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mmu_circU2surp_407
Basic information of circular RNA
PanCircBase ID:
mmu_circU2surp_407
mm39_Chr. Position ID:
chr9|95363705|95366386|-
Gene name:
U2surp
Transcript:
ENSMUST00000079659.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
18,17,16
Exon/intron offsets:
0,439,2517
Genomic length:
2681
Exon/intron sizes in nt:
8,01,63,164
Flanking exon/introns:
chr9:95361407-95363705|chr9:95366386-95366460
Splice length:
407
Other database IDs:
CIRCpedia: MMU_CIRCpedia_40801, circAtlas: mmu-U2surp_0025
Human Ortholog IDs:
Mature spliced Sequence:
GGAGATTCTCCAACGAAATGGCGGACAGAAGATTTTCGAATGTTCAAAAATGGATCTTTTTGGAGGCCACCACCTTTAAATCCATACCTTCATGGGATGTCAGAGGAGCAAGAGACAGAAGCGTTTGTAGAAGAACCTAGTAAGAAGGGAGCACTCAAGGAAGAACAGCGGGATAAGTTAGAAGAAATCTTGCGAGGATTAACTCCAAGGAAAAATGATATTGGAGATGCCATGGTTTTCTGTCTTAATAATGCTGAAGCTGCTGAAGAAATAGTGGATTGCATTACTGAGTCGCTGTCCATCTTAAAGACACCTCTTCCCAAGAAGATTGCCAGATTATATTTGGTTTCTGATGTTTTATACAACTCTTCAGCCAAAGTTGCCAATGCTTCATATTACAGGAAATT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCCCAAGAAGATTGCCAGA
56.73
AAGGTGGTGGCCTCCAAAAA
60.03
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCCCAAGAAGATTGCCAGA
56.73
AAAGGTGGTGGCCTCCAAAA
60.03
168
PCR template sequence:
AGACACCTCTTCCCAAGAAGATTGCCAGATTATATTTGGTTTCTGATGTTTTATACAACTCTTCAGCCAAAGTTGCCAATGCTTCATATTACAGGAAATTGGAGATTCTCCAACGAAATGGCGGACAGAAGATTTTCGAATGTTCAAAAATGGATCTTTTTGGAGGCCACCACCTTTAAATCCATACCTTCATGGGATGT
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-182-5p(1), mmu-miR-340-5p(1), mmu-miR-680(1)
siRNAs for circular RNA silencing
Junction sequence
ATTACAGGAAATTGGAGATTCTCCAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCU2SURP_407_ORF_1
0.8902
0.054948742
0.46099624
447
ORF sequence:
ATGTTCAAAAATGGATCTTTTTGGAGGCCACCACCTTTAAATCCATACCTTCATGGGATGTCAGAGGAGCAAGAGACAGAAGCGTTTGTAGAAGAACCTAGTAAGAAGGGAGCACTCAAGGAAGAACAGCGGGATAAGTTAGAAGAAATCTTGCGAGGATTAACTCCAAGGAAAAATGATATTGGAGATGCCATGGTTTTCTGTCTTAATAATGCTGAAGCTGCTGAAGAAATAGTGGATTGCATTACTGAGTCGCTGTCCATCTTAAAGACACCTCTTCCCAAGAAGATTGCCAGATTATATTTGGTTTCTGATGTTTTATACAACTCTTCAGCCAAAGTTGCCAATGCTTCATATTACAGGAAATTGGAGATTCTCCAACGAAATGGCGGACAGAAGATTTTCGAATGTTCAAAAATGGATCTTTTTGGAGGCCACCACCTTTAA
Peptide sequence:
MFKNGSFWRPPPLNPYLHGMSEEQETEAFVEEPSKKGALKEEQRDKLEEILRGLTPRKNDIGDAMVFCLNNAEAAEEIVDCITESLSILKTPLPKKIARLYLVSDVLYNSSAKVANASYYRKLEILQRNGGQKIFECSKMDLFGGHHL
IRESfinder result
IRESfinder score
0.57327917
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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