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mmu_circAfmid_583
Basic information of circular RNA
PanCircBase ID:
mmu_circAfmid_583
mm39_Chr. Position ID:
chr11|117725592|117727338|+
Gene name:
Afmid
Transcript:
ENSMUST00000073388.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
5,6,7,8,9,10
Exon/intron offsets:
0,179,378,736,899,1641
Genomic length:
1746
Exon/intron sizes in nt:
8,67,39,87,91,42,105
Flanking exon/introns:
chr11:117723402-117725592|chr11:117727338-117729318
Splice length:
583
Other database IDs:
CIRCpedia: MMU_CIRCpedia_38961, circAtlas: mmu-Afmid_0003
Human Ortholog IDs:
Mature spliced Sequence:
TAAAGATGACTCGGCCTTCATGGTAAACCCACTGACTGCACAGGGAATCGTGGTGGTGATAGTGGCTTATGACATTGCACCCAAAGGCACACTGGACCAGATGGTGGACCAGGTGACCCGCAGTGTCGTGTTTCTACAGAGGCGCTATCCAAGCAATGAGGGAATCTACCTCTGCGGACACTCTGCGGGAGCTCACCTGGCTGCTATGGTGCTCCTGGCCCGCTGGACCAAGCATGGCGTCACACCCAACCTCCAAGGCTTTCTCCTGGTGAGTGGGATCTACGACCTGGAGCCCCTCATAGCCACCTCCCAGAATGACCCTCTGCGCATGACCCTGGAAGATGCTCAGAGAAACAGTCCACAGCGACACTTGGATGTGGTTCCAGCACAGCCTGTGGCTCCAGCCTGCCCTGTGCTGGTGCTTGTGGGTCAGCATGACTCCCCAGAGTTCCACCGGCAGTCCAAGGAGTTCTACGAGACACTTCTCCGCGTGGGATGGAAGGCCTCTTTCCAGCAGCTGCGTGGTGTGGATCACTTTGACATCATAGAGAATCTGACCCGGGAGGATGACGTGCTCACCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAAGGCCTCTTTCCAGC
60.03
AAGCCACTATCACCACCACG
60.04
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGATGGAAGGCCTCTTTCC
60.11
AAGCCACTATCACCACCACG
60.04
159
PCR template sequence:
TCTCCGCGTGGGATGGAAGGCCTCTTTCCAGCAGCTGCGTGGTGTGGATCACTTTGACATCATAGAGAATCTGACCCGGGAGGATGACGTGCTCACCCAGTAAAGATGACTCGGCCTTCATGGTAAACCCACTGACTGCACAGGGAATCGTGGTGGTGATAGTGGCTTATGACATTGCACCCAAAGGCACACTGGACCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-130a-3p(1), mmu-miR-298-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTGCTCACCCAGTAAAGATGACTCG
siRNA sets
TCTTTACTGGGTGAGCACG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFMID_583_ORF_1
1.2392
0.438999589
0.959253449
600
ORF sequence:
ATGACGTGCTCACCCAGTAAAGATGACTCGGCCTTCATGGTAAACCCACTGACTGCACAGGGAATCGTGGTGGTGATAGTGGCTTATGACATTGCACCCAAAGGCACACTGGACCAGATGGTGGACCAGGTGACCCGCAGTGTCGTGTTTCTACAGAGGCGCTATCCAAGCAATGAGGGAATCTACCTCTGCGGACACTCTGCGGGAGCTCACCTGGCTGCTATGGTGCTCCTGGCCCGCTGGACCAAGCATGGCGTCACACCCAACCTCCAAGGCTTTCTCCTGGTGAGTGGGATCTACGACCTGGAGCCCCTCATAGCCACCTCCCAGAATGACCCTCTGCGCATGACCCTGGAAGATGCTCAGAGAAACAGTCCACAGCGACACTTGGATGTGGTTCCAGCACAGCCTGTGGCTCCAGCCTGCCCTGTGCTGGTGCTTGTGGGTCAGCATGACTCCCCAGAGTTCCACCGGCAGTCCAAGGAGTTCTACGAGACACTTCTCCGCGTGGGATGGAAGGCCTCTTTCCAGCAGCTGCGTGGTGTGGATCACTTTGACATCATAGAGAATCTGACCCGGGAGGATGACGTGCTCACCCAG
Peptide sequence:
MTCSPSKDDSAFMVNPLTAQGIVVVIVAYDIAPKGTLDQMVDQVTRSVVFLQRRYPSNEGIYLCGHSAGAHLAAMVLLARWTKHGVTPNLQGFLLVSGIYDLEPLIATSQNDPLRMTLEDAQRNSPQRHLDVVPAQPVAPACPVLVLVGQHDSPEFHRQSKEFYETLLRVGWKASFQQLRGVDHFDIIENLTREDDVLTQ
IRESfinder result
IRESfinder score
0.315988805
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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