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mmu_circUsh2a_684
Basic information of circular RNA
PanCircBase ID:
mmu_circUsh2a_684
mm39_Chr. Position ID:
chr1|188487261|188517003|+
Gene name:
Ush2a
Transcript:
ENSMUST00000060479.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
45,46,47,48
Exon/intron offsets:
0,4682,27255,29573
Genomic length:
29742
Exon/intron sizes in nt:
2,03,11,31,99,169
Flanking exon/introns:
chr1:188485919-188487261|chr1:188517003-188529924
Splice length:
684
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGCCTCAGGGCATGCTTCCCCCAGAGGTTGTCATCATCAACAGTACAGCTGTACGTGTCATCTGGACATCGCCTTCAAACCCAAATGCCGTTGTCACCGAGTCTTCTGTCTATGTAAATAATAAGCTCTACAAGACTGGAACGGATGCGCCCGGGTCGTTTGTTCTGGAAGACCTGTCTCCCTTCACTATCTATGACATTCAGGTGGAAGTCTGTACAAAAGACGCCTGCGTGAAAAGCAATGGAACGCAAGTCAGCACAGCGGAAGATACTCCAAGTGACATTTCAATACCTGTAATCCGAGGTATTACTTCAAGATCCCTTCAAATAGATTGGACAACACCAGCAAATCCAAATGGTATCATTCTTGGGTATGACGTTTTGCGGAAAACATGGCGCCCATGCTCTGAAACCCAGAAGTTAACAGACAAACCGCGTGATGAGCTTTGCAAAGCAGTCAAGTGCCAATACCCTGGAAAAGTCTGTGGGCACACGTGCTACTCTCCAGGAACTAAGGTATGTTGTGACGGACTTCTGTATGACCCTCAGCCTGGATACAGCTGCTGTGAGGACAAATACATCGCACTCTCTCCGAATGCCACTGGGGTTTGCTGTGGAGGGCGAATGTGGGAGGCACAGCCAGACCACCAGTGCTGCTCTGGGCATTACGCTAGAATCCTTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTCTCCGAATGCCACTGG
60.18
CCAGATGACACGTACAGCTGT
60.07
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTCTCCGAATGCCACTGG
60.18
TGAAGGCGATGTCCAGATGAC
60.13
177
PCR template sequence:
CTCTCTCCGAATGCCACTGGGGTTTGCTGTGGAGGGCGAATGTGGGAGGCACAGCCAGACCACCAGTGCTGCTCTGGGCATTACGCTAGAATCCTTCCAGAGCCTCAGGGCATGCTTCCCCCAGAGGTTGTCATCATCAACAGTACAGCTGTACGTGTCATCTGGACATCGCCTTCAAACCCAAATGCCGTTGTCACCGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-203-3p(1), mmu-miR-138-5p(1), mmu-miR-96-5p(1), mmu-miR-541-5p(1), mmu-miR-425-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAATCCTTCCAGAGCCTCAGGGCAT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSH2A_684_ORF_1
0.7997
0.102176919
0.998366108
1356
ORF sequence:
ATGCTTCCCCCAGAGGTTGTCATCATCAACAGTACAGCTGTACGTGTCATCTGGACATCGCCTTCAAACCCAAATGCCGTTGTCACCGAGTCTTCTGTCTATGTAAATAATAAGCTCTACAAGACTGGAACGGATGCGCCCGGGTCGTTTGTTCTGGAAGACCTGTCTCCCTTCACTATCTATGACATTCAGGTGGAAGTCTGTACAAAAGACGCCTGCGTGAAAAGCAATGGAACGCAAGTCAGCACAGCGGAAGATACTCCAAGTGACATTTCAATACCTGTAATCCGAGGTATTACTTCAAGATCCCTTCAAATAGATTGGACAACACCAGCAAATCCAAATGGTATCATTCTTGGGTATGACGTTTTGCGGAAAACATGGCGCCCATGCTCTGAAACCCAGAAGTTAACAGACAAACCGCGTGATGAGCTTTGCAAAGCAGTCAAGTGCCAATACCCTGGAAAAGTCTGTGGGCACACGTGCTACTCTCCAGGAACTAAGGTATGTTGTGACGGACTTCTGTATGACCCTCAGCCTGGATACAGCTGCTGTGAGGACAAATACATCGCACTCTCTCCGAATGCCACTGGGGTTTGCTGTGGAGGGCGAATGTGGGAGGCACAGCCAGACCACCAGTGCTGCTCTGGGCATTACGCTAGAATCCTTCCAGAGCCTCAGGGCATGCTTCCCCCAGAGGTTGTCATCATCAACAGTACAGCTGTACGTGTCATCTGGACATCGCCTTCAAACCCAAATGCCGTTGTCACCGAGTCTTCTGTCTATGTAAATAATAAGCTCTACAAGACTGGAACGGATGCGCCCGGGTCGTTTGTTCTGGAAGACCTGTCTCCCTTCACTATCTATGACATTCAGGTGGAAGTCTGTACAAAAGACGCCTGCGTGAAAAGCAATGGAACGCAAGTCAGCACAGCGGAAGATACTCCAAGTGACATTTCAATACCTGTAATCCGAGGTATTACTTCAAGATCCCTTCAAATAGATTGGACAACACCAGCAAATCCAAATGGTATCATTCTTGGGTATGACGTTTTGCGGAAAACATGGCGCCCATGCTCTGAAACCCAGAAGTTAACAGACAAACCGCGTGATGAGCTTTGCAAAGCAGTCAAGTGCCAATACCCTGGAAAAGTCTGTGGGCACACGTGCTACTCTCCAGGAACTAAGGTATGTTGTGACGGACTTCTGTATGACCCTCAGCCTGGATACAGCTGCTGTGAGGACAAATACATCGCACTCTCTCCGAATGCCACTGGGGTTTGCTGTGGAGGGCGAATGTGGGAGGCACAGCCAGACCACCAGTGCTGCTCTGGGCATTACGCTAGAATCCTTCCA
Peptide sequence:
MLPPEVVIINSTAVRVIWTSPSNPNAVVTESSVYVNNKLYKTGTDAPGSFVLEDLSPFTIYDIQVEVCTKDACVKSNGTQVSTAEDTPSDISIPVIRGITSRSLQIDWTTPANPNGIILGYDVLRKTWRPCSETQKLTDKPRDELCKAVKCQYPGKVCGHTCYSPGTKVCCDGLLYDPQPGYSCCEDKYIALSPNATGVCCGGRMWEAQPDHQCCSGHYARILPEPQGMLPPEVVIINSTAVRVIWTSPSNPNAVVTESSVYVNNKLYKTGTDAPGSFVLEDLSPFTIYDIQVEVCTKDACVKSNGTQVSTAEDTPSDISIPVIRGITSRSLQIDWTTPANPNGIILGYDVLRKTWRPCSETQKLTDKPRDELCKAVKCQYPGKVCGHTCYSPGTKVCCDGLLYDPQPGYSCCEDKYIALSPNATGVCCGGRMWEAQPDHQCCSGHYARILP
IRESfinder result
IRESfinder score
0.402581246
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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