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mmu_circHerc1_369
Basic information of circular RNA
PanCircBase ID:
mmu_circHerc1_369
mm39_Chr. Position ID:
chr9|66295442|66298769|+
Gene name:
Herc1
Transcript:
ENSMUST00000042824.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,7,8
Exon/intron offsets:
0,594,3199
Genomic length:
3327
Exon/intron sizes in nt:
9,71,44,128
Flanking exon/introns:
chr9:66294192-66295442|chr9:66298769-66301941
Splice length:
369
Other database IDs:
CIRCpedia: MMU_CIRCpedia_26503, circAtlas: mmu-Herc1_0050
Human Ortholog IDs:
Mature spliced Sequence:
GTAGTAGTTTGTGTATCAGCTGGATACAGACATAGTGCTGCTGTCACAGAGGATGGTGAATTATATACTTGGGGTGAAGGAGACTTCGGAAGATTAGGTCATGGTGACAGTAACAGCCGTAACATTCCAACATTAGTAAAAGACATTAGCAATGTAGGAGAGGTTTCTTGTGGAAGTTCACATACGATTGCTTTGTCCAAAGATGGAAGAACTGTGTGGTCTTTTGGAGGAGGTGACAATGGCAAACTTGGCCATGGTGATACCAACAGAGTATATAAACCTAAAGTTATTGAAGCTTTACAAGGAATGTTTATTCGCAAAGTCTGTGCTGGGAGCCAATCTTCACTTGCTTTGACATCAACAGGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCGCAAAGTCTGTGCTGG
59.12
CGAAGTCTCCTTCACCCCAA
59.31
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCGCAAAGTCTGTGCTGG
59.12
TCCGAAGTCTCCTTCACCCC
60.9
147
PCR template sequence:
AGTATATAAACCTAAAGTTATTGAAGCTTTACAAGGAATGTTTATTCGCAAAGTCTGTGCTGGGAGCCAATCTTCACTTGCTTTGACATCAACAGGGCAGGTAGTAGTTTGTGTATCAGCTGGATACAGACATAGTGCTGCTGTCACAGAGGATGGTGAATTATATACTTGGGGTGAAGGAGACTTCGGAAGATTAGGTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCAACAGGGCAGGTAGTAGTTTGTG
siRNA sets
CACAAACTACTACCTGCCC, AAACTACTACCTGCCCTGT, CTACTACCTGCCCTGTTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHERC1_369_ORF_1
1.0695
-0.103167109
0.359897303
432
ORF sequence:
ATGTTTATTCGCAAAGTCTGTGCTGGGAGCCAATCTTCACTTGCTTTGACATCAACAGGGCAGGTAGTAGTTTGTGTATCAGCTGGATACAGACATAGTGCTGCTGTCACAGAGGATGGTGAATTATATACTTGGGGTGAAGGAGACTTCGGAAGATTAGGTCATGGTGACAGTAACAGCCGTAACATTCCAACATTAGTAAAAGACATTAGCAATGTAGGAGAGGTTTCTTGTGGAAGTTCACATACGATTGCTTTGTCCAAAGATGGAAGAACTGTGTGGTCTTTTGGAGGAGGTGACAATGGCAAACTTGGCCATGGTGATACCAACAGAGTATATAAACCTAAAGTTATTGAAGCTTTACAAGGAATGTTTATTCGCAAAGTCTGTGCTGGGAGCCAATCTTCACTTGCTTTGACATCAACAGGGCAG
Peptide sequence:
MFIRKVCAGSQSSLALTSTGQVVVCVSAGYRHSAAVTEDGELYTWGEGDFGRLGHGDSNSRNIPTLVKDISNVGEVSCGSSHTIALSKDGRTVWSFGGGDNGKLGHGDTNRVYKPKVIEALQGMFIRKVCAGSQSSLALTSTGQ
IRESfinder result
IRESfinder score
0.637445999
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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