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mmu_circSergef_562
Basic information of circular RNA
PanCircBase ID:
mmu_circSergef_562
mm39_Chr. Position ID:
chr7|46270984|46284980|-
Gene name:
Sergef
Transcript:
ENSMUST00000033127.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,4648,11099,12194,13860
Genomic length:
13996
Exon/intron sizes in nt:
11,46,19,51,56,136
Flanking exon/introns:
chr7:46268182-46270984|chr7:46284980-46289136
Splice length:
562
Other database IDs:
circBase: mmu_circ_0014226, CIRCpedia: MMU_CIRCpedia_20910, circAtlas: mmu-Sergef_0004
circAtlas: hsa-SERGEF_0005
Human Ortholog IDs:
Mature spliced Sequence:
GGTGCAAACAGCTATGGGCAACTTGGCCTTGGCCATAAGGAAGATGTGTTTCTGCCCCAGCAACTGAGTGACTTCTGTCAAGCTGGGTGTATCAAGAGTGTCACAGGAGGAGGAGGGCATTCTGCAGTTGTCACAGATGGAGGAGATCTTTTTGTTTGTGGCCTGAATAAAGATGGGCAGTTGGGGCTTGGTCACACAGAGGAAGTTCTGCGTTTTACCATCTGCAAGCCTCTCCGTGGTTGTCCCATCCGACAGGTGGCCTGTGGCTGGGACTTCACCATCATGCTTACAGAAAAAGGTCAAGTTCTGTCCTGTGGATCCAATGCCTTTGGCCAGTTAGGTGTGCCTCACGGCCCTCGCAAATGCGTGGTCCCCCAGGCCATTGAGTGCCTGAGAGAGAAGGTTGTTTGTGTCGCTGCTGGACTGAGGCATGCCTTAGCCACTACAGCGACTGGCAGTGTGTTCCAGTGGGGGACTGGCTTGGCATCTTCTGGTCGACGCCTGTGCCCTGGGCAGAATCTCCCACTGTTTTTGACAGCAAAGGAACCCAGCAGAGTGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACTGGCTTGGCATCTTCT
60.03
AAGTCACTCAGTTGCTGGGG
59.89
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCTTGGCATCTTCTGGTC
60.32
AAGTCACTCAGTTGCTGGGG
59.89
160
PCR template sequence:
TTCCAGTGGGGGACTGGCTTGGCATCTTCTGGTCGACGCCTGTGCCCTGGGCAGAATCTCCCACTGTTTTTGACAGCAAAGGAACCCAGCAGAGTGACAGGGTGCAAACAGCTATGGGCAACTTGGCCTTGGCCATAAGGAAGATGTGTTTCTGCCCCAGCAACTGAGTGACTTCTGTCAAGCTGGGTGTATCAAGAGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-503-5p(1), mmu-miR-382-5p(1), mmu-miR-324-3p(1), mmu-miR-224-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCAGAGTGACAGGGTGCAAACAGCT
siRNA sets
TTTGCACCCTGTCACTCTG,TGTTTGCACCCTGTCACTC,TTGCACCCTGTCACTCTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSERGEF_562_ORF_1
0.52
-0.020224355
0.110043034
318
ORF sequence:
ATGCTTACAGAAAAAGGTCAAGTTCTGTCCTGTGGATCCAATGCCTTTGGCCAGTTAGGTGTGCCTCACGGCCCTCGCAAATGCGTGGTCCCCCAGGCCATTGAGTGCCTGAGAGAGAAGGTTGTTTGTGTCGCTGCTGGACTGAGGCATGCCTTAGCCACTACAGCGACTGGCAGTGTGTTCCAGTGGGGGACTGGCTTGGCATCTTCTGGTCGACGCCTGTGCCCTGGGCAGAATCTCCCACTGTTTTTGACAGCAAAGGAACCCAGCAGAGTGACAGGGTGCAAACAGCTATGGGCAACTTGGCCTTGGCCATAA
Peptide sequence:
MLTEKGQVLSCGSNAFGQLGVPHGPRKCVVPQAIECLREKVVCVAAGLRHALATTATGSVFQWGTGLASSGRRLCPGQNLPLFLTAKEPSRVTGCKQLWATWPWP
IRESfinder result
IRESfinder score
0.588767654
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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