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mmu_circSerinc3_274
Basic information of circular RNA
PanCircBase ID:
mmu_circSerinc3_274
mm39_Chr. Position ID:
chr2|163476354|163478924|-
Gene name:
Serinc3
Transcript:
ENSMUST00000017851.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,3
Exon/intron offsets:
0,2376
Genomic length:
2570
Exon/intron sizes in nt:
80,194
Flanking exon/introns:
chr2:163474163-163476354|chr2:163478924-163481085
Splice length:
274
Other database IDs:
CIRCpedia: MMU_CIRCpedia_218407, circAtlas: mmu-Serinc3_0019
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_95932
Human Ortholog IDs:
Mature spliced Sequence:
ATTCCTGGATTCTGTGAAGGAGGATTTCAAATCAAGATGGTTGATACAAAGGCAGAGAAAGATTGTGACGTGCTGGTCGGTTTTAAAGCTGTGTATCGGATCAACTTTGCTGTGGCCATCTTTTTCTTTGCCTTCTTTTTGCTCATGTTAAAAGTTAAAACAAGTAAAGATCCCAGAGCAGCAGTGCACAACGGGTTTTGGTTCTTCAAAATCGCTGCCATTATTGGTATCATGATTGGATCTTTCTACATCCCTGGGGGCAGTTTTACTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCACAACGGGTTTTGGTT
60.11
TAAAACCGACCAGCACGTCA
59.9
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCACAACGGGTTTTGGTTC
59.83
TAAAACCGACCAGCACGTCA
59.9
175
PCR template sequence:
AGAGCAGCAGTGCACAACGGGTTTTGGTTCTTCAAAATCGCTGCCATTATTGGTATCATGATTGGATCTTTCTACATCCCTGGGGGCAGTTTTACTGAAGATTCCTGGATTCTGTGAAGGAGGATTTCAAATCAAGATGGTTGATACAAAGGCAGAGAAAGATTGTGACGTGCTGGTCGGTTTTAAAGCTGTGTATCGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
AGTTTTACTGAAGATTCCTGGATTCT
siRNA sets
AGAATCCAGGAATCTTCAG, GAATCCAGGAATCTTCAGT, AATCCAGGAATCTTCAGTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSERINC3_274_ORF_1
1.0569
0.096613402
0.258210717
255
ORF sequence:
ATGGTTGATACAAAGGCAGAGAAAGATTGTGACGTGCTGGTCGGTTTTAAAGCTGTGTATCGGATCAACTTTGCTGTGGCCATCTTTTTCTTTGCCTTCTTTTTGCTCATGTTAAAAGTTAAAACAAGTAAAGATCCCAGAGCAGCAGTGCACAACGGGTTTTGGTTCTTCAAAATCGCTGCCATTATTGGTATCATGATTGGATCTTTCTACATCCCTGGGGGCAGTTTTACTGAAGATTCCTGGATTCTGTGA
Peptide sequence:
MVDTKAEKDCDVLVGFKAVYRINFAVAIFFFAFFLLMLKVKTSKDPRAAVHNGFWFFKIAAIIGIMIGSFYIPGGSFTEDSWIL
IRESfinder result
IRESfinder score
0.865626374
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
RPF, cORF, MS
mmu_circSerinc3_001
Evidence
Peptide sequence:
MVDTKAEKDCDVLVGFKAVYRINFAVAIFFFAFFLLMLKVKTSKDPRAAVHNGFWFFKIAAIIGIMIGSFYIPGGSFTEDSWIL*
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