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mmu_circPign_250
Basic information of circular RNA
PanCircBase ID:
mmu_circPign_250
mm39_Chr. Position ID:
chr1|105565234|105572244|-
Gene name:
Pign
Transcript:
ENSMUST00000070699.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,11,10,9
Exon/intron offsets:
0,673,3155,6969
Genomic length:
7010
Exon/intron sizes in nt:
56,93,60,41
Flanking exon/introns:
chr1:105526852-105565234|chr1:105572244-105574422
Splice length:
250
Other database IDs:
circBase: hsa_circ_0047857, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AATGGAGATTGGAAAACTGGAAAAGGAGAGATGTCAATCAGGCTGATATTGCACCTCTGATGGCATCCCTTATTGGAGTCCCCTTTCCTCTTAATTCGGTGGGAATACTTCCTGTGGGTTATCTTAACAACACTGGTCTCTTCAAAGCAGAGAGCATGTTTACCAATGCAGTACAGATTCTTGAACAGTTCAAGGTGAAAATGACTCAGAAAAAAGAAGCCACTTTACCGTTTTTGTTTACACCATTTAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGCATGTTTACCAATGCAGT
58.58
GGATGCCATCAGAGGTGCAA
60.39
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGCATGTTTACCAATGCAGT
58.58
AAGGGATGCCATCAGAGGTG
59.45
171
PCR template sequence:
AGAGCATGTTTACCAATGCAGTACAGATTCTTGAACAGTTCAAGGTGAAAATGACTCAGAAAAAAGAAGCCACTTTACCGTTTTTGTTTACACCATTTAAAATGGAGATTGGAAAACTGGAAAAGGAGAGATGTCAATCAGGCTGATATTGCACCTCTGATGGCATCCCTTATTGGAGTCCCCTTTCCTCTTAATTCGGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-30d-5p(1), mmu-miR-30b-5p(1), mmu-miR-342-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTACACCATTTAAAATGGAGATTGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPIGN_250_ORF_1
0.9671
-0.048654941
0.125099935
237
ORF sequence:
ATGGCATCCCTTATTGGAGTCCCCTTTCCTCTTAATTCGGTGGGAATACTTCCTGTGGGTTATCTTAACAACACTGGTCTCTTCAAAGCAGAGAGCATGTTTACCAATGCAGTACAGATTCTTGAACAGTTCAAGGTGAAAATGACTCAGAAAAAAGAAGCCACTTTACCGTTTTTGTTTACACCATTTAAAATGGAGATTGGAAAACTGGAAAAGGAGAGATGTCAATCAGGCTGA
Peptide sequence:
MASLIGVPFPLNSVGILPVGYLNNTGLFKAESMFTNAVQILEQFKVKMTQKKEATLPFLFTPFKMEIGKLEKERCQSG
IRESfinder result
IRESfinder score
0.747444401
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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