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mmu_circHdac9_641
Basic information of circular RNA
PanCircBase ID:
mmu_circHdac9_641
mm39_Chr. Position ID:
chr12|34265009|34337574|-
Gene name:
Hdac9
Transcript:
ENSMUST00000209902.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
20,19,18,17,16,15,14
Exon/intron offsets:
0,410,5861,6193,33312,67636,72444
Genomic length:
72565
Exon/intron sizes in nt:
98,12,08,85,61,08,50,100
Flanking exon/introns:
chr12:34220112-34265009|chr12:34337574-34353171
Splice length:
641
Other database IDs:
circBase: mmu_circ_0003914, CIRCpedia: MMU_CIRCpedia_17150, circAtlas: mmu-intergenic_000134
circBase: hsa_circ_0079529, circAtlas: hsa-HDAC9_0024, CIRCpedia: HSA_CIRCpedia_57560
Human Ortholog IDs:
Mature spliced Sequence:
CGAATTCAAGGTCGAAAAGCCAGCCTGGAGGAAATACAGCTTGTTCATTCTGAACATCACTCACTATTGTATGGCACCAGCCCCCTGGATGGACAGAAGCTGGACCCCAGGACACTCTTAGGTGATGATTCTCGGAAATTCTTTTCCTCGTTGCCTTGTGGTGGACTCGGGGTGGACAGTGACACCATTTGGAATGAGCTGCACTCGTCCGGTGCTGCACGCATGGCTGTTGGCTGTGTCATTGAGCTGGCTTCCAAAGTGGCCTCAGGAGAGCTGAAGAATGGGTTTGCCGTTGTGAGGCCCCCAGGCCATCATGCGGAAGAGTCTGCAGCCATGGGGTTCTGCTTTTTTAATTCAGTTGCAATTACCGCCAAATACTTGAGAGACCAACTAAATATAAGCAAGATATTGATTGTAGATCTGGATGTTCACCATGGAAACGGTACACAGCAGGCCTTTTATGCTGACCCCAGCATCCTGTACATTTCACTCCATCGCTATGATGAAGGGAACTTTTTCCCTGGCAGTGGAGCCCCGAATGAGGTTGGAGTAGGTCTGGGAGAAGGCTACAATGTAAACATTGCCTGGACAGGTGGCCTCGACCCCCCTATGGGAGATGTTGAGTACCTTGAAGCGTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTTGGAGTAGGTCTGGGA
59.21
AGCTGTATTTCCTCCAGGCTG
59.79
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTTGGAGTAGGTCTGGGA
59.21
AGCTGTATTTCCTCCAGGCT
58.41
141
PCR template sequence:
AGGTTGGAGTAGGTCTGGGAGAAGGCTACAATGTAAACATTGCCTGGACAGGTGGCCTCGACCCCCCTATGGGAGATGTTGAGTACCTTGAAGCGTTCAGCGAATTCAAGGTCGAAAAGCCAGCCTGGAGGAAATACAGCTTGTTCATTCTGAACATCACTCACTATTGTATGGCACCAGCCCCCTGGATGGACAGAAGC
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-205-5p(1), mmu-miR-204-5p(1), mmu-miR-203-3p(1), mmu-miR-138-5p(1), mmu-miR-26b-5p(1), mmu-miR-425-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
TTGAAGCGTTCAGCGAATTCAAGGTC
siRNA sets
CTTGAATTCGCTGAACGCT, CCTTGAATTCGCTGAACGC, TTGAATTCGCTGAACGCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHDAC9_641_ORF_1
1.0806
0.134444822
0.765480525
540
ORF sequence:
ATGGCTGTTGGCTGTGTCATTGAGCTGGCTTCCAAAGTGGCCTCAGGAGAGCTGAAGAATGGGTTTGCCGTTGTGAGGCCCCCAGGCCATCATGCGGAAGAGTCTGCAGCCATGGGGTTCTGCTTTTTTAATTCAGTTGCAATTACCGCCAAATACTTGAGAGACCAACTAAATATAAGCAAGATATTGATTGTAGATCTGGATGTTCACCATGGAAACGGTACACAGCAGGCCTTTTATGCTGACCCCAGCATCCTGTACATTTCACTCCATCGCTATGATGAAGGGAACTTTTTCCCTGGCAGTGGAGCCCCGAATGAGGTTGGAGTAGGTCTGGGAGAAGGCTACAATGTAAACATTGCCTGGACAGGTGGCCTCGACCCCCCTATGGGAGATGTTGAGTACCTTGAAGCGTTCAGCGAATTCAAGGTCGAAAAGCCAGCCTGGAGGAAATACAGCTTGTTCATTCTGAACATCACTCACTATTGTATGGCACCAGCCCCCTGGATGGACAGAAGCTGGACCCCAGGACACTCTTAG
Peptide sequence:
MAVGCVIELASKVASGELKNGFAVVRPPGHHAEESAAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYISLHRYDEGNFFPGSGAPNEVGVGLGEGYNVNIAWTGGLDPPMGDVEYLEAFSEFKVEKPAWRKYSLFILNITHYCMAPAPWMDRSWTPGHS
IRESfinder result
IRESfinder score
0.500457872
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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