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mmu_circNisch_291
Basic information of circular RNA
PanCircBase ID:
mmu_circNisch_291
mm39_Chr. Position ID:
chr14|30894393|30895149|-
Gene name:
Nisch
Transcript:
ENSMUST00000168206.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
16,15
Exon/intron offsets:
0,627
Genomic length:
756
Exon/intron sizes in nt:
1,62,129
Flanking exon/introns:
chr14:30894135-30894393|chr14:30895149-30895543
Splice length:
291
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATTTCTGGCACCAGAAAAACACCGACTATAACAACAGTCCTTTCCACGTCTCTCAGTGCTTTGTGTTGAAACTCAGTGACCTGCAGTCAGTCAACGTCGGCCTTTTCGACCAGTACTTCCGGCTGACGGGCTCCTCCCCGACGCAGGTGGTCACGTGCTTGACTCGCGACAGCTACCTGACGCACTGCTTCCTCCAGCATCTGATGCTTGTGCTGTCCTCCCTGGAGCGCACACCCTCGCCTGAGCCTGTTGACAAGGACTTCTACTCAGAATTTGGGGACAAGAATACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGAGCCTGTTGACAAGGA
59.6
ACGTTGACTGACTGCAGGTC
60.25
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGAGCCTGTTGACAAGGA
59.6
GACGTTGACTGACTGCAGGT
60.25
150
PCR template sequence:
CTCCAGCATCTGATGCTTGTGCTGTCCTCCCTGGAGCGCACACCCTCGCCTGAGCCTGTTGACAAGGACTTCTACTCAGAATTTGGGGACAAGAATACAGATTTCTGGCACCAGAAAAACACCGACTATAACAACAGTCCTTTCCACGTCTCTCAGTGCTTTGTGTTGAAACTCAGTGACCTGCAGTCAGTCAACGTCGG
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-34a-5p(1), mmu-miR-484(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACAAGAATACAGATTTCTGGCACCA
siRNA sets
AGAAATCTGTATTCTTGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNISCH_291_ORF_1
1.243
0.422398283
0.819001336
378
ORF sequence:
ATGCTTGTGCTGTCCTCCCTGGAGCGCACACCCTCGCCTGAGCCTGTTGACAAGGACTTCTACTCAGAATTTGGGGACAAGAATACAGATTTCTGGCACCAGAAAAACACCGACTATAACAACAGTCCTTTCCACGTCTCTCAGTGCTTTGTGTTGAAACTCAGTGACCTGCAGTCAGTCAACGTCGGCCTTTTCGACCAGTACTTCCGGCTGACGGGCTCCTCCCCGACGCAGGTGGTCACGTGCTTGACTCGCGACAGCTACCTGACGCACTGCTTCCTCCAGCATCTGATGCTTGTGCTGTCCTCCCTGGAGCGCACACCCTCGCCTGAGCCTGTTGACAAGGACTTCTACTCAGAATTTGGGGACAAGAATACA
Peptide sequence:
MLVLSSLERTPSPEPVDKDFYSEFGDKNTDFWHQKNTDYNNSPFHVSQCFVLKLSDLQSVNVGLFDQYFRLTGSSPTQVVTCLTRDSYLTHCFLQHLMLVLSSLERTPSPEPVDKDFYSEFGDKNT
IRESfinder result
IRESfinder score
0.602214146
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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