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mmu_circNipsnap2_692
Basic information of circular RNA
PanCircBase ID:
mmu_circNipsnap2_692
mm39_Chr. Position ID:
chr5|129821768|129834316|+
Gene name:
Nipsnap2
Transcript:
ENSMUST00000124342.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
4,5,6,7,8,9,10
Exon/intron offsets:
0,511,1622,3297,8521,10137,12374
Genomic length:
12548
Exon/intron sizes in nt:
9,57,11,41,32,95,84,170
Flanking exon/introns:
chr5:129816827-129821768|chr5:129834316-129834715
Splice length:
692
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TCAAGAAGTGTTACCAAAGATCCACGAAGGCAAGCAGTACCCTTGTACCCTGGTGGGGACGTGGAACACGTGGTATGGCGAGCAGGATCAAGCAGTCCACCTCTGGAGGTATGAAGGAGGCTATCCAGCCCTCACGGAGGTCATGAATAAACTCAAAGAAAACCAGGAATTTGTAAATTTCCGAAAGGCCAGAAGTGACATGCTTCTCTCCAGGAAGAACCAGCTGCTGCTGGAGTTCAGTTTCTGGAATGAGCCAGTGCCAAGACCGGGCCCCAATATATACGAACTCAGGTCCTACCAACTCCGACCAGGAACAATGATCGAGTGGGGCAACTACTGGGCCCGGGCCATTCGCTTTAGACAGGACAGTAATGAGGCAGTTGGGGGATTCTTCTCTCAAATTGGGCAGCTCTATATGGTGCACCATCTTTGGGCTTATAAAGATCTTCAGACCCGGGAGGACATCCGGAACGCGGCCTGGCACAAGCATGGCTGGGAGGAGCTCGTGTACTATACAGTCCCACTCATTCAGGAAATGGAGTCCAGGATCATGATCCCGCTCAAGACCTCCCCGCTCCAGTGACGCTGCCGTGTGCCTACGCAGATTACAGTGACGAATACGTGTCATGATTTCATCTCACCCAGTCACCGAGTGGAAAGCAAGCCGAGGTGTAAACTGCTGTACATAGCTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATCTCACCCAGTCACCGAG
59.83
GTGGACTGCTTGATCCTGCT
60.04
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATCTCACCCAGTCACCGAG
59.83
TTGATCCTGCTCGCCATACC
59.89
150
PCR template sequence:
GTGCCTACGCAGATTACAGTGACGAATACGTGTCATGATTTCATCTCACCCAGTCACCGAGTGGAAAGCAAGCCGAGGTGTAAACTGCTGTACATAGCTTTCAAGAAGTGTTACCAAAGATCCACGAAGGCAAGCAGTACCCTTGTACCCTGGTGGGGACGTGGAACACGTGGTATGGCGAGCAGGATCAAGCAGTCCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-205-5p(1), mmu-miR-322-5p(1), mmu-miR-185-5p(1), mmu-miR-136-5p(1), mmu-miR-433-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-22-3p(1), mmu-miR-96-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-425-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGTACATAGCTTTCAAGAAGTGTTA
siRNA sets
TCTTGAAAGCTATGTACAG, CTTCTTGAAAGCTATGTAC, TAACACTTCTTGAAAGCTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.468951236
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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