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mmu_circGsap_544
Basic information of circular RNA
PanCircBase ID:
mmu_circGsap_544
mm39_Chr. Position ID:
chr5|21474899|21486600|+
Gene name:
Gsap
Transcript:
ENSMUST00000036031.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
20,21,22,23,24,25,26
Exon/intron offsets:
0,654,1315,3080,8143,11094,11606
Genomic length:
11701
Exon/intron sizes in nt:
129,59,32,62,96,71,95
Flanking exon/introns:
chr5:21462921-21474899|chr5:21486600-21492674
Splice length:
544
Other database IDs:
CIRCpedia: MMU_CIRCpedia_219332, circAtlas: mmu-Gsap_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_59007
Human Ortholog IDs:
Mature spliced Sequence:
GTCTACGGCTTGAAGGGGTACTGGGCAAAGCTGAACTCCAACCTTGAGTACATTAAGTATACAAAACCTCACTTGCACTATCACAACAGCGTCGTGAGGAGGGAATGGCATAACCTGATCTCTGAAGAGAGAACGGGCAAAAGGAGATCCACAATGTACGTGAGGAACATTCTTGAAAACGCAATGAAGGTGATTGCTAGCATGGAAACGAGGACACTGGAGCCAAGATTAATACCATTCTTACAAGAGGAAGACCGGCACCAGAGGCTGCTCATGGGCTTGATGGTGTCTGAGCTAAGAGACCACCTACTGAGACACCTGCAGGGTGTAGAAAAGAAGAAAATTGAACAGATGGTTCTGGACTACATTTCAAAACTGCTGGATCTCATTTGGTGCTTGCTGGAAACCAGTTGGAGGAAACACAGTATGCATCCATTGGTTCTCCACCTCAATAGCCATTGCAGTGCTGCAGATTTTGAAGTCTTTCATCTCATGACCAGGATTTTGGATGCTGCTAGCAGTTTGTGTTTGCCTCTGCCTCCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCAATAGCCATTGCAGTGC
59.93
GTTGGAGTTCAGCTTTGCCC
59.68
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCAATAGCCATTGCAGTGC
59.93
GGTTGGAGTTCAGCTTTGCC
59.68
141
PCR template sequence:
CACCTCAATAGCCATTGCAGTGCTGCAGATTTTGAAGTCTTTCATCTCATGACCAGGATTTTGGATGCTGCTAGCAGTTTGTGTTTGCCTCTGCCTCCTGGTCTACGGCTTGAAGGGGTACTGGGCAAAGCTGAACTCCAACCTTGAGTACATTAAGTATACAAAACCTCACTTGCACTATCACAACAGCGTCGTGAGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-7b-5p(1), mmu-miR-103-3p(1), mmu-miR-322-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-709(1), mmu-miR-203-3p(1), mmu-miR-143-3p(1), mmu-miR-149-5p(1), mmu-miR-301b-3p(1), mmu-miR-107-3p(1), mmu-miR-301a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTCTGCCTCCTGGTCTACGGCTTGA
siRNA sets
GTAGACCAGGAGGCAGAGG, CAAGCCGTAGACCAGGAGG, TCAAGCCGTAGACCAGGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGSAP_544_ORF_1
1.1714
0.093254446
0.812964853
579
ORF sequence:
ATGCTGCTAGCAGTTTGTGTTTGCCTCTGCCTCCTGGTCTACGGCTTGAAGGGGTACTGGGCAAAGCTGAACTCCAACCTTGAGTACATTAAGTATACAAAACCTCACTTGCACTATCACAACAGCGTCGTGAGGAGGGAATGGCATAACCTGATCTCTGAAGAGAGAACGGGCAAAAGGAGATCCACAATGTACGTGAGGAACATTCTTGAAAACGCAATGAAGGTGATTGCTAGCATGGAAACGAGGACACTGGAGCCAAGATTAATACCATTCTTACAAGAGGAAGACCGGCACCAGAGGCTGCTCATGGGCTTGATGGTGTCTGAGCTAAGAGACCACCTACTGAGACACCTGCAGGGTGTAGAAAAGAAGAAAATTGAACAGATGGTTCTGGACTACATTTCAAAACTGCTGGATCTCATTTGGTGCTTGCTGGAAACCAGTTGGAGGAAACACAGTATGCATCCATTGGTTCTCCACCTCAATAGCCATTGCAGTGCTGCAGATTTTGAAGTCTTTCATCTCATGACCAGGATTTTGGATGCTGCTAGCAGTTTGTGTTTGCCTCTGCCTCCT
Peptide sequence:
MLLAVCVCLCLLVYGLKGYWAKLNSNLEYIKYTKPHLHYHNSVVRREWHNLISEERTGKRRSTMYVRNILENAMKVIASMETRTLEPRLIPFLQEEDRHQRLLMGLMVSELRDHLLRHLQGVEKKKIEQMVLDYISKLLDLIWCLLETSWRKHSMHPLVLHLNSHCSAADFEVFHLMTRILDAASSLCLPLPP
IRESfinder result
IRESfinder score
0.52873955
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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