top of page
mmu_circHdlbp_441
Basic information of circular RNA
PanCircBase ID:
mmu_circHdlbp_441
mm39_Chr. Position ID:
chr1|93345189|93348009|-
Gene name:
Hdlbp
Transcript:
ENSMUST00000170883.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
18,17
Exon/intron offsets:
0,2601
Genomic length:
2820
Exon/intron sizes in nt:
2,22,219
Flanking exon/introns:
chr1:93345112-93345189|chr1:93348009-93348805
Splice length:
441
Other database IDs:
circAtlas: mmu-Hdlbp_0048
Human Ortholog IDs:
Mature spliced Sequence:
GCCAACATAGCTGAAGTGGAGGTCTCAATTCCTGCCAAACTACACAACTCTCTCATTGGCACAAAGGGCCGTCTGATCCGCTCCATCATGGAGGAATGTGGTGGCGTCCATATTCACTTTCCTGTGGAAGGTTCTGGAAGCGACACTGTTGTCATCAGGGGTCCTTCCTCAGATGTAGAGAAGGCCAAGAAGCAGCTCCTGCACCTGGCTGAGGAGAAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACCAGGACCTGATCACA
59.88
ATGATGGAGCGGATCAGACG
59.68
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACCAGGACCTGATCACA
59.88
GCCCTTTGTGCCAATGAGAG
59.47
155
PCR template sequence:
GGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTGGCCAACATAGCTGAAGTGGAGGTCTCAATTCCTGCCAAACTACACAACTCTCTCATTGGCACAAAGGGCCGTCTGATCCGCTCCATCATGGAGGAATGTG
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-383-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GATCCAGAACCTGGCCAACATAGCTG
siRNA sets
CTATGTTGGCCAGGTTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHDLBP_441_ORF_1
1.2602
0.457410663
0.990869229
795
ORF sequence:
ATGGAGGAATGTGGTGGCGTCCATATTCACTTTCCTGTGGAAGGTTCTGGAAGCGACACTGTTGTCATCAGGGGTCCTTCCTCAGATGTAGAGAAGGCCAAGAAGCAGCTCCTGCACCTGGCTGAGGAGAAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTGGCCAACATAGCTGAAGTGGAGGTCTCAATTCCTGCCAAACTACACAACTCTCTCATTGGCACAAAGGGCCGTCTGATCCGCTCCATCATGGAGGAATGTGGTGGCGTCCATATTCACTTTCCTGTGGAAGGTTCTGGAAGCGACACTGTTGTCATCAGGGGTCCTTCCTCAGATGTAGAGAAGGCCAAGAAGCAGCTCCTGCACCTGGCTGAGGAGAAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTG
Peptide sequence:
MEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARIIFPAAEDKDQDLITIIGKEDAVREAQKELEALIQNLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARIIFPAAEDKDQDLITIIGKEDAVREAQKELEALIQNL
IRESfinder result
IRESfinder score
0.463797278
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page