https://www.alphaknockout.com
Mouse Ppp1r9b Knockout Project (CRISPR/Cas9)
Objective: To create a Ppp1r9b knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Ppp1r9b gene (NCBI Reference Sequence: NM_172261 ; Ensembl: ENSMUSG00000038976 ) is located on Mouse chromosome 11. 10 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 10 (Transcript: ENSMUST00000038696). Exon 1~10 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygotes for a targeted null mutation exhibit abnormal glutamatergic synaptic transmission, reduced long-term depression, resistance to kainate-induced seizures, impaired taste aversion learning, and increased dendritic spine density.
Exon 1 starts from about 0.04% of the coding region. Exon 1~10 covers 100.0% of the coding region. The size of effective KO region: ~13808 bp. The KO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele 5' gRNA region gRNA region 3'
1 6 7 8 9 10
Legends Exon of mouse Ppp1r9b Knockout region
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Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 2000 bp section upstream of start codon is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis.
Overview of the Dot Plot (down) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 2000 bp section downstream of stop codon is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(22.5% 450) | C(26.0% 520) | T(19.95% 399) | G(31.55% 631)
Note: The 2000 bp section upstream of start codon is analyzed to determine the GC content. Significant high GC-content regions are found. The gRNA site is selected outside of these high GC-content regions.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(19.0% 380) | C(31.25% 625) | T(24.95% 499) | G(24.8% 496)
Note: The 2000 bp section downstream of stop codon is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis.
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BLAT Search Results (up)
QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ------browser details YourSeq 2000 1 2000 2000 100.0% chr11 + 94989549 94991548 2000 browser details YourSeq 47 199 281 2000 94.3% chr11 + 101910787 101911288 502 browser details YourSeq 43 223 281 2000 92.4% chr4 - 137457797 137457884 88 browser details YourSeq 37 236 281 2000 90.3% chr6 - 37179756 37179800 45 browser details YourSeq 30 240 277 2000 91.7% chrX + 94844151 94844189 39 browser details YourSeq 29 560 590 2000 96.8% chr1 + 154798447 154798477 31 browser details YourSeq 23 1477 1500 2000 100.0% chr4 - 154071836 154071861 26 browser details YourSeq 23 858 880 2000 100.0% chr6 + 5158590 5158612 23 browser details YourSeq 22 859 880 2000 100.0% chr10 - 66278871 66278892 22 browser details YourSeq 22 858 879 2000 100.0% chrX + 139576090 139576111 22 browser details YourSeq 22 961 982 2000 100.0% chr15 + 23651701 23651722 22 browser details YourSeq 22 1682 1704 2000 100.0% chr1 + 88018504 88018532 29 browser details YourSeq 21 858 878 2000 100.0% chr13 + 50365131 50365151 21 browser details YourSeq 20 67 86 2000 100.0% chr1 - 47073534 47073553 20
Note: The 2000 bp section upstream of start codon is BLAT searched against the genome. No significant similarity is found.
BLAT Search Results (down)
QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ------browser details YourSeq 2000 1 2000 2000 100.0% chr11 + 95005357 95007356 2000 browser details YourSeq 35 48 149 2000 66.7% chr1 - 60750243 60750300 58 browser details YourSeq 27 527 553 2000 100.0% chr19 + 57189094 57189120 27 browser details YourSeq 24 1459 1482 2000 100.0% chr12 + 103102751 103102774 24 browser details YourSeq 24 766 792 2000 96.3% chr1 + 16099580 16099607 28 browser details YourSeq 23 1248 1271 2000 100.0% chr12 - 16705526 16705551 26 browser details YourSeq 22 117 148 2000 84.4% chr17 + 48464036 48464067 32 browser details YourSeq 22 1176 1197 2000 100.0% chr1 + 164208910 164208931 22 browser details YourSeq 21 1167 1187 2000 100.0% chr9 - 111357331 111357351 21 browser details YourSeq 21 1569 1589 2000 100.0% chr7 + 108883431 108883451 21 browser details YourSeq 20 926 945 2000 100.0% chr1 - 113330984 113331003 20 browser details YourSeq 20 527 548 2000 95.5% chr1 - 113159330 113159351 22 browser details YourSeq 20 63 82 2000 100.0% chr1 + 72234902 72234921 20
Note: The 2000 bp section downstream of stop codon is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Ppp1r9b protein phosphatase 1, regulatory subunit 9B [ Mus musculus (house mouse) ] Gene ID: 217124, updated on 12-Aug-2019
Gene summary
Official Symbol Ppp1r9b provided by MGI Official Full Name protein phosphatase 1, regulatory subunit 9B provided by MGI Primary source MGI:MGI:2387581 See related Ensembl:ENSMUSG00000038976 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as SPL; Spn Expression Ubiquitous expression in frontal lobe adult (RPKM 75.4), cortex adult (RPKM 71.9) and 27 other tissues See more Orthologs human all
Genomic context
Location: 11; 11 D See Ppp1r9b in Genome Data Viewer Exon count: 10
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (94991212..95006898)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (94852526..94868212)
Chromosome 11 - NC_000077.6
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Transcript information: This gene has 3 transcripts
Gene: Ppp1r9b ENSMUSG00000038976
Description protein phosphatase 1, regulatory subunit 9B [Source:MGI Symbol;Acc:MGI:2387581] Gene Synonyms SPL, Spn, neurabin II, spinophilin Location Chromosome 11: 94,991,035-95,006,899 forward strand. GRCm38:CM001004.2 About this gene This gene has 3 transcripts (splice variants), 249 orthologues, 2 paralogues, is a member of 1 Ensembl protein family and is associated with 33 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Ppp1r9b-201 ENSMUST00000038696.11 4508 817aa ENSMUSP00000041732.5 Protein coding CCDS25268 Q6R891 TSL:1 GENCODE basic APPRIS P2
Ppp1r9b-202 ENSMUST00000107748.1 3095 393aa ENSMUSP00000103377.1 Protein coding - Q6R891 TSL:1 GENCODE basic APPRIS ALT2
Ppp1r9b-203 ENSMUST00000151771.1 610 No protein - lncRNA - - TSL:5
35.87 kb Forward strand
94.99Mb 95.00Mb 95.01Mb Genes (Comprehensive set... Ppp1r9b-201 >protein coding Samd14-201 >protein coding
Ppp1r9b-203 >lncRNA Samd14-203 >lncRNA
Ppp1r9b-202 >protein coding Samd14-202 >protein coding
Contigs AL606480.11 > Regulatory Build
94.99Mb 95.00Mb 95.01Mb Reverse strand 35.87 kb
Regulation Legend CTCF Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
RNA gene
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Transcript: ENSMUST00000038696
15.87 kb Forward strand
Ppp1r9b-201 >protein coding
ENSMUSP00000041... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily PDZ superfamily SMART PDZ domain Pfam PDZ domain
Neurabin-1/2, PDZ domain PROSITE profiles PDZ domain PANTHER PTHR16154
Neurabin-2 Gene3D 2.30.42.10 CDD cd00992
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 817
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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