top of page
mmu_ciChordc1_395
Basic information of circular RNA
PanCircBase ID:
mmu_ciChordc1_395
mm39_Chr. Position ID:
chr9|18223327|18223722|+
Gene name:
Chordc1
Transcript:
ENSMUST00000001825.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
9
Exon/intron offsets:
0
Genomic length:
395
Exon/intron sizes in nt:
395
Flanking exon/introns:
chr9:18223327-18223725
Splice length:
395
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTAAACATGTTCTCAAAAGTTCTTCATTCTGATCAGAAAATCACAAATGACTTTCATAGAAACAGTATTTTAAGTGAAACTCACAGTGTAGTAGACTTTATTCCAAAGTTATCTAGAAGTATAGTAGCTTAGAAAAATCACAAAATACATATTTGTGTCTCAGTATCAATCTTCTAGCTAATTCTTCCTGTTAATCATTTTCTTAAATGAAACAGTGGGGCTCAATATTGACATTTTGTCATAGCTTGAGCAATGCCAGTATTGTCTTTATAATTAGTACTTAGTCTACTCTTGGCTTGGTGTGGTTCAATGTTTCACTGCATGGTTATTGTGTATTATGGTCATATTTTCAATACTTAGCACCAAAATAATGACGATACATTATCTATTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCTTGGTGTGGTTCAATG
58.96
AGTCATTTGTGATTTTCTGATCAGA
57.01
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTTGGTGTGGTTCAATGT
58.96
AGTCATTTGTGATTTTCTGATCAGA
57.01
154
PCR template sequence:
TTGGCTTGGTGTGGTTCAATGTTTCACTGCATGGTTATTGTGTATTATGGTCATATTTTCAATACTTAGCACCAAAATAATGACGATACATTATCTATTTGTGAGTAAACATGTTCTCAAAAGTTCTTCATTCTGATCAGAAAATCACAAATGACTTTCATAGAAACAGTATTTTAAGTGAAACTCACAGTGTAGTAGAC
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-429-3p(2), mmu-miR-434-3p(1), mmu-miR-340-5p(1), mmu-miR-383-5p(1), mmu-miR-369-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACATTATCTATTTGTGAGTAAACATG
siRNA sets
CATGTTTACTCACAAATAG,TACTCACAAATAGATAATG,ATGTTTACTCACAAATAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CICHORDC1_395_ORF_3
0.7013
-0.473763349
0.005246415
90
ORF sequence:
ATGGTCATATTTTCAATACTTAGCACCAAAATAATGACGATACATTATCTATTTGTGAGTAAACATGTTCTCAAAAGTTCTTCATTCTGA
Peptide sequence:
MVIFSILSTKIMTIHYLFVSKHVLKSSSF
IRESfinder result
IRESfinder score
0.908643194
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page