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mmu_circScly_395
Basic information of circular RNA
PanCircBase ID:
mmu_circScly_395
mm39_Chr. Position ID:
chr1|91228249|91233176|+
Gene name:
Scly
Transcript:
ENSMUST00000027532.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,2241,4746
Genomic length:
4927
Exon/intron sizes in nt:
11,31,01,181
Flanking exon/introns:
chr1:91226170-91228249|chr1:91233176-91236035
Splice length:
395
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34038
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_94005
Human Ortholog IDs:
Mature spliced Sequence:
GAAGGTCTATATGGACTATAATGCCACCACACCTCTAGAGCCCGAAGTCATCCAGGCTGTGACAGAGGCCATGAAGGAAGCCTGGGGAAACCCCAGCAGCTCCTATGTGTCAGGTAGGAAGGCCAAGGACATTATAAATGCAGCTCGAGCGAGCCTGGCCAAGATGATAGGTGGAAAGCCCCAGGACATCATCTTCACTTCTGGGGGCACCGAGTCAAATAATTTAGTAATCCACTCTATGGTAAGATGCTTCCATGAACAGCAGACCCTGAAGGGGAACATGGTTGACCAGCACAGCCCAGAAGAGGGGACCAGGCCCCATTTTATCACTTGCACAGTGGAACACGACTCCATCCGGCTGCCCCTGGAGCACCTGGTGGAAAATCAAATGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACCAGGCCCCATTTTAT
59.74
GCTTCCTTCATGGCCTCTGT
60.03
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACCAGGCCCCATTTTAT
59.74
CCTCTGTCACAGCCTGGATG
60.11
156
PCR template sequence:
AGCCCAGAAGAGGGGACCAGGCCCCATTTTATCACTTGCACAGTGGAACACGACTCCATCCGGCTGCCCCTGGAGCACCTGGTGGAAAATCAAATGGCAGGAAGGTCTATATGGACTATAATGCCACCACACCTCTAGAGCCCGAAGTCATCCAGGCTGTGACAGAGGCCATGAAGGAAGCCTGGGGAAACCCCAGCAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-130a-3p(1), mmu-miR-130b-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATCAAATGGCAGGAAGGTCTATATG
siRNA sets
CATATAGACCTTCCTGCCA, ATATAGACCTTCCTGCCAT, TAGACCTTCCTGCCATTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCLY_395_ORF_1
1.0985
0.242250094
0.69512758
423
ORF sequence:
ATGGACTATAATGCCACCACACCTCTAGAGCCCGAAGTCATCCAGGCTGTGACAGAGGCCATGAAGGAAGCCTGGGGAAACCCCAGCAGCTCCTATGTGTCAGGTAGGAAGGCCAAGGACATTATAAATGCAGCTCGAGCGAGCCTGGCCAAGATGATAGGTGGAAAGCCCCAGGACATCATCTTCACTTCTGGGGGCACCGAGTCAAATAATTTAGTAATCCACTCTATGGTAAGATGCTTCCATGAACAGCAGACCCTGAAGGGGAACATGGTTGACCAGCACAGCCCAGAAGAGGGGACCAGGCCCCATTTTATCACTTGCACAGTGGAACACGACTCCATCCGGCTGCCCCTGGAGCACCTGGTGGAAAATCAAATGGCAGGAAGGTCTATATGGACTATAATGCCACCACACCTCTAG
Peptide sequence:
MDYNATTPLEPEVIQAVTEAMKEAWGNPSSSYVSGRKAKDIINAARASLAKMIGGKPQDIIFTSGGTESNNLVIHSMVRCFHEQQTLKGNMVDQHSPEEGTRPHFITCTVEHDSIRLPLEHLVENQMAGRSIWTIMPPHL
IRESfinder result
IRESfinder score
0.394121716
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
RPF, cORF, MS
mmu_circScly_001
Evidence
Peptide sequence:
MDYNATTPLEPEVIQAVTEAMKEAWGNPSSSYVSGRKAKDIINAARASLAKMIGGKPQDIIFTSGGTESNNLVIHSMVRCFHEQQTLKGNMVDQHSPEEGTRPHFITCTVEHDSIRLPLEHLVENQMAGRSIWTIMPPHL*
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