top of page
mmu_circScaf8_566
Basic information of circular RNA
PanCircBase ID:
mmu_circScaf8_566
mm39_Chr. Position ID:
chr17|3228429|3238020|+
Gene name:
Scaf8
Transcript:
ENSMUST00000076734.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,13,14,15
Exon/intron offsets:
0,6909,7606,9434
Genomic length:
9591
Exon/intron sizes in nt:
194,101,114,157
Flanking exon/introns:
chr17:3227998-3228429|chr17:3238020-3240421
Splice length:
566
Other database IDs:
circAtlas: mmu-Scaf8_0058
CIRCpedia: HSA_CIRCpedia_178224
Human Ortholog IDs:
Mature spliced Sequence:
GTCACCAAGAAAACGAAGGTCCAGGTCACGCTCTGGGTCCCGAAAGCGAAAGCACAGGAAGCGGTCTCGGTCCCACTCGAGAGAGAAAAAGAGAAAAGCCTCACGCTCCTACTCCAGTGAGCGCAGAGCCAGGGAAAGGGAGAAAGAGCGCCAGAAAAAGGGCTTGCCTCCTGTCAGGTCAAAAACACTAAGTGTATGCAGCACTACTCTCTGGGTTGGCCAAGTGGACAAGAAGGCTACACAGCAAGATTTAACCAACCTTTTTGAGGAATTTGGACAAATTGAATCCATTAATATGATTCCACCCAGGGGCTGTGCATATGTCTGCATGGTTCATCGACAAGATTCATTTCGGGCTCTTCAGAAACTGAGTTCAGGATCCTATAAAATTGGTTCCAAGGTCATTAAGATTGCCTGGGCTTTGAACAAAGGTGTAAAGACAGAATACAAACAGTTCTGGGATGTGGATCTTGGCGTCACATATATACCCTGGGAAAAAGTGAAAGTAGATGACTTGGATGGCTTTGCAGAGGGCGGCATGATTGATCAGGAGACTGTAAATGCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGGATGGCTTTGCAGAGG
59.18
TTCTCTCTCGAGTGGGACCG
60.68
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGACTTGGATGGCTTTGCAGA
60.2
TTCTCTCTCGAGTGGGACCG
60.68
143
PCR template sequence:
GATCTTGGCGTCACATATATACCCTGGGAAAAAGTGAAAGTAGATGACTTGGATGGCTTTGCAGAGGGCGGCATGATTGATCAGGAGACTGTAAATGCTGGTCACCAAGAAAACGAAGGTCCAGGTCACGCTCTGGGTCCCGAAAGCGAAAGCACAGGAAGCGGTCTCGGTCCCACTCGAGAGAGAAAAAGAGAAAAGCC
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-211-5p(1), mmu-miR-204-5p(1), mmu-miR-149-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGTAAATGCTGGTCACCAAGAAAA
siRNA sets
TTTTCTTGGTGACCAGCAT, TTTCTTGGTGACCAGCATT, CTTGGTGACCAGCATTTAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCAF8_566_ORF_1
0.9367
0.082273676
0.535609158
462
ORF sequence:
ATGATTCCACCCAGGGGCTGTGCATATGTCTGCATGGTTCATCGACAAGATTCATTTCGGGCTCTTCAGAAACTGAGTTCAGGATCCTATAAAATTGGTTCCAAGGTCATTAAGATTGCCTGGGCTTTGAACAAAGGTGTAAAGACAGAATACAAACAGTTCTGGGATGTGGATCTTGGCGTCACATATATACCCTGGGAAAAAGTGAAAGTAGATGACTTGGATGGCTTTGCAGAGGGCGGCATGATTGATCAGGAGACTGTAAATGCTGGTCACCAAGAAAACGAAGGTCCAGGTCACGCTCTGGGTCCCGAAAGCGAAAGCACAGGAAGCGGTCTCGGTCCCACTCGAGAGAGAAAAAGAGAAAAGCCTCACGCTCCTACTCCAGTGAGCGCAGAGCCAGGGAAAGGGAGAAAGAGCGCCAGAAAAAGGGCTTGCCTCCTGTCAGGTCAAAAACACTAA
Peptide sequence:
MIPPRGCAYVCMVHRQDSFRALQKLSSGSYKIGSKVIKIAWALNKGVKTEYKQFWDVDLGVTYIPWEKVKVDDLDGFAEGGMIDQETVNAGHQENEGPGHALGPESESTGSGLGPTRERKREKPHAPTPVSAEPGKGRKSARKRACLLSGQKH
IRESfinder result
IRESfinder score
0.487357106
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page