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mmu_ciHdac4_797
Basic information of circular RNA
PanCircBase ID:
mmu_ciHdac4_797
mm39_Chr. Position ID:
chr1|91861526|91862323|-
Gene name:
Hdac4
Transcript:
ENSMUST00000097644.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
25
Exon/intron offsets:
0
Genomic length:
797
Exon/intron sizes in nt:
797
Flanking exon/introns:
chr1:91861519-91862323
Splice length:
797
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTGGCTGGCCAAGTCATCGTGGGGACCCAGGGCAGAAGCAGAAGGCCTCACCTCCCCTGGCATGTGATCAGCTAGTAGAGACTCCCTGAACCAGGTCCTACTGTACAGGGCTTCGAAAGAATCTGGGCACCAATAGTCTCAAACTACTTGGTTCAGTTGCATAGAACTTACTTGGACTGAAAAATCTATGTCATGCTAGAGGTACCTAGCACAGGGTAGAACTCATCCCCCATTCAGTCAACAAATCCCAGGCAACAGGTACACAGCCAGATACCCACACATGGCCCTGCCTCAGGTAAAACCTGCTACTCCTTGCCTGGCTCTCTGATATGCTATCCTGGCACATAAGCTCACAAAGATGATGCACACCTGAAGGCTTCACCCAGGTACCTACTGACCATTTAGTTCTGCCTTCAAAACTGTTTCACCTAATGCCCCTAACTCTAGAAAGCTGCTTCAGCGGGGCTCCAAGTGCTGAACCTGGATGTGATCTATCCACAGCACCTATAAGGCTCCAGGTAGGAAACTCCCTAAGTCTGGATGCCAGCAAGTCTCCATGTGTCTGCTCCCAGAATTTCTGGTCACCCACAGCAAGGCAGAATCCCACAGACGTGGAGAGCCAGGTTCCACAACAGTTCACAGCCCTGTGTTCAGGTGACCTGTAATGCAGAAATTACACCACAAGGGCCTGTGAGGGCAGTGCCAGCCAGCACTCTTCAGAAAGGCGCTTTTCAGACACAAGTGAGTCTCCCATTAACCTGCAGAAGTGGGGAGTCACTGAGTGTTTCCCTCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGCCAGCACTCTTCAGAA
59.96
CTGATCACATGCCAGGGGAG
60.18
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGCCAGCACTCTTCAGAA
59.96
TAGCTGATCACATGCCAGGG
59.53
169
PCR template sequence:
AGGGCAGTGCCAGCCAGCACTCTTCAGAAAGGCGCTTTTCAGACACAAGTGAGTCTCCCATTAACCTGCAGAAGTGGGGAGTCACTGAGTGTTTCCCTCTGTAAGTGGCTGGCCAAGTCATCGTGGGGACCCAGGGCAGAAGCAGAAGGCCTCACCTCCCCTGGCATGTGATCAGCTAGTAGAGACTCCCTGAACCAGGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-196a-5p(1), mmu-miR-709(1), mmu-miR-149-5p(1), mmu-miR-324-3p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-490-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGTGTTTCCCTCTGTAAGTGGCTGGC
siRNA sets
ACTTACAGAGGGAAACACT,CACTTACAGAGGGAAACAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIHDAC4_797_ORF_1
0.6372
-0.065574104
0.116557945
324
ORF sequence:
ATGCCAGCAAGTCTCCATGTGTCTGCTCCCAGAATTTCTGGTCACCCACAGCAAGGCAGAATCCCACAGACGTGGAGAGCCAGGTTCCACAACAGTTCACAGCCCTGTGTTCAGGTGACCTGTAATGCAGAAATTACACCACAAGGGCCTGTGAGGGCAGTGCCAGCCAGCACTCTTCAGAAAGGCGCTTTTCAGACACAAGTGAGTCTCCCATTAACCTGCAGAAGTGGGGAGTCACTGAGTGTTTCCCTCTGTAAGTGGCTGGCCAAGTCATCGTGGGGACCCAGGGCAGAAGCAGAAGGCCTCACCTCCCCTGGCATGTGA
Peptide sequence:
MPASLHVSAPRISGHPQQGRIPQTWRARFHNSSQPCVQVTCNAEITPQGPVRAVPASTLQKGAFQTQVSLPLTCRSGESLSVSLCKWLAKSSWGPRAEAEGLTSPGM
IRESfinder result
IRESfinder score
0.661839446
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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