top of page
mmu_circDgkd_250
Basic information of circular RNA
PanCircBase ID:
mmu_circDgkd_250
mm39_Chr. Position ID:
chr1|87866917|87868028|+
Gene name:
Dgkd
Transcript:
ENSMUST00000027517.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
27,28
Exon/intron offsets:
0,981
Genomic length:
1111
Exon/intron sizes in nt:
1,20,130
Flanking exon/introns:
chr1:87866160-87866917|chr1:87868028-87869090
Splice length:
250
Other database IDs:
circAtlas: mmu-Dgkd_0037
Human Ortholog IDs:
Mature spliced Sequence:
CAATTGGATCCCCCTCAGAAGGAACGGCTCGGGGCTGCCCTAATTGAGATGGACCAGCAGCTCAGGAAGCTGACAGACACTCCCTGGCTTTGCCAGCCCTTGGAGCCTGGTGAGGAAGAGTCTCTCCAACAGAATGTGATGCTGGATCTTACTAAACGCAGCCGTAGTGGTAAATTCCGCCTTGTGACCAAGTTTAAAAAGGAGAAAAACAATAAGAACAAAGAAGTTCACAGTAACCTAGGAGGCCCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCGCCTTGTGACCAAGTTT
60.11
GGGAGTGTCTGTCAGCTTCC
60.04
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCCGCCTTGTGACCAAGTT
60.11
GGGAGTGTCTGTCAGCTTCC
60.04
160
PCR template sequence:
ACTAAACGCAGCCGTAGTGGTAAATTCCGCCTTGTGACCAAGTTTAAAAAGGAGAAAAACAATAAGAACAAAGAAGTTCACAGTAACCTAGGAGGCCCTGCAATTGGATCCCCCTCAGAAGGAACGGCTCGGGGCTGCCCTAATTGAGATGGACCAGCAGCTCAGGAAGCTGACAGACACTCCCTGGCTTTGCCAGCCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTAGGAGGCCCTGCAATTGGATCCCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDGKD_250_ORF_1
0.9615
0.195876366
0.295452705
249
ORF sequence:
ATGGACCAGCAGCTCAGGAAGCTGACAGACACTCCCTGGCTTTGCCAGCCCTTGGAGCCTGGTGAGGAAGAGTCTCTCCAACAGAATGTGATGCTGGATCTTACTAAACGCAGCCGTAGTGGTAAATTCCGCCTTGTGACCAAGTTTAAAAAGGAGAAAAACAATAAGAACAAAGAAGTTCACAGTAACCTAGGAGGCCCTGCAATTGGATCCCCCTCAGAAGGAACGGCTCGGGGCTGCCCTAATTGA
Peptide sequence:
MDQQLRKLTDTPWLCQPLEPGEEESLQQNVMLDLTKRSRSGKFRLVTKFKKEKNNKNKEVHSNLGGPAIGSPSEGTARGCPN
IRESfinder result
IRESfinder score
0.584151817
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page