCATCTCTTGGAAGCAGACATCAAACTCTTCCGGAAATATTTCTGGGACAGAGCCTTTCTTGTCAAGGCTCTTGAGCAAGAAGCCAAGACTGAGAAAGCAACCATGCCTTCTGGAGCTGCAGAAACTGAAGAAGAGGTTAGGAATTTGGAGTCTGGCAGATCACCATCGGAGGAGGAGGAGGATGCAAAGAGCATCAAAAGCCAGGTGGATGGGCCGAGTGAACACGAAGACCAGGACCGCCTACCTCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGATCACCATCGGAGGAG
59.97
CCATCTCACAGCCAGATGCA
60.11
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGCAGATCACCATCGGAG
60.25
CCATCTCACAGCCAGATGCA
60.11
143
PCR template sequence:
TCTGGCAGATCACCATCGGAGGAGGAGGAGGATGCAAAGAGCATCAAAAGCCAGGTGGATGGGCCGAGTGAACACGAAGACCAGGACCGCCTACCTCTGGTATCTCTACACAGAGAGTCTCTCCTGCATCTGGCTGTGAGATGGGCCCTCCCTAAGCTATTCCACTTCCTCTTGTGTCTCCCTGGAGGAGTCAAGGCCTT
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
CGCCTACCTCTGGTATCTCTACACAG
siRNA sets
TGTGTAGAGATACCAGAGG, TAGAGATACCAGAGGTAGG, GTAGAGATACCAGAGGTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGEF28_549_ORF_1
1.0228
0.243116938
0.934000281
696
ORF sequence:
ATGCCTTCTGGAGCTGCAGAAACTGAAGAAGAGGTTAGGAATTTGGAGTCTGGCAGATCACCATCGGAGGAGGAGGAGGATGCAAAGAGCATCAAAAGCCAGGTGGATGGGCCGAGTGAACACGAAGACCAGGACCGCCTACCTCTGGTATCTCTACACAGAGAGTCTCTCCTGCATCTGGCTGTGAGATGGGCCCTCCCTAAGCTATTCCACTTCCTCTTGTGTCTCCCTGGAGGAGTCAAGGCCTTGAAGCTACCTAATGAAGAGGCCACCACACCATTAGACTTAGCTTTGCAAGGTGGACACTCCACACTGGTAGAAGACATCACAAATTTTCAGGGTAGCCATTCCCCAGGCTTCTCCCGACTGCGTCTTAACGAAGAGGCCACTCTGCAGTTTGTTCATTCATCGGAAACATTGACCCTGACCGTTAACCACACAGCTGAGCATCTCTTGGAAGCAGACATCAAACTCTTCCGGAAATATTTCTGGGACAGAGCCTTTCTTGTCAAGGCTCTTGAGCAAGAAGCCAAGACTGAGAAAGCAACCATGCCTTCTGGAGCTGCAGAAACTGAAGAAGAGGTTAGGAATTTGGAGTCTGGCAGATCACCATCGGAGGAGGAGGAGGATGCAAAGAGCATCAAAAGCCAGGTGGATGGGCCGAGTGAACACGAAGACCAGGACCGCCTACCTCTG
Peptide sequence:
MPSGAAETEEEVRNLESGRSPSEEEEDAKSIKSQVDGPSEHEDQDRLPLVSLHRESLLHLAVRWALPKLFHFLLCLPGGVKALKLPNEEATTPLDLALQGGHSTLVEDITNFQGSHSPGFSRLRLNEEATLQFVHSSETLTLTVNHTAEHLLEADIKLFRKYFWDRAFLVKALEQEAKTEKATMPSGAAETEEEVRNLESGRSPSEEEEDAKSIKSQVDGPSEHEDQDRLPL
IRESfinder result
IRESfinder score
0.555594489
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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