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mmu_circArhgef1_907
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgef1_907
mm39_Chr. Position ID:
chr7|24607735|24616366|+
Gene name:
Arhgef1
Transcript:
ENSMUST00000117796.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,3746,3999,4244,4829,5088,5309,7707,8490
Genomic length:
8631
Exon/intron sizes in nt:
1,14,99,43,24,73,01,00,00,00,000
Flanking exon/introns:
chr7:24607359-24607735|chr7:24616366-24617319
Splice length:
907
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AACTCAGAAGATCAAAACAGCCAGTTCCAGAGCCTAGAGCAAGTGAAGCGCCGCCCTGCCCACCTCATGGCCCTCCTGCAGCATGTGGCCCTGCAGTTCGAGCCAGGACCACTGCTCTGCTGCCTGCATGCAGACATGCTGAGCTCTCTGGGCCCCAAAGAAGCCAAGAAGGCCTTCCTTGACTTCTATCACAGTTTCCTGGAGAAGACTGCGGTTCTACGGGTGCCGGTCCCTCCCAGTGTCGCTTTTGAACTTGATCGTACTCGACCTGATCTGATCTCTGAGGATGTCCAGAGGCGGTTCATACAAGAGGTGGTGCAGAGCCAGCAGGCAGCCGTGAGCCGTCAGCTAGAGGACTTCCGCTCCAAGCGGCTCATGGGCATGACGCCCTGGGAGCAGGAACTGAGCCTGCTGGAGCCCTGGATTGGGAAAGACCGAGGCAACTATGAGGCCCGGGAGCGGCATGTTGCGGAGCGGCTGCTGTCCCACCTGGAGGAGACCCAGCATACCATCTCTACAGATGAAGAGAAAAGTGCTGCTGTGGTCACTGCCATCAGCCTGTATATGCGCCACCTTGGAGTCCGGACCAAGAGTGGGGACAAGAAGTCGGGAAGGAACTTCTTCCGGAAAAAGGTGATGGGGAATCGGAGGTCAGACGAACCCCCAAAGACAAAGAAAGGGCTGAGCAGTATCCTAGATCCTGCACGTTGGAACCGGGGAGAGCCATCCGCTCCAGATTGTCGACATCTAAAGGTCGAGGCTGATGCAGAGAAGCCAGGCCCTGCAGACCGGAAGGGAGGCCTGGGTATGTCTTCTCGGGACAGGACTGTTGGGACTCCTGGACAGGACAACCCAGGAGTCTCCCTGCACCCTCTGTCTACAGACAGCGTCGACTCCCGGGAACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCTTCTCGGGACAGGACT
59.89
CGCTTCACTTGCTCTAGGCT
60.11
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCTTCTCGGGACAGGACTG
59.47
CGCTTCACTTGCTCTAGGCT
60.11
148
PCR template sequence:
ATGTCTTCTCGGGACAGGACTGTTGGGACTCCTGGACAGGACAACCCAGGAGTCTCCCTGCACCCTCTGTCTACAGACAGCGTCGACTCCCGGGAACCAGAACTCAGAAGATCAAAACAGCCAGTTCCAGAGCCTAGAGCAAGTGAAGCGCCGCCCTGCCCACCTCATGGCCCTCCTGCAGCATGTGGCCCTGCAGTTCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-34a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-214-3p(1), mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-212-3p(1), mmu-miR-370-3p(1), mmu-miR-383-5p(1), mmu-miR-484(1), mmu-miR-99a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCCGGGAACCAGAACTCAGAAGATC
siRNA sets
TCTTCTGAGTTCTGGTTCC, ATCTTCTGAGTTCTGGTTC, TTCTGAGTTCTGGTTCCCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGEF1_907_ORF_1
1.0795
0.39320371
0.997286385
1050
ORF sequence:
ATGCAGAGAAGCCAGGCCCTGCAGACCGGAAGGGAGGCCTGGGTATGTCTTCTCGGGACAGGACTGTTGGGACTCCTGGACAGGACAACCCAGGAGTCTCCCTGCACCCTCTGTCTACAGACAGCGTCGACTCCCGGGAACCAGAACTCAGAAGATCAAAACAGCCAGTTCCAGAGCCTAGAGCAAGTGAAGCGCCGCCCTGCCCACCTCATGGCCCTCCTGCAGCATGTGGCCCTGCAGTTCGAGCCAGGACCACTGCTCTGCTGCCTGCATGCAGACATGCTGAGCTCTCTGGGCCCCAAAGAAGCCAAGAAGGCCTTCCTTGACTTCTATCACAGTTTCCTGGAGAAGACTGCGGTTCTACGGGTGCCGGTCCCTCCCAGTGTCGCTTTTGAACTTGATCGTACTCGACCTGATCTGATCTCTGAGGATGTCCAGAGGCGGTTCATACAAGAGGTGGTGCAGAGCCAGCAGGCAGCCGTGAGCCGTCAGCTAGAGGACTTCCGCTCCAAGCGGCTCATGGGCATGACGCCCTGGGAGCAGGAACTGAGCCTGCTGGAGCCCTGGATTGGGAAAGACCGAGGCAACTATGAGGCCCGGGAGCGGCATGTTGCGGAGCGGCTGCTGTCCCACCTGGAGGAGACCCAGCATACCATCTCTACAGATGAAGAGAAAAGTGCTGCTGTGGTCACTGCCATCAGCCTGTATATGCGCCACCTTGGAGTCCGGACCAAGAGTGGGGACAAGAAGTCGGGAAGGAACTTCTTCCGGAAAAAGGTGATGGGGAATCGGAGGTCAGACGAACCCCCAAAGACAAAGAAAGGGCTGAGCAGTATCCTAGATCCTGCACGTTGGAACCGGGGAGAGCCATCCGCTCCAGATTGTCGACATCTAAAGGTCGAGGCTGATGCAGAGAAGCCAGGCCCTGCAGACCGGAAGGGAGGCCTGGGTATGTCTTCTCGGGACAGGACTGTTGGGACTCCTGGACAGGACAACCCAGGAGTCTCCCTGCACCCTCTGTCTACAGACAGCGTCGACTCCCGGGAACCA
Peptide sequence:
MQRSQALQTGREAWVCLLGTGLLGLLDRTTQESPCTLCLQTASTPGNQNSEDQNSQFQSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLSSLGPKEAKKAFLDFYHSFLEKTAVLRVPVPPSVAFELDRTRPDLISEDVQRRFIQEVVQSQQAAVSRQLEDFRSKRLMGMTPWEQELSLLEPWIGKDRGNYEARERHVAERLLSHLEETQHTISTDEEKSAAVVTAISLYMRHLGVRTKSGDKKSGRNFFRKKVMGNRRSDEPPKTKKGLSSILDPARWNRGEPSAPDCRHLKVEADAEKPGPADRKGGLGMSSRDRTVGTPGQDNPGVSLHPLSTDSVDSREP
IRESfinder result
IRESfinder score
0.319770594
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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