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mmu_circNup188_560
Basic information of circular RNA
PanCircBase ID:
mmu_circNup188_560
mm39_Chr. Position ID:
chr2|30211893|30213646|+
Gene name:
Nup188
Transcript:
ENSMUST00000064447.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
16,17,18,19,20
Exon/intron offsets:
0,290,604,789,1638
Genomic length:
1753
Exon/intron sizes in nt:
15,31,27,88,77,115
Flanking exon/introns:
chr2:30207319-30211893|chr2:30213646-30215239
Splice length:
560
Other database IDs:
circAtlas: mmu-Nup188_0006
Human Ortholog IDs:
Mature spliced Sequence:
GGGGTCAGACCAACCTTCGCATTCCTCAGGGCACTGTGGGCCAAGTCATGCTGGATGACAGGGCTTACCTTGTCCGCTGGGAGTACTCTTACAGCAGCTGGACCCTCTTCACCTGCGAGATTGAAATGCTGCTCCACGTTGTCTCCACAGCAGATGTGATCCAGCATTGCCAGCGGGTCAAGCCCATCATTGATTTGGTTCATAAGGTCATCAGCACAGACTTGTCCATAGCAGACTGCCTGCTGCCCATCACATCCCGCATCTACATGCTGTTGCAGCGGCTGACGACGGTGATCTCCCCTCCTGTAAACGTCATTGCTTCTTGTGTCAACTGCTTAACTGTCTTGGCTGCTCGAAACCCAGCAAAGGTCTGGACTGATCTTCGTCACACAGGTTTTTTGCCATTCGTGGCCCACCCTGTCTCCAACATGACTCAGATGATTAGTGCGGAGGGAATGAATGCTGGAGGGTATGGCAGCCTTCTGATGAACAGTGAGCAGCCCCAGGGCGAATATGGGGTCACCATTGCCTTTCTGCGCCTGGTCACCACGCTTGTCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGATGAACAGTGAGCAGCCC
60.32
TACTCCCAGCGGACAAGGTA
59.96
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGATGAACAGTGAGCAGCCC
60.32
CTCCCAGCGGACAAGGTAAG
60.11
160
PCR template sequence:
TGCTGGAGGGTATGGCAGCCTTCTGATGAACAGTGAGCAGCCCCAGGGCGAATATGGGGTCACCATTGCCTTTCTGCGCCTGGTCACCACGCTTGTCAAGGGGGTCAGACCAACCTTCGCATTCCTCAGGGCACTGTGGGCCAAGTCATGCTGGATGACAGGGCTTACCTTGTCCGCTGGGAGTACTCTTACAGCAGCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-322-5p(1), mmu-miR-138-5p(1), mmu-miR-339-5p(1), mmu-miR-214-3p(1), mmu-miR-351-5p(1), mmu-miR-676-3p(1), mmu-miR-182-5p(1), mmu-miR-3061-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CACGCTTGTCAAGGGGGTCAGACCAA
siRNA sets
TTGGTCTGACCCCCTTGAC, TGACCCCCTTGACAAGCGT, TCTGACCCCCTTGACAAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNUP188_560_ORF_1
1.0441
0.224256893
0.919725492
672
ORF sequence:
ATGCTGGATGACAGGGCTTACCTTGTCCGCTGGGAGTACTCTTACAGCAGCTGGACCCTCTTCACCTGCGAGATTGAAATGCTGCTCCACGTTGTCTCCACAGCAGATGTGATCCAGCATTGCCAGCGGGTCAAGCCCATCATTGATTTGGTTCATAAGGTCATCAGCACAGACTTGTCCATAGCAGACTGCCTGCTGCCCATCACATCCCGCATCTACATGCTGTTGCAGCGGCTGACGACGGTGATCTCCCCTCCTGTAAACGTCATTGCTTCTTGTGTCAACTGCTTAACTGTCTTGGCTGCTCGAAACCCAGCAAAGGTCTGGACTGATCTTCGTCACACAGGTTTTTTGCCATTCGTGGCCCACCCTGTCTCCAACATGACTCAGATGATTAGTGCGGAGGGAATGAATGCTGGAGGGTATGGCAGCCTTCTGATGAACAGTGAGCAGCCCCAGGGCGAATATGGGGTCACCATTGCCTTTCTGCGCCTGGTCACCACGCTTGTCAAGGGGGTCAGACCAACCTTCGCATTCCTCAGGGCACTGTGGGCCAAGTCATGCTGGATGACAGGGCTTACCTTGTCCGCTGGGAGTACTCTTACAGCAGCTGGACCCTCTTCACCTGCGAGATTGAAATGCTGCTCCACGTTGTCTCCACAGCAGATGTGA
Peptide sequence:
MLDDRAYLVRWEYSYSSWTLFTCEIEMLLHVVSTADVIQHCQRVKPIIDLVHKVISTDLSIADCLLPITSRIYMLLQRLTTVISPPVNVIASCVNCLTVLAARNPAKVWTDLRHTGFLPFVAHPVSNMTQMISAEGMNAGGYGSLLMNSEQPQGEYGVTIAFLRLVTTLVKGVRPTFAFLRALWAKSCWMTGLTLSAGSTLTAAGPSSPARLKCCSTLSPQQM
IRESfinder result
IRESfinder score
0.541781254
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
RPF, cORF, m6A
mmu_circNup188_001
Evidence
Peptide sequence:
MGSPLPFCAWSPRLSRGSDQPSHSSGHCGPSHAG*
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