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mmu_circAfmid_737
Basic information of circular RNA
PanCircBase ID:
mmu_circAfmid_737
mm39_Chr. Position ID:
chr11|117723170|117727338|+
Gene name:
Afmid
Transcript:
ENSMUST00000073388.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
3,4,5,6,7,8,9,10
Exon/intron offsets:
0,183,2422,2601,2800,3158,3321,4063
Genomic length:
4168
Exon/intron sizes in nt:
10,54,98,67,39,87,91,40,000
Flanking exon/introns:
chr11:117718995-117723170|chr11:117727338-117729318
Splice length:
737
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223671, circAtlas: mmu-Afmid_0002
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_365389
Human Ortholog IDs:
Mature spliced Sequence:
CCACCCAGAAGGCCCGGGCCACCAGGAGGAACCAGCTGGATGTCCCCTATGGAGATGGCGAAGGGGAGAAACTGGACATCTACTTTCCCGATGAGGATTCCAAGGCTTTCCCTCTGTTCCTGTTCTTGCATGGAGGATACTGGCAGAGTGGAAGTAAAGATGACTCGGCCTTCATGGTAAACCCACTGACTGCACAGGGAATCGTGGTGGTGATAGTGGCTTATGACATTGCACCCAAAGGCACACTGGACCAGATGGTGGACCAGGTGACCCGCAGTGTCGTGTTTCTACAGAGGCGCTATCCAAGCAATGAGGGAATCTACCTCTGCGGACACTCTGCGGGAGCTCACCTGGCTGCTATGGTGCTCCTGGCCCGCTGGACCAAGCATGGCGTCACACCCAACCTCCAAGGCTTTCTCCTGGTGAGTGGGATCTACGACCTGGAGCCCCTCATAGCCACCTCCCAGAATGACCCTCTGCGCATGACCCTGGAAGATGCTCAGAGAAACAGTCCACAGCGACACTTGGATGTGGTTCCAGCACAGCCTGTGGCTCCAGCCTGCCCTGTGCTGGTGCTTGTGGGTCAGCATGACTCCCCAGAGTTCCACCGGCAGTCCAAGGAGTTCTACGAGACACTTCTCCGCGTGGGATGGAAGGCCTCTTTCCAGCAGCTGCGTGGTGTGGATCACTTTGACATCATAGAGAATCTGACCCGGGAGGATGACGTGCTCACCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAAGGCCTCTTTCCAGC
60.03
CAGTTTCTCCCCTTCGCCAT
60.04
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGATGGAAGGCCTCTTTCC
60.11
ATAGGGGACATCCAGCTGGT
60.03
141
PCR template sequence:
TCTCCGCGTGGGATGGAAGGCCTCTTTCCAGCAGCTGCGTGGTGTGGATCACTTTGACATCATAGAGAATCTGACCCGGGAGGATGACGTGCTCACCCAGCCACCCAGAAGGCCCGGGCCACCAGGAGGAACCAGCTGGATGTCCCCTATGGAGATGGCGAAGGGGAGAAACTGGACATCTACTTTCCCGATGAGGATTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-130a-3p(1), mmu-miR-298-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-300-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTGCTCACCCAGCCACCCAGAAGGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFMID_737_ORF_1
1.0974
0.318874278
0.968807726
744
ORF sequence:
ATGGTAAACCCACTGACTGCACAGGGAATCGTGGTGGTGATAGTGGCTTATGACATTGCACCCAAAGGCACACTGGACCAGATGGTGGACCAGGTGACCCGCAGTGTCGTGTTTCTACAGAGGCGCTATCCAAGCAATGAGGGAATCTACCTCTGCGGACACTCTGCGGGAGCTCACCTGGCTGCTATGGTGCTCCTGGCCCGCTGGACCAAGCATGGCGTCACACCCAACCTCCAAGGCTTTCTCCTGGTGAGTGGGATCTACGACCTGGAGCCCCTCATAGCCACCTCCCAGAATGACCCTCTGCGCATGACCCTGGAAGATGCTCAGAGAAACAGTCCACAGCGACACTTGGATGTGGTTCCAGCACAGCCTGTGGCTCCAGCCTGCCCTGTGCTGGTGCTTGTGGGTCAGCATGACTCCCCAGAGTTCCACCGGCAGTCCAAGGAGTTCTACGAGACACTTCTCCGCGTGGGATGGAAGGCCTCTTTCCAGCAGCTGCGTGGTGTGGATCACTTTGACATCATAGAGAATCTGACCCGGGAGGATGACGTGCTCACCCAGCCACCCAGAAGGCCCGGGCCACCAGGAGGAACCAGCTGGATGTCCCCTATGGAGATGGCGAAGGGGAGAAACTGGACATCTACTTTCCCGATGAGGATTCCAAGGCTTTCCCTCTGTTCCTGTTCTTGCATGGAGGATACTGGCAGAGTGGAAGTAAAGATGACTCGGCCTTCATGGTAA
Peptide sequence:
MVNPLTAQGIVVVIVAYDIAPKGTLDQMVDQVTRSVVFLQRRYPSNEGIYLCGHSAGAHLAAMVLLARWTKHGVTPNLQGFLLVSGIYDLEPLIATSQNDPLRMTLEDAQRNSPQRHLDVVPAQPVAPACPVLVLVGQHDSPEFHRQSKEFYETLLRVGWKASFQQLRGVDHFDIIENLTREDDVLTQPPRRPGPPGGTSWMSPMEMAKGRNWTSTFPMRIPRLSLCSCSCMEDTGRVEVKMTRPSW
IRESfinder result
IRESfinder score
0.318711777
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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