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mmu_circHdac5_470
Basic information of circular RNA
PanCircBase ID:
mmu_circHdac5_470
mm39_Chr. Position ID:
chr11|102088164|102090299|-
Gene name:
Hdac5
Transcript:
ENSMUST00000107151.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
20,19,18,17,16
Exon/intron offsets:
0,327,1458,1666,2027
Genomic length:
2135
Exon/intron sizes in nt:
9,81,20,88,56,108
Flanking exon/introns:
chr11:102088003-102088164|chr11:102090299-102090461
Splice length:
470
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGGACAGTGACACGGTGTGGAATGAGATGCACTCCTCAAGTGCCGTGCGAATGGCAGTGGGCTGCCTGGTGGAGCTGGCCTTCAAGGTGGCTGCAGGAGAGCTCAAGAATGGATTTGCTATCATCCGGCCCCCAGGACACCATGCTGAGGAGTCCACAGCCATGGGATTCTGCTTCTTCAACTCCGTAGCCATCACAGCTAAACTCCTGCAGCAGAAGCTGAGCGTGGGCAAGGTCCTCATCGTGGACTGGGATATTCACCATGGCAACGGCACCCAGCAAGCATTCTACAACGATCCCTCTGTGCTCTACATCTCCCTGCATCGCTACGACAACGGGAACTTCTTTCCAGGCTCTGGGGCTCCTGAAGAGGTTGGTGGAGGGCCAGGTGTGGGGTACAACGTAAATGTGGCGTGGACAGGAGGTGTGGATCCCCCCATTGGAGATGTGGAATACCTGACAGCCTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTAAATGTGGCGTGGACA
60.25
CTCCTGCAGCCACCTTGAAG
60.96
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGACAGGAGGTGTGGATC
59.75
CTCCTGCAGCCACCTTGAAG
60.96
157
PCR template sequence:
AGGTTGGTGGAGGGCCAGGTGTGGGGTACAACGTAAATGTGGCGTGGACAGGAGGTGTGGATCCCCCCATTGGAGATGTGGAATACCTGACAGCCTTCAGGTGGACAGTGACACGGTGTGGAATGAGATGCACTCCTCAAGTGCCGTGCGAATGGCAGTGGGCTGCCTGGTGGAGCTGGCCTTCAAGGTGGCTGCAGGAG
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-328-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGACAGCCTTCAGGTGGACAGTGACA
siRNA sets
TCACTGTCCACCTGAAGGC, CACTGTCCACCTGAAGGCT, GTCACTGTCCACCTGAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHDAC5_470_ORF_1
0.8292
0.297608961
0.887118085
633
ORF sequence:
ATGCACTCCTCAAGTGCCGTGCGAATGGCAGTGGGCTGCCTGGTGGAGCTGGCCTTCAAGGTGGCTGCAGGAGAGCTCAAGAATGGATTTGCTATCATCCGGCCCCCAGGACACCATGCTGAGGAGTCCACAGCCATGGGATTCTGCTTCTTCAACTCCGTAGCCATCACAGCTAAACTCCTGCAGCAGAAGCTGAGCGTGGGCAAGGTCCTCATCGTGGACTGGGATATTCACCATGGCAACGGCACCCAGCAAGCATTCTACAACGATCCCTCTGTGCTCTACATCTCCCTGCATCGCTACGACAACGGGAACTTCTTTCCAGGCTCTGGGGCTCCTGAAGAGGTTGGTGGAGGGCCAGGTGTGGGGTACAACGTAAATGTGGCGTGGACAGGAGGTGTGGATCCCCCCATTGGAGATGTGGAATACCTGACAGCCTTCAGGTGGACAGTGACACGGTGTGGAATGAGATGCACTCCTCAAGTGCCGTGCGAATGGCAGTGGGCTGCCTGGTGGAGCTGGCCTTCAAGGTGGCTGCAGGAGAGCTCAAGAATGGATTTGCTATCATCCGGCCCCCAGGACACCATGCTGAGGAGTCCACAGCCATGGGATTCTGCTTCTTCAACTCCGTAG
Peptide sequence:
MHSSSAVRMAVGCLVELAFKVAAGELKNGFAIIRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLSVGKVLIVDWDIHHGNGTQQAFYNDPSVLYISLHRYDNGNFFPGSGAPEEVGGGPGVGYNVNVAWTGGVDPPIGDVEYLTAFRWTVTRCGMRCTPQVPCEWQWAAWWSWPSRWLQESSRMDLLSSGPQDTMLRSPQPWDSASSTP
IRESfinder result
IRESfinder score
0.356004082
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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