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mmu_circChm_365
Basic information of circular RNA
PanCircBase ID:
mmu_circChm_365
mm39_Chr. Position ID:
chrX|111962758|111981718|-
Gene name:
Chm
Transcript:
ENSMUST00000026607.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
13,12,11,10
Exon/intron offsets:
0,11785,16517,18855
Genomic length:
18960
Exon/intron sizes in nt:
99,97,64,105
Flanking exon/introns:
chrX:111957193-111962758|chrX:111981718-111989834
Splice length:
365
Other database IDs:
circAtlas: mmu-Chm_0014
Human Ortholog IDs:
Mature spliced Sequence:
ATGTAAAGCAATTGTAGATCAGTTTGGTCAAAGGATAATCTCTAAACATTTCGTTATTGAAGACAGTTACCTTTCTGAGAATACATGTTCCGGTGTACAGTACAGGCAAATTTCCAGGGCAGTCCTGATTACAGATGGATCAGTACTAAAACCCGATTCTGATCAACAGGTCTCCATTTTGACAGTGCCAGCAGAAGAGTCAGGAAGTTTTGCTGTTCGAGTCATTGAGTTATGCTCTTCAACAATGACATGCATGAAAGGCACATACTTGGTACATTTGACTTGCATGTCTTCTAAAACAGCAAGAGAAGATTTAGAACGAGTAGTCCAGAAATTGTTTACTCCATATACAGAAATCGAAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCATGTCTTCTAAAACAGCAAGA
59.18
ACACCGGAACATGTATTCTCAGA
59.49
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCATGTCTTCTAAAACAGCA
56.09
ACACCGGAACATGTATTCTCAGA
59.49
178
PCR template sequence:
TACTTGGTACATTTGACTTGCATGTCTTCTAAAACAGCAAGAGAAGATTTAGAACGAGTAGTCCAGAAATTGTTTACTCCATATACAGAAATCGAAGCAGATGTAAAGCAATTGTAGATCAGTTTGGTCAAAGGATAATCTCTAAACATTTCGTTATTGAAGACAGTTACCTTTCTGAGAATACATGTTCCGGTGTACAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-203-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAATCGAAGCAGATGTAAAGCAATT
siRNA sets
ATTGCTTTACATCTGCTTC, TTGCTTTACATCTGCTTCG, TTACATCTGCTTCGATTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHM_365_ORF_1
0.8833
-0.144017679
0.038771581
138
ORF sequence:
ATGACATGCATGAAAGGCACATACTTGGTACATTTGACTTGCATGTCTTCTAAAACAGCAAGAGAAGATTTAGAACGAGTAGTCCAGAAATTGTTTACTCCATATACAGAAATCGAAGCAGATGTAAAGCAATTGTAG
Peptide sequence:
MTCMKGTYLVHLTCMSSKTAREDLERVVQKLFTPYTEIEADVKQL
IRESfinder result
IRESfinder score
0.657467221
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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