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mmu_circSdad1_488
Basic information of circular RNA
PanCircBase ID:
mmu_circSdad1_488
mm39_Chr. Position ID:
chr5|92451524|92453696|-
Gene name:
Sdad1
Transcript:
ENSMUST00000031364.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,218,1307,1538,2067
Genomic length:
2172
Exon/intron sizes in nt:
10,17,21,11,99,105
Flanking exon/introns:
chr5:92450555-92451524|chr5:92453696-92457650
Splice length:
488
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_137469
Human Ortholog IDs:
Mature spliced Sequence:
TTCCTTCAGCAATATAACCACTATAAATCCAATATGGAGATTTTCAAGTTACAACCAAATAAGCCCAGCAAAGAGCTGGCAGAGCTGGTGATGTTCATGGCGCAGATTGGCCAGTGCTACCCGGAGCATCTCAGTAACTTCCCGCAGGAGCTGAAGGACCTGCTCTCCTACAACCACACTGTCTTAGACCCAGATCTCCGCATGACGTTTTGCAAAGCCTTGATCTTACTGAGAAACAAGAATCTCATCAATCCATCAAGTTTGCTAGAGCTCTTCTTTGAGCTGCTGCGCTGCCACGACAAGCTCCTGCGGAAGACTCTGTACACACACATTGTGACTGACATCAAGAACATCAACGCCAAACACAAGAACAACAAAGTGAACGTGGTGCTGCAGAACTTCATGTACACCATGTTGAGAGACAGCAATGCAACCGCAGCCAAGATGTCCTTGGATGTGATGATCGAACTCTACAGAAGGAACATCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGAGACAGCAATGCAACCG
59.55
GAACATCACCAGCTCTGCCA
60.32
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGAGACAGCAATGCAACCG
59.55
TGAACATCACCAGCTCTGCC
60.32
169
PCR template sequence:
TGCTGCAGAACTTCATGTACACCATGTTGAGAGACAGCAATGCAACCGCAGCCAAGATGTCCTTGGATGTGATGATCGAACTCTACAGAAGGAACATCTGTTCCTTCAGCAATATAACCACTATAAATCCAATATGGAGATTTTCAAGTTACAACCAAATAAGCCCAGCAAAGAGCTGGCAGAGCTGGTGATGTTCATGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-33-5p(1), mmu-miR-27a-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAGGAACATCTGTTCCTTCAGCAAT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSDAD1_488_ORF_1
1.2521
0.327937215
0.91241239
546
ORF sequence:
ATGGAGATTTTCAAGTTACAACCAAATAAGCCCAGCAAAGAGCTGGCAGAGCTGGTGATGTTCATGGCGCAGATTGGCCAGTGCTACCCGGAGCATCTCAGTAACTTCCCGCAGGAGCTGAAGGACCTGCTCTCCTACAACCACACTGTCTTAGACCCAGATCTCCGCATGACGTTTTGCAAAGCCTTGATCTTACTGAGAAACAAGAATCTCATCAATCCATCAAGTTTGCTAGAGCTCTTCTTTGAGCTGCTGCGCTGCCACGACAAGCTCCTGCGGAAGACTCTGTACACACACATTGTGACTGACATCAAGAACATCAACGCCAAACACAAGAACAACAAAGTGAACGTGGTGCTGCAGAACTTCATGTACACCATGTTGAGAGACAGCAATGCAACCGCAGCCAAGATGTCCTTGGATGTGATGATCGAACTCTACAGAAGGAACATCTGTTCCTTCAGCAATATAACCACTATAAATCCAATATGGAGATTTTCAAGTTACAACCAAATAAGCCCAGCAAAGAGCTGGCAGAGCTGGTGA
Peptide sequence:
MEIFKLQPNKPSKELAELVMFMAQIGQCYPEHLSNFPQELKDLLSYNHTVLDPDLRMTFCKALILLRNKNLINPSSLLELFFELLRCHDKLLRKTLYTHIVTDIKNINAKHKNNKVNVVLQNFMYTMLRDSNATAAKMSLDVMIELYRRNICSFSNITTINPIWRFSSYNQISPAKSWQSW
IRESfinder result
IRESfinder score
0.375320683
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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