top of page
mmu_ciClstn1_204
Basic information of circular RNA
PanCircBase ID:
mmu_ciClstn1_204
mm39_Chr. Position ID:
chr4|149727809|149728013|+
Gene name:
Clstn1
Transcript:
ENSMUST00000105691.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
11
Exon/intron offsets:
0
Genomic length:
204
Exon/intron sizes in nt:
204
Flanking exon/introns:
chr4:149727809-149728037
Splice length:
204
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGAGCTCCCCTGACCTTACTCCTAGCCTCGCCCTCTGAGAGTGGGGCCAGCAGGGTAGGGCGGACACGGGGTCCTGGACTTTACCCTATGTGAGCATCTTGTTCTTGGGGACTAAACAGCTTCTCCGAGACTCAGCCCCGGCTGATGACTCCACTGCCTCTCAGTTTTGGCCGCTCTCAGTTGGGACCTGGTTCCCCTCTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCTTCTCCGAGACTCAGC
60.18
GTAAAGTCCAGGACCCCGTG
60.04
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGATGACTCCACTGCCTC
60.46
GTAAAGTCCAGGACCCCGTG
60.04
148
PCR template sequence:
TTCTTGGGGACTAAACAGCTTCTCCGAGACTCAGCCCCGGCTGATGACTCCACTGCCTCTCAGTTTTGGCCGCTCTCAGTTGGGACCTGGTTCCCCTCTCGTGAGAGCTCCCCTGACCTTACTCCTAGCCTCGCCCTCTGAGAGTGGGGCCAGCAGGGTAGGGCGGACACGGGGTCCTGGACTTTACCCTATGTGAGCAT
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-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-31-5p(1), mmu-miR-34b-5p(1), mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGGTTCCCCTCTCGTGAGAGCTCCCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CICLSTN1_204_ORF_1
0.9556
-0.045939119
0.071804031
153
ORF sequence:
ATGACTCCACTGCCTCTCAGTTTTGGCCGCTCTCAGTTGGGACCTGGTTCCCCTCTCGTGAGAGCTCCCCTGACCTTACTCCTAGCCTCGCCCTCTGAGAGTGGGGCCAGCAGGGTAGGGCGGACACGGGGTCCTGGACTTTACCCTATGTGA
Peptide sequence:
MTPLPLSFGRSQLGPGSPLVRAPLTLLLASPSESGASRVGRTRGPGLYPM
IRESfinder result
IRESfinder score
0.68204125
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page