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mmu_circHnrnpd_345
Basic information of circular RNA
PanCircBase ID:
mmu_circHnrnpd_345
mm39_Chr. Position ID:
chr5|100110373|100111942|-
Gene name:
Hnrnpd
Transcript:
ENSMUST00000172361.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
8,7,6
Exon/intron offsets:
0,1216,1469
Genomic length:
1569
Exon/intron sizes in nt:
9,81,47,100
Flanking exon/introns:
chr5:100109192-100110373|chr5:100111942-100112528
Splice length:
345
Other database IDs:
CIRCpedia: MMU_CIRCpedia_36214, circAtlas: mmu-Hnrnpd_0008
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_49267
Human Ortholog IDs:
Mature spliced Sequence:
TGTGAAATAAAAGTAGCCATGTCAAAGGAACAGTATCAGCAGCAGCAGCAGTGGGGATCTAGAGGAGGGTTTGCAGGCAGAGCTCGCGGAAGAGGTGGAGGCCCCAGTCAAAACTGGAACCAGGGATATAGTAACTATTGGAATCAAGGCTATGGCAACTATGGATATAACAGCCAAGGTTACGGAGGTTATGGAGGATATGACTACACTGGTTACAACAACTACTATGGATATGGTGATTATAGCAATCAGCAGAGTGGTTATGGGAAAGTATCCAGGCGAGGTGGACATCAAAATAGCTACAAACCATACTAAATTATTCCATTTGCAACTTATCCCCAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGCGAGGTGGACATCAAA
60.32
GCCTGCAAACCCTCCTCTAG
60.11
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCGAGGTGGACATCAAAA
59.6
GCCTGCAAACCCTCCTCTAG
60.11
147
PCR template sequence:
CAATCAGCAGAGTGGTTATGGGAAAGTATCCAGGCGAGGTGGACATCAAAATAGCTACAAACCATACTAAATTATTCCATTTGCAACTTATCCCCAACAGTGTGAAATAAAAGTAGCCATGTCAAAGGAACAGTATCAGCAGCAGCAGCAGTGGGGATCTAGAGGAGGGTTTGCAGGCAGAGCTCGCGGAAGAGGTGGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
TTATCCCCAACAGTGTGAAATAAAAG
siRNA sets
TTTTATTTCACACTGTTGG, TATTTCACACTGTTGGGGA, TTATTTCACACTGTTGGGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHNRNPD_345_ORF_3
1.1836
0.065303708
0.210981109
204
ORF sequence:
ATGGCAACTATGGATATAACAGCCAAGGTTACGGAGGTTATGGAGGATATGACTACACTGGTTACAACAACTACTATGGATATGGTGATTATAGCAATCAGCAGAGTGGTTATGGGAAAGTATCCAGGCGAGGTGGACATCAAAATAGCTACAAACCATACTAAATTATTCCATTTGCAACTTATCCCCAACAGTGTGAAATAA
Peptide sequence:
MATMDITAKVTEVMEDMTTLVTTTTMDMVIIAISRVVMGKYPGEVDIKIATNHTKLFHLQLIPNSVK
IRESfinder result
IRESfinder score
0.346516781
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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