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mmu_circRae1_380
Basic information of circular RNA
PanCircBase ID:
mmu_circRae1_380
mm39_Chr. Position ID:
chr2|172844451|172848760|+
Gene name:
Rae1
Transcript:
ENSMUST00000029013.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,848,2501,4222
Genomic length:
4309
Exon/intron sizes in nt:
95,105,93,87
Flanking exon/introns:
chr2:172842169-172844451|chr2:172848760-172849852
Splice length:
380
Other database IDs:
circAtlas: mmu-Rae1_0007
Human Ortholog IDs:
Mature spliced Sequence:
CCAACATGAGTCTGTTTGGATCAACCTCTGGATTTGGGACTGGTGGGACCAGCATGTTTGGGAGCACAACCACAGATAACCACAATCCAATGAAGGATATCGAAGTGACATCTTCTCCTGATGACAGCATCGGTTGTCTGTCTTTCAGCCCGCCAACTTTACCAGGCAACTTCCTTATTGCAGGATCATGGGCGAATGATGTTCGCTGCTGGGAAGTGCAGGACAGTGGGCAAACCATTCCAAAGGCCCAGCAGATGCACACGGGGCCAGTGCTTGACGTCTGCTGGAGTGATGATGGGAGCAAAGTATTCACAGCATCGTGTGACAAGACAGCCAAGATGTGGGACCTGAACAGCAACCAGGCCATTCAGATAGCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCATCGTGTGACAAGACAGC
59.84
TCTGTGGTTGTGCTCCCAAA
59.74
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCATCGTGTGACAAGACAGC
59.84
TGTGGTTGTGCTCCCAAACA
60.32
140
PCR template sequence:
CTGCTGGAGTGATGATGGGAGCAAAGTATTCACAGCATCGTGTGACAAGACAGCCAAGATGTGGGACCTGAACAGCAACCAGGCCATTCAGATAGCACAGCCAACATGAGTCTGTTTGGATCAACCTCTGGATTTGGGACTGGTGGGACCAGCATGTTTGGGAGCACAACCACAGATAACCACAATCCAATGAAGGATAT
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-150-5p(1), mmu-miR-503-5p(1), mmu-miR-149-5p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGATAGCACAGCCAACATGAGTCT
siRNA sets
ATGTTGGCTGTGCTATCTG, CATGTTGGCTGTGCTATCT, AGACTCATGTTGGCTGTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAE1_380_ORF_1
0.6337
0.197016296
0.376160588
384
ORF sequence:
ATGAGTCTGTTTGGATCAACCTCTGGATTTGGGACTGGTGGGACCAGCATGTTTGGGAGCACAACCACAGATAACCACAATCCAATGAAGGATATCGAAGTGACATCTTCTCCTGATGACAGCATCGGTTGTCTGTCTTTCAGCCCGCCAACTTTACCAGGCAACTTCCTTATTGCAGGATCATGGGCGAATGATGTTCGCTGCTGGGAAGTGCAGGACAGTGGGCAAACCATTCCAAAGGCCCAGCAGATGCACACGGGGCCAGTGCTTGACGTCTGCTGGAGTGATGATGGGAGCAAAGTATTCACAGCATCGTGTGACAAGACAGCCAAGATGTGGGACCTGAACAGCAACCAGGCCATTCAGATAGCACAGCCAACATGA
Peptide sequence:
MSLFGSTSGFGTGGTSMFGSTTTDNHNPMKDIEVTSSPDDSIGCLSFSPPTLPGNFLIAGSWANDVRCWEVQDSGQTIPKAQQMHTGPVLDVCWSDDGSKVFTASCDKTAKMWDLNSNQAIQIAQPT
IRESfinder result
IRESfinder score
0.529873771
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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