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mmu_circHgs_316
Basic information of circular RNA
PanCircBase ID:
mmu_circHgs_316
mm39_Chr. Position ID:
chr11|120370624|120371024|+
Gene name:
Hgs
Transcript:
ENSMUST00000106203.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
17,18
Exon/intron offsets:
0,225
Genomic length:
400
Exon/intron sizes in nt:
1,41,175
Flanking exon/introns:
chr11:120370551-120370624|chr11:120371024-120373355
Splice length:
316
Other database IDs:
CIRCpedia: MMU_CIRCpedia_5136, circAtlas: mmu-Hgs_0006
Human Ortholog IDs:
Mature spliced Sequence:
GAGTACCTGGAGGTGCAGAGACAGCTAGCTATCCAGCGCCTGCAGGAACAGGAGAAGGAACGGCAGATGCGTCTGGAGCAACAGAAGCAGACTGTCCAGATGCGCGCCCAGATGCCTGCCTTTCCCTTGCCTTATGCCCAGCTCCAGGCTATGCCCACGGCTGGGGGTGTACTCTACCAGCCCTCAGGCCCAACCAGCTTCCCTGCCACCTTCAGCCCAGCAGGCTCAGTAGAGGGCTCTCCGATGCATGGTGTGTATATGAGCCAGCCAGCCCCAGCCACTGGCCCCTACCCCAGCATGCCTGGCACAACAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCTCAGTAGAGGGCTCTC
60.11
TGCCGTTCCTTCTCCTGTTC
59.97
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCTCAGTAGAGGGCTCTC
60.11
CTGCCGTTCCTTCTCCTGTT
59.96
161
PCR template sequence:
CCAGCAGGCTCAGTAGAGGGCTCTCCGATGCATGGTGTGTATATGAGCCAGCCAGCCCCAGCCACTGGCCCCTACCCCAGCATGCCTGGCACAACAGCAGGAGTACCTGGAGGTGCAGAGACAGCTAGCTATCCAGCGCCTGCAGGAACAGGAGAAGGAACGGCAGATGCGTCTGGAGCAACAGAAGCAGACTGTCCAGA
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-149-5p(1), mmu-miR-370-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
GGCACAACAGCAGGAGTACCTGGAGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHGS_316_ORF_1
0.811
0.138936532
0.708544271
564
ORF sequence:
ATGCGTCTGGAGCAACAGAAGCAGACTGTCCAGATGCGCGCCCAGATGCCTGCCTTTCCCTTGCCTTATGCCCAGCTCCAGGCTATGCCCACGGCTGGGGGTGTACTCTACCAGCCCTCAGGCCCAACCAGCTTCCCTGCCACCTTCAGCCCAGCAGGCTCAGTAGAGGGCTCTCCGATGCATGGTGTGTATATGAGCCAGCCAGCCCCAGCCACTGGCCCCTACCCCAGCATGCCTGGCACAACAGCAGGAGTACCTGGAGGTGCAGAGACAGCTAGCTATCCAGCGCCTGCAGGAACAGGAGAAGGAACGGCAGATGCGTCTGGAGCAACAGAAGCAGACTGTCCAGATGCGCGCCCAGATGCCTGCCTTTCCCTTGCCTTATGCCCAGCTCCAGGCTATGCCCACGGCTGGGGGTGTACTCTACCAGCCCTCAGGCCCAACCAGCTTCCCTGCCACCTTCAGCCCAGCAGGCTCAGTAGAGGGCTCTCCGATGCATGGTGTGTATATGAGCCAGCCAGCCCCAGCCACTGGCCCCTACCCCAGCATGCCTGGCACAACAGC
Peptide sequence:
MRLEQQKQTVQMRAQMPAFPLPYAQLQAMPTAGGVLYQPSGPTSFPATFSPAGSVEGSPMHGVYMSQPAPATGPYPSMPGTTAGVPGGAETASYPAPAGTGEGTADASGATEADCPDARPDACLSLALCPAPGYAHGWGCTLPALRPNQLPCHLQPSRLSRGLSDAWCVYEPASPSHWPLPQHAWHNS
IRESfinder result
IRESfinder score
0.197270242
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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