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mmu_circNckap1_527
Basic information of circular RNA
PanCircBase ID:
mmu_circNckap1_527
mm39_Chr. Position ID:
chr2|80360501|80370569|-
Gene name:
Nckap1
Transcript:
ENSMUST00000028386.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
16,15,14,13,12
Exon/intron offsets:
0,3487,5316,7946,9961
Genomic length:
10068
Exon/intron sizes in nt:
14,65,98,21,33,107
Flanking exon/introns:
chr2:80359011-80360501|chr2:80370569-80370853
Splice length:
527
Other database IDs:
CIRCpedia: MMU_CIRCpedia_30527, circAtlas: mmu-Nckap1_0045
Human Ortholog IDs:
Mature spliced Sequence:
GCACTTTTTGTTTTCATGGCGTTATCTTTTGCCCGTGATGAAATTATCTGGCTGCTCCGTCACGCGGACAACATGCCAAAGAAGAGTGCAGATGACTTTATAGATAAGCACATTGCTGAGCTAATATTTTACATGGAAGAGCTTAGAGCACATGTCAGGAAGTATGGGCCTGTCATGCAGAGGTACTACGTGCAATACCTCTCTGGCTTTGATGCTGTTGTCCTCAATGAACTTGTGCAGAACCTGTCTGTTTGCCCTGAGGATGAATCGATCATCATGTCCTCTTTTGTGAACACCATGACCTCCCTAAGTGTGAAGCAAGTTGAAGATGGAGAAGTGTTTGATTTCAGAGGGATGAGATTAGATTGGTTTAGGTTACAGGCGTACACTAGCGTCTCCAAAGCTTCACTTAGCCTTGCAGATCACAGAGAACTTGGAAAGATGATGAACACAATCATATTCCATACAAAAATGGTAGATTCCTTGGTTGAAATGTTGGTGGAAACATCCGATCTCTCCATATTTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTTGGTTGAAATGTTGGTGGA
59.3
CATCTGCACTCTTCTTTGGCA
58.84
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTTGGTTGAAATGTTGGTGG
59.3
CATCTGCACTCTTCTTTGGCA
58.84
141
PCR template sequence:
GAGAACTTGGAAAGATGATGAACACAATCATATTCCATACAAAAATGGTAGATTCCTTGGTTGAAATGTTGGTGGAAACATCCGATCTCTCCATATTTTGGCACTTTTTGTTTTCATGGCGTTATCTTTTGCCCGTGATGAAATTATCTGGCTGCTCCGTCACGCGGACAACATGCCAAAGAAGAGTGCAGATGACTTTA
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-92a-3p(1), mmu-miR-25-3p(1), mmu-miR-185-5p(1), mmu-miR-363-3p(1), mmu-miR-127-5p(1), mmu-miR-218-5p(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTCCATATTTTGGCACTTTTTGTTT
siRNA sets
AAAAAGTGCCAAAATATGG, AAAAGTGCCAAAATATGGA, CAAAAAGTGCCAAAATATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNCKAP1_527_ORF_1
0.8895
0.063942488
0.747603705
615
ORF sequence:
ATGGCGTTATCTTTTGCCCGTGATGAAATTATCTGGCTGCTCCGTCACGCGGACAACATGCCAAAGAAGAGTGCAGATGACTTTATAGATAAGCACATTGCTGAGCTAATATTTTACATGGAAGAGCTTAGAGCACATGTCAGGAAGTATGGGCCTGTCATGCAGAGGTACTACGTGCAATACCTCTCTGGCTTTGATGCTGTTGTCCTCAATGAACTTGTGCAGAACCTGTCTGTTTGCCCTGAGGATGAATCGATCATCATGTCCTCTTTTGTGAACACCATGACCTCCCTAAGTGTGAAGCAAGTTGAAGATGGAGAAGTGTTTGATTTCAGAGGGATGAGATTAGATTGGTTTAGGTTACAGGCGTACACTAGCGTCTCCAAAGCTTCACTTAGCCTTGCAGATCACAGAGAACTTGGAAAGATGATGAACACAATCATATTCCATACAAAAATGGTAGATTCCTTGGTTGAAATGTTGGTGGAAACATCCGATCTCTCCATATTTTGGCACTTTTTGTTTTCATGGCGTTATCTTTTGCCCGTGATGAAATTATCTGGCTGCTCCGTCACGCGGACAACATGCCAAAGAAGAGTGCAGATGACTTTATAG
Peptide sequence:
MALSFARDEIIWLLRHADNMPKKSADDFIDKHIAELIFYMEELRAHVRKYGPVMQRYYVQYLSGFDAVVLNELVQNLSVCPEDESIIMSSFVNTMTSLSVKQVEDGEVFDFRGMRLDWFRLQAYTSVSKASLSLADHRELGKMMNTIIFHTKMVDSLVEMLVETSDLSIFWHFLFSWRYLLPVMKLSGCSVTRTTCQRRVQMTL
IRESfinder result
IRESfinder score
0.558744433
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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