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mmu_circRgl1_495
Basic information of circular RNA
PanCircBase ID:
mmu_circRgl1_495
mm39_Chr. Position ID:
chr1|152415687|152428387|-
Gene name:
Rgl1
Transcript:
ENSMUST00000111859.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,10,9,8
Exon/intron offsets:
0,4414,9130,12484
Genomic length:
12700
Exon/intron sizes in nt:
9,08,51,04,216
Flanking exon/introns:
chr1:152413568-152415687|chr1:152428387-152430046
Splice length:
495
Other database IDs:
circAtlas: mmu-Rgl1_0008
Human Ortholog IDs:
Mature spliced Sequence:
CAACTATTCAAGAAGGTAGTGCCTCACCATTGCCTGGGCTGTATTTGGTCTCAGCGGGATAAAAAGGAAAACAAGCATTTGGCTCCTACGATCCGTGCCACCATCTCTCAGTTTAATACGCTCACCAAGTGTGTTGTCAGCACCGTCCTGGGGAGCAAGGAACTCAAAACTCAGCAGCGAGCCAGAGTCATCGAGAAGTGGATCAACATTGCTCACGAATGTAGAATCCTGAAGAATTTTTCCTCCTTGAGGGCCATCGTTTCCGCACTGCAGTCTAATTCCATCTATCGGTTGAAAAAGGCTTGGGCTGCTGTCCCGAAGGACAGAATGCTGATGTTTGAAGAACTTTCAGATATCTTCTCTGATCACAATAACCATCTAACCAGTCGGGAGCTACTAATGAAGGAAGGAACTTCAAAATTTGCAAACCTGGACAGCAGCGTGAAAGAAAACCAGAAGCGGACCCAGAGGCGCCTGCAACTGCAGAAGGATATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGACAGCAGCGTGAAAGAA
60.18
GCACGGATCGTAGGAGCC
59.97
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGACAGCAGCGTGAAAGAA
60.18
GGCACGGATCGTAGGAGC
59.97
164
PCR template sequence:
ACTAATGAAGGAAGGAACTTCAAAATTTGCAAACCTGGACAGCAGCGTGAAAGAAAACCAGAAGCGGACCCAGAGGCGCCTGCAACTGCAGAAGGATATGCAACTATTCAAGAAGGTAGTGCCTCACCATTGCCTGGGCTGTATTTGGTCTCAGCGGGATAAAAAGGAAAACAAGCATTTGGCTCCTACGATCCGTGCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-326-3p(1), mmu-miR-383-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGAAGGATATGCAACTATTCAAGA
siRNA sets
CTTGAATAGTTGCATATCC, TTGAATAGTTGCATATCCT, GAATAGTTGCATATCCTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRGL1_495_ORF_1
1.2425
0.301836649
0.955334931
663
ORF sequence:
ATGCTGATGTTTGAAGAACTTTCAGATATCTTCTCTGATCACAATAACCATCTAACCAGTCGGGAGCTACTAATGAAGGAAGGAACTTCAAAATTTGCAAACCTGGACAGCAGCGTGAAAGAAAACCAGAAGCGGACCCAGAGGCGCCTGCAACTGCAGAAGGATATGCAACTATTCAAGAAGGTAGTGCCTCACCATTGCCTGGGCTGTATTTGGTCTCAGCGGGATAAAAAGGAAAACAAGCATTTGGCTCCTACGATCCGTGCCACCATCTCTCAGTTTAATACGCTCACCAAGTGTGTTGTCAGCACCGTCCTGGGGAGCAAGGAACTCAAAACTCAGCAGCGAGCCAGAGTCATCGAGAAGTGGATCAACATTGCTCACGAATGTAGAATCCTGAAGAATTTTTCCTCCTTGAGGGCCATCGTTTCCGCACTGCAGTCTAATTCCATCTATCGGTTGAAAAAGGCTTGGGCTGCTGTCCCGAAGGACAGAATGCTGATGTTTGAAGAACTTTCAGATATCTTCTCTGATCACAATAACCATCTAACCAGTCGGGAGCTACTAATGAAGGAAGGAACTTCAAAATTTGCAAACCTGGACAGCAGCGTGAAAGAAAACCAGAAGCGGACCCAGAGGCGCCTGCAACTGCAGAAGGATATG
Peptide sequence:
MLMFEELSDIFSDHNNHLTSRELLMKEGTSKFANLDSSVKENQKRTQRRLQLQKDMQLFKKVVPHHCLGCIWSQRDKKENKHLAPTIRATISQFNTLTKCVVSTVLGSKELKTQQRARVIEKWINIAHECRILKNFSSLRAIVSALQSNSIYRLKKAWAAVPKDRMLMFEELSDIFSDHNNHLTSRELLMKEGTSKFANLDSSVKENQKRTQRRLQLQKDM
IRESfinder result
IRESfinder score
0.678192539
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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