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mmu_circPms1_483
Basic information of circular RNA
PanCircBase ID:
mmu_circPms1_483
mm39_Chr. Position ID:
chr1|53306986|53329582|-
Gene name:
Pms1
Transcript:
ENSMUST00000135246.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,7242,14113,22551
Genomic length:
22596
Exon/intron sizes in nt:
103,183,152,45
Flanking exon/introns:
chr1:53295951-53306986|chr1:53329582-53336044
Splice length:
483
Other database IDs:
CIRCpedia: MMU_CIRCpedia_37761, circAtlas: mmu-Pms1_0012
Human Ortholog IDs:
Mature spliced Sequence:
TGACTCAGTGAGCTGATATGGTGAGCTTGGACCAGGACATTTAAGCTACTCAGGTGCAAGCTAGGATGAAACAGTTGCCTGCAGCAACAGTTCGCCTCCTGTCCAGTTCTCAGACAATCACGTCAGTGGTCAGCGTTGTGAAAGAGCTCATTGAAAACTCCTTGGATGCCGGAGCCACCAGCATTGAAGTTAAACTGGAGAACTATGGATTTGATAAAATTGAGATTCGGGACAATGGTGAGGGCATCAAGGCTGTAGATGTCCCTGTAATGGCAGTGAAGTACTACACCTCGAAGATCAGCAGTCATGAAGACCTTGGAAATCTGACAACTTATGGTTTTCGTGGTGAAGCCTTGGGGTCAATATGTAATGTTGCGGAGGTGGTAGTTACAACAAGGACATCTGCTGATGACTTTAGCACTCAGTATGTTTTAGATGGCAGTGGCCACATACTTTCTCAGAAGCCTTCACATCTTGGTCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGTGGCCACATACTTTCTC
59.26
AGGAGGCGAACTGTTGCTG
60.3
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGTGGCCACATACTTTCT
58.17
AGGAGGCGAACTGTTGCTG
60.3
145
PCR template sequence:
GTAGTTACAACAAGGACATCTGCTGATGACTTTAGCACTCAGTATGTTTTAGATGGCAGTGGCCACATACTTTCTCAGAAGCCTTCACATCTTGGTCAAGTGACTCAGTGAGCTGATATGGTGAGCTTGGACCAGGACATTTAAGCTACTCAGGTGCAAGCTAGGATGAAACAGTTGCCTGCAGCAACAGTTCGCCTCCT
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-673-5p(1), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CATCTTGGTCAAGTGACTCAGTGAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPMS1_483_ORF_1
1.0942
0.208933168
0.672425182
429
ORF sequence:
ATGAAACAGTTGCCTGCAGCAACAGTTCGCCTCCTGTCCAGTTCTCAGACAATCACGTCAGTGGTCAGCGTTGTGAAAGAGCTCATTGAAAACTCCTTGGATGCCGGAGCCACCAGCATTGAAGTTAAACTGGAGAACTATGGATTTGATAAAATTGAGATTCGGGACAATGGTGAGGGCATCAAGGCTGTAGATGTCCCTGTAATGGCAGTGAAGTACTACACCTCGAAGATCAGCAGTCATGAAGACCTTGGAAATCTGACAACTTATGGTTTTCGTGGTGAAGCCTTGGGGTCAATATGTAATGTTGCGGAGGTGGTAGTTACAACAAGGACATCTGCTGATGACTTTAGCACTCAGTATGTTTTAGATGGCAGTGGCCACATACTTTCTCAGAAGCCTTCACATCTTGGTCAAGTGACTCAGTGA
Peptide sequence:
MKQLPAATVRLLSSSQTITSVVSVVKELIENSLDAGATSIEVKLENYGFDKIEIRDNGEGIKAVDVPVMAVKYYTSKISSHEDLGNLTTYGFRGEALGSICNVAEVVVTTRTSADDFSTQYVLDGSGHILSQKPSHLGQVTQ
IRESfinder result
IRESfinder score
0.411255009
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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