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mmu_circSynj1_355
Basic information of circular RNA
PanCircBase ID:
mmu_circSynj1_355
mm39_Chr. Position ID:
chr16|90788267|90790915|-
Gene name:
Synj1
Transcript:
ENSMUST00000121759.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,3
Exon/intron offsets:
0,2561
Genomic length:
2648
Exon/intron sizes in nt:
268,87
Flanking exon/introns:
chr16:90785255-90788267|chr16:90790915-90806911
Splice length:
355
Other database IDs:
CIRCpedia: MMU_CIRCpedia_33924, circAtlas: mmu-Synj1_0026
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_35253
Human Ortholog IDs:
Mature spliced Sequence:
CATCTGCAGAAAAGGAGGCTATTAAAGGCACATATGCCAAAGTACTGGATGCATACGGACTTTTGGGAGTTTTACGATTAAATCTTGGTGATACCATGCTGCACTATCTGGTCCTAGTCACTGGATGCATGTCTGTGGGGAAAATCCAAGAATCTGAAGTTTTCCGAGTTACTTCCACTGAGTTTATATCATTGCGAGTTGATGCTTCAGATGAGGACCGCATTTCGGAAGTACGAAAAGTTTTGAACTCGGGAAACTTTTATTTTGCATGGTCTGCATCTGGAGTCAGCTTAGATCTGAGTCTGAATGCACATCGAAGCATGCAAGAGCACACAACCGACAATAGGTTTTTCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTCTGCATCTGGAGTCAGC
60.46
ACTCCCAAAAGTCCGTATGCA
59.65
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCTGCATCTGGAGTCAGCT
59.46
ACTCCCAAAAGTCCGTATGCA
59.65
154
PCR template sequence:
ACTTTTATTTTGCATGGTCTGCATCTGGAGTCAGCTTAGATCTGAGTCTGAATGCACATCGAAGCATGCAAGAGCACACAACCGACAATAGGTTTTTCTGCATCTGCAGAAAAGGAGGCTATTAAAGGCACATATGCCAAAGTACTGGATGCATACGGACTTTTGGGAGTTTTACGATTAAATCTTGGTGATACCATGCT
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-134-5p(1), mmu-miR-7b-5p(1), mmu-miR-103-3p(1), mmu-miR-107-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATAGGTTTTTCTGCATCTGCAGAAAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYNJ1_355_ORF_1
0.8798
0.085665383
0.40796278
402
ORF sequence:
ATGCACATCGAAGCATGCAAGAGCACACAACCGACAATAGGTTTTTCTGCATCTGCAGAAAAGGAGGCTATTAAAGGCACATATGCCAAAGTACTGGATGCATACGGACTTTTGGGAGTTTTACGATTAAATCTTGGTGATACCATGCTGCACTATCTGGTCCTAGTCACTGGATGCATGTCTGTGGGGAAAATCCAAGAATCTGAAGTTTTCCGAGTTACTTCCACTGAGTTTATATCATTGCGAGTTGATGCTTCAGATGAGGACCGCATTTCGGAAGTACGAAAAGTTTTGAACTCGGGAAACTTTTATTTTGCATGGTCTGCATCTGGAGTCAGCTTAGATCTGAGTCTGAATGCACATCGAAGCATGCAAGAGCACACAACCGACAATAGGTTTTTC
Peptide sequence:
MHIEACKSTQPTIGFSASAEKEAIKGTYAKVLDAYGLLGVLRLNLGDTMLHYLVLVTGCMSVGKIQESEVFRVTSTEFISLRVDASDEDRISEVRKVLNSGNFYFAWSASGVSLDLSLNAHRSMQEHTTDNRFF
IRESfinder result
IRESfinder score
0.491141521
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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