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mmu_circSetd2_275
Basic information of circular RNA
PanCircBase ID:
mmu_circSetd2_275
mm39_Chr. Position ID:
chr9|110428186|110431330|+
Gene name:
Setd2
Transcript:
ENSMUST00000153838.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
16,17
Exon/intron offsets:
0,3004
Genomic length:
3144
Exon/intron sizes in nt:
1,35,140
Flanking exon/introns:
chr9:110423828-110428186|chr9:110431330-110433187
Splice length:
275
Other database IDs:
circBase: mmu_circ_0015305, CIRCpedia: MMU_CIRCpedia_2930, circAtlas: mmu-Setd2_0027
circAtlas: hsa-SETD2_0054, CIRCpedia: HSA_CIRCpedia_159280
Human Ortholog IDs:
Mature spliced Sequence:
AGTTATGCCCAGCCAAGTCTTCAGTATATCCAGGGACAGCAGATTTTCACAGCTCACCCACAAGGAGTGGTGGTACAGCCAACTGCAGCCGTGACTTCAATAGTTGCACCAGGGCAGCCTCAGTCCTTACAGCCACCTGAAATGGTTGTAACAAATAATCTACTGGACCTGCCACCACCCTCCCCTCCAAAACCAAAAACGATTGTTTTACCTCCCAACTGGAAGACAGCCCGAGACCCTGAGGGGAAGATCTACTACTACCACGTGATCACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTCCCCTCCAAAACCAAA
59.81
CCTTGTGGGTGAGCTGTGAA
60.18
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTCCCCTCCAAAACCAAA
59.81
GGCTGTACCACCACTCCTTG
60.32
178
PCR template sequence:
CACCCTCCCCTCCAAAACCAAAAACGATTGTTTTACCTCCCAACTGGAAGACAGCCCGAGACCCTGAGGGGAAGATCTACTACTACCACGTGATCACAAGAGTTATGCCCAGCCAAGTCTTCAGTATATCCAGGGACAGCAGATTTTCACAGCTCACCCACAAGGAGTGGTGGTACAGCCAACTGCAGCCGTGACTTCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
ACGTGATCACAAGAGTTATGCCCAGC
siRNA sets
ATAACTCTTGTGATCACGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSETD2_275_ORF_1
0.7833
0.137430432
0.169085961
228
ORF sequence:
ATGGTTGTAACAAATAATCTACTGGACCTGCCACCACCCTCCCCTCCAAAACCAAAAACGATTGTTTTACCTCCCAACTGGAAGACAGCCCGAGACCCTGAGGGGAAGATCTACTACTACCACGTGATCACAAGAGTTATGCCCAGCCAAGTCTTCAGTATATCCAGGGACAGCAGATTTTCACAGCTCACCCACAAGGAGTGGTGGTACAGCCAACTGCAGCCGTGA
Peptide sequence:
MVVTNNLLDLPPPSPPKPKTIVLPPNWKTARDPEGKIYYYHVITRVMPSQVFSISRDSRFSQLTHKEWWYSQLQP
IRESfinder result
IRESfinder score
0.71124956
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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