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mmu_ciHdlbp_638
Basic information of circular RNA
PanCircBase ID:
mmu_ciHdlbp_638
mm39_Chr. Position ID:
chr1|93358038|93358676|-
Gene name:
Hdlbp
Transcript:
ENSMUST00000170883.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
7
Exon/intron offsets:
0
Genomic length:
638
Exon/intron sizes in nt:
638
Flanking exon/introns:
chr1:93358026-93358676
Splice length:
638
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACAGTGTGGAGGTGGCAGAGCCCATGAGCAAAACGGTTAATGGGATTTGAGTGTGGGAATTTGGCTAATTCCACAGTTCACCCTGCACCCTTTTGTCCTTGGAGACAAAGTTTGGTATGTGTCTACCTTAAGTGTCAATGTTTAGTGGTTGGTGGCCACATTTCCCTTCTGGTCTACTGGGTACACTATAGAGTGCTGTCCTGGTTTTTTATGTGTGTATCCTTTCTCAGGTCTATGACTATACTGGTAGGTTGCTACCACAGAATCAGCACAGACTTTTTGAAGTGTTTTTTTTTTAGCTTATTCTGACTTTGAGATGTAAAACCTGTTCCTTATTTGGAAGAAGTAAGGTTGGCAAATAGCTCTGTAGCAGAGCACTTGTCTAACAAGCATAACCCTATGTCAGCCCCCAACACTGTATGAAAAATGTAAGGGAACAAATGGAAAACAGTCTGGTTACTCAAAAAGTGACCAGACTCTGGGCCAGTCCAGTAGAGAGAAGTAGAATTTCTGGGGAGGCCAATCCTAACTTCACTTACTGAGAACCGCTTCTCAGTCCCCTTCACACTTTGTTAGCAGCAGTGGATGGTCTGTCATGCTGCCCATGCACAGATGTTTCCTGCTGACTGCCTTATA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCAGTGGATGGTCTGTCA
59.68
ACAAAAGGGTGCAGGGTGAA
60.03
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATGGTCTGTCATGCTGC
60.39
ACAAAAGGGTGCAGGGTGAA
60.03
152
PCR template sequence:
TACTGAGAACCGCTTCTCAGTCCCCTTCACACTTTGTTAGCAGCAGTGGATGGTCTGTCATGCTGCCCATGCACAGATGTTTCCTGCTGACTGCCTTATAGTACAGTGTGGAGGTGGCAGAGCCCATGAGCAAAACGGTTAATGGGATTTGAGTGTGGGAATTTGGCTAATTCCACAGTTCACCCTGCACCCTTTTGTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-149-5p(1), mmu-miR-107-3p(1), mmu-miR-383-5p(1), mmu-miR-342-3p(1), mmu-miR-188-3p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGACTGCCTTATAGTACAGTGTGGAG
siRNA sets
TCCACACTGTACTATAAGG, CCACACTGTACTATAAGGC, CACACTGTACTATAAGGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIHDLBP_638_ORF_5
1.1734
-0.131718218
0.049349379
93
ORF sequence:
ATGGTCTGTCATGCTGCCCATGCACAGATGTTTCCTGCTGACTGCCTTATAGTACAGTGTGGAGGTGGCAGAGCCCATGAGCAAAACGGTTAA
Peptide sequence:
MVCHAAHAQMFPADCLIVQCGGGRAHEQNG
IRESfinder result
IRESfinder score
0.802625325
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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