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mmu_circChn1_491
Basic information of circular RNA
PanCircBase ID:
mmu_circChn1_491
mm39_Chr. Position ID:
chr2|73509958|73546763|-
Gene name:
Chn1
Transcript:
ENSMUST00000112024.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,27304,30840,36749
Genomic length:
36805
Exon/intron sizes in nt:
289,114,32,56
Flanking exon/introns:
chr2:73490101-73509958|chr2:73546763-73551746
Splice length:
491
Other database IDs:
circAtlas: mmu-Chn1_0015
circAtlas: hsa-CHN1_0011, CIRCpedia: HSA_CIRCpedia_135081
Human Ortholog IDs:
Mature spliced Sequence:
TATACCAGCTGCAGCAGGAAGCCCCTCACCCTCGAAGGGTCACCTGCACTTGTGAGGTAGAAAACAGACCAAAGTATTATGGAAGAGAGTATCATGGCATGATCTCTAGAGAAGAGACTGACCAGCTCCTGAGTGTGGCTGAGGGGAGCTACCTCATCCGTGAGAGCCAGCGGCAGCCAGGAACGTACACTTTGGCTTTAAGATTTGGAAGTCAGACCAGAAACTTCAGGCTGTACTACGATGGAAAGCACTTTGTTGGGGAGAAACGCTTTGAGTCCATCCACGATCTGGTGACTGATGGCTTGATTACTCTCTATATTGAAACCAAGGCAGCAGAATACATTGCCAAGATGACGATAAACCCAATTTATGAGCACATAGGATACACAACCTTAAACAGAGAGCCAGCATACAAACAGCACATGGCAGTCCTGAAAGAGACACATGATGAGAAAGAGGCTACAGGCCAGGATGGGGTATCAGAGAAAAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGCATACAAACAGCACA
59.4
ACAAGTGCAGGTGACCCTTC
60.18
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGCATACAAACAGCACA
59.4
ACCTCACAAGTGCAGGTGAC
60.18
146
PCR template sequence:
CTTAAACAGAGAGCCAGCATACAAACAGCACATGGCAGTCCTGAAAGAGACACATGATGAGAAAGAGGCTACAGGCCAGGATGGGGTATCAGAGAAAAGGTATACCAGCTGCAGCAGGAAGCCCCTCACCCTCGAAGGGTCACCTGCACTTGTGAGGTAGAAAACAGACCAAAGTATTATGGAAGAGAGTATCATGGCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-34c-5p(1), mmu-miR-106b-5p(1), mmu-miR-149-5p(1), mmu-miR-182-5p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-369-3p(1), mmu-miR-452-3p(1), mmu-miR-697(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
ATCAGAGAAAAGGTATACCAGCTGCA
siRNA sets
CTGGTATACCTTTTCTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHN1_491_ORF_1
0.8502
0.224973918
0.623352
453
ORF sequence:
ATGATCTCTAGAGAAGAGACTGACCAGCTCCTGAGTGTGGCTGAGGGGAGCTACCTCATCCGTGAGAGCCAGCGGCAGCCAGGAACGTACACTTTGGCTTTAAGATTTGGAAGTCAGACCAGAAACTTCAGGCTGTACTACGATGGAAAGCACTTTGTTGGGGAGAAACGCTTTGAGTCCATCCACGATCTGGTGACTGATGGCTTGATTACTCTCTATATTGAAACCAAGGCAGCAGAATACATTGCCAAGATGACGATAAACCCAATTTATGAGCACATAGGATACACAACCTTAAACAGAGAGCCAGCATACAAACAGCACATGGCAGTCCTGAAAGAGACACATGATGAGAAAGAGGCTACAGGCCAGGATGGGGTATCAGAGAAAAGGTATACCAGCTGCAGCAGGAAGCCCCTCACCCTCGAAGGGTCACCTGCACTTGTGAGGTAG
Peptide sequence:
MISREETDQLLSVAEGSYLIRESQRQPGTYTLALRFGSQTRNFRLYYDGKHFVGEKRFESIHDLVTDGLITLYIETKAAEYIAKMTINPIYEHIGYTTLNREPAYKQHMAVLKETHDEKEATGQDGVSEKRYTSCSRKPLTLEGSPALVR
IRESfinder result
IRESfinder score
0.407059493
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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