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mmu_circSmc4_686
Basic information of circular RNA
PanCircBase ID:
mmu_circSmc4_686
mm39_Chr. Position ID:
chr3|68913408|68916993|+
Gene name:
Smc4
Transcript:
ENSMUST00000042901.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,1113,1853,3408
Genomic length:
3585
Exon/intron sizes in nt:
1,38,17,91,92,177
Flanking exon/introns:
chr3:68912423-68913408|chr3:68916993-68923425
Splice length:
686
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CCACCATGCGGCGTAAGGGCACCAAGCCCTCCACTGCCTGCCACCAGGAGGAAGGGCCGCCGCCCTCCCAGGACGGTGCCCACAGCGACGAAGAGATGGAGCAACCGGCCGGCGAAGCGGAGAGCGCTGCACCCGCAAAGCCTCCAGGTGAGGAGCTGGATAACAGAAGTTTAGAGGAGATTTTGAATAGTATCCCTCCACCCCCACCTCCAGCCATGGCCAGTGAAGCTGGAGCTCCTCGTCTCATGATAACTCATATTGTAAACCAAAACTTCAAGTCCTATGCTGGAGAGAAAGTTCTGGGACCTTTCCATAAGCGCTTTTCCTGTATTATTGGACCAAATGGCAGTGGAAAATCCAATGTTATTGATTCCATGCTTTTTGTGTTTGGCTATCGAGCACAAAAAATAAGGTCTAAAAAGCTATCGGTACTGATACATAATTCTGATGAACACAAGGATATTCAGAGTTGTACTGTAGAAGTTCATTTTCAAAAGATAATTGATAAGGAAGGAGATGATTACGAAGTCCTTCCTAACAGCAACTTCTATGTATCCAGAACCGCCTACAGAGATAGCACTTCTGTCTACCACATAAGTGGGAAGAAGAAGACGTTTAAAGATGTTGGAAATCTCCTTAGAAGCCATGGCATTGACTTAGACCATAATCGATTTTTAATCTTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCCTTAGAAGCCATGGCA
58.42
TCCATCTCTTCGTCGCTGTG
59.83
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCATGGCATTGACTTAGACC
59.32
TCCATCTCTTCGTCGCTGTG
59.83
144
PCR template sequence:
CTACCACATAAGTGGGAAGAAGAAGACGTTTAAAGATGTTGGAAATCTCCTTAGAAGCCATGGCATTGACTTAGACCATAATCGATTTTTAATCTTGCAGCCACCATGCGGCGTAAGGGCACCAAGCCCTCCACTGCCTGCCACCAGGAGGAAGGGCCGCCGCCCTCCCAGGACGGTGCCCACAGCGACGAAGAGATGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-20a-5p(1), mmu-miR-135a-5p(1), mmu-miR-139-5p(1), mmu-miR-218-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTAATCTTGCAGCCACCATGCGGCG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMC4_686_ORF_1
0.9459
0.15429624
0.963898902
855
ORF sequence:
ATGCGGCGTAAGGGCACCAAGCCCTCCACTGCCTGCCACCAGGAGGAAGGGCCGCCGCCCTCCCAGGACGGTGCCCACAGCGACGAAGAGATGGAGCAACCGGCCGGCGAAGCGGAGAGCGCTGCACCCGCAAAGCCTCCAGGTGAGGAGCTGGATAACAGAAGTTTAGAGGAGATTTTGAATAGTATCCCTCCACCCCCACCTCCAGCCATGGCCAGTGAAGCTGGAGCTCCTCGTCTCATGATAACTCATATTGTAAACCAAAACTTCAAGTCCTATGCTGGAGAGAAAGTTCTGGGACCTTTCCATAAGCGCTTTTCCTGTATTATTGGACCAAATGGCAGTGGAAAATCCAATGTTATTGATTCCATGCTTTTTGTGTTTGGCTATCGAGCACAAAAAATAAGGTCTAAAAAGCTATCGGTACTGATACATAATTCTGATGAACACAAGGATATTCAGAGTTGTACTGTAGAAGTTCATTTTCAAAAGATAATTGATAAGGAAGGAGATGATTACGAAGTCCTTCCTAACAGCAACTTCTATGTATCCAGAACCGCCTACAGAGATAGCACTTCTGTCTACCACATAAGTGGGAAGAAGAAGACGTTTAAAGATGTTGGAAATCTCCTTAGAAGCCATGGCATTGACTTAGACCATAATCGATTTTTAATCTTGCAGCCACCATGCGGCGTAAGGGCACCAAGCCCTCCACTGCCTGCCACCAGGAGGAAGGGCCGCCGCCCTCCCAGGACGGTGCCCACAGCGACGAAGAGATGGAGCAACCGGCCGGCGAAGCGGAGAGCGCTGCACCCGCAAAGCCTCCAGGTGAGGAGCTGGATAACAGAAGTTTAG
Peptide sequence:
MRRKGTKPSTACHQEEGPPPSQDGAHSDEEMEQPAGEAESAAPAKPPGEELDNRSLEEILNSIPPPPPPAMASEAGAPRLMITHIVNQNFKSYAGEKVLGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHNSDEHKDIQSCTVEVHFQKIIDKEGDDYEVLPNSNFYVSRTAYRDSTSVYHISGKKKTFKDVGNLLRSHGIDLDHNRFLILQPPCGVRAPSPPLPATRRKGRRPPRTVPTATKRWSNRPAKRRALHPQSLQVRSWITEV
IRESfinder result
IRESfinder score
0.422880888
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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