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mmu_ciHnrnpdl_316
Basic information of circular RNA
PanCircBase ID:
mmu_ciHnrnpdl_316
mm39_Chr. Position ID:
chr5|100185110|100185426|-
Gene name:
Hnrnpdl
Transcript:
ENSMUST00000128187.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
316
Exon/intron sizes in nt:
316
Flanking exon/introns:
chr5:100185075-100185426
Splice length:
316
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGGGCTGTGTTTGTGTATGTATGTGTGTCTGTGCTCGTGTTTGGTCAAGTCTGGGGGGGTTCATTAATATTTCACCGGATGGGACTGAATTCTCTTGCTTCGTCTTCACTGCTGCTTTCTATGTTGTAGTGGAAACCAGTATCTAATCTTACTTAGCCAAAGCCCCAAAGGTGTAAAGTGTTTCACCAATTGGTGGCCTCTGGGGTGTAAGGTACTATAAAAAGATAAAACACAACTTTTTAGAACATGGTGGTCAGTAGATGTGTCTGGTGTTTGTGAAGAGCCTGTGGCATTATATAATCTTTATTAACTGGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTGTTTGTGAAGAGCCTGT
60.06
GAATTCAGTCCCATCCGGTGA
59.79
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTGTTTGTGAAGAGCCTGT
60.06
AGAATTCAGTCCCATCCGGTG
59.79
142
PCR template sequence:
TATAAAAAGATAAAACACAACTTTTTAGAACATGGTGGTCAGTAGATGTGTCTGGTGTTTGTGAAGAGCCTGTGGCATTATATAATCTTTATTAACTGGTGTGGGCTGTGTTTGTGTATGTATGTGTGTCTGTGCTCGTGTTTGGTCAAGTCTGGGGGGGTTCATTAATATTTCACCGGATGGGACTGAATTCTCTTGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-203-3p(1), mmu-miR-466d-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-466b-3p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTATTAACTGGTGTGGGCTGTGTTT
siRNA sets
AAACACAGCCCACACCAGT, AACACAGCCCACACCAGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIHNRNPDL_316_ORF_3
0.9532
-0.447282549
0.011816334
123
ORF sequence:
ATGTGTCTGGTGTTTGTGAAGAGCCTGTGGCATTATATAATCTTTATTAACTGGTGTGGGCTGTGTTTGTGTATGTATGTGTGTCTGTGCTCGTGTTTGGTCAAGTCTGGGGGGGTTCATTAA
Peptide sequence:
MCLVFVKSLWHYIIFINWCGLCLCMYVCLCSCLVKSGGVH
IRESfinder result
IRESfinder score
0.856814043
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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