https://www.alphaknockout.com
Mouse Ppp2r2c Knockout Project (CRISPR/Cas9)
Objective: To create a Ppp2r2c knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Ppp2r2c gene (NCBI Reference Sequence: NM_172994 ; Ensembl: ENSMUSG00000029120 ) is located on Mouse chromosome 5. 9 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 9 (Transcript: ENSMUST00000031003). Exon 2~4 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:
Exon 2 starts from about 5.29% of the coding region. Exon 2~4 covers 28.11% of the coding region. The size of effective KO region: ~4676 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 2 3 4 9
Legends Exon of mouse Ppp2r2c 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 Exon 2 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats.
Overview of the Dot Plot (down) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 2000 bp section downstream of Exon 4 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(22.1% 442) | C(25.2% 504) | T(24.1% 482) | G(28.6% 572)
Note: The 2000 bp section upstream of Exon 2 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.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(24.15% 483) | C(24.15% 483) | T(26.4% 528) | G(25.3% 506)
Note: The 2000 bp section downstream of Exon 4 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% chr5 + 36920969 36922968 2000 browser details YourSeq 37 664 700 2000 100.0% chr15 + 77755311 77755347 37 browser details YourSeq 37 664 700 2000 100.0% chr13 + 40597123 40597159 37 browser details YourSeq 27 663 695 2000 84.4% chr14 + 9990918 9990949 32
Note: The 2000 bp section upstream of Exon 2 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% chr5 + 36927645 36929644 2000 browser details YourSeq 152 207 603 2000 87.4% chr1 + 88566662 88567061 400 browser details YourSeq 140 208 641 2000 87.4% chr6 - 51348680 51349178 499 browser details YourSeq 138 111 632 2000 83.5% chr4 + 140510350 140510816 467 browser details YourSeq 135 208 602 2000 83.7% chr16 - 89804102 89804488 387 browser details YourSeq 130 244 632 2000 83.0% chr19 + 3689725 3690105 381 browser details YourSeq 128 212 605 2000 82.8% chr19 + 42480860 42481251 392 browser details YourSeq 126 663 885 2000 90.4% chr1 + 155227089 155227312 224 browser details YourSeq 125 647 880 2000 91.4% chr11 + 30274492 30274849 358 browser details YourSeq 117 660 890 2000 90.5% chr13 + 21622294 21913324 291031 browser details YourSeq 116 648 879 2000 81.5% chrX + 47977996 47978201 206 browser details YourSeq 115 538 886 2000 81.0% chr16 + 20178528 20178798 271 browser details YourSeq 114 669 894 2000 85.7% chr15 + 32242387 32242610 224 browser details YourSeq 113 669 840 2000 89.0% chr7 - 6360562 6360737 176 browser details YourSeq 113 664 1063 2000 80.8% chr3 - 94781733 94782032 300 browser details YourSeq 113 239 602 2000 86.9% chr2 - 132418370 132418727 358 browser details YourSeq 112 252 603 2000 92.4% chr15 + 94574977 94575356 380 browser details YourSeq 111 239 631 2000 88.6% chrX - 56565332 56565723 392 browser details YourSeq 111 680 887 2000 83.5% chr16 - 35679906 35680114 209 browser details YourSeq 110 663 852 2000 87.0% chr5 + 118319590 118319776 187
Note: The 2000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Ppp2r2c protein phosphatase 2, regulatory subunit B, gamma [ Mus musculus (house mouse) ] Gene ID: 269643, updated on 12-Aug-2019
Gene summary
Official Symbol Ppp2r2c provided by MGI Official Full Name protein phosphatase 2, regulatory subunit B, gamma provided by MGI Primary source MGI:MGI:2442660 See related Ensembl:ENSMUSG00000029120 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 PR52; IMYPNO; IMYPNO1; 6330548O06Rik Expression Biased expression in cortex adult (RPKM 105.0), frontal lobe adult (RPKM 88.2) and 6 other tissues See more Orthologs human all
Genomic context
Location: 5; 5 B3 See Ppp2r2c in Genome Data Viewer Exon count: 11
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (36866846..36955078)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (37259809..37346317)
Chromosome 5 - NC_000071.6
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Transcript information: This gene has 3 transcripts
Gene: Ppp2r2c ENSMUSG00000029120
Description protein phosphatase 2, regulatory subunit B, gamma [Source:MGI Symbol;Acc:MGI:2442660] Gene Synonyms 6330548O06Rik, IMYPNO1, PR52 Location Chromosome 5: 36,868,513-36,955,078 forward strand. GRCm38:CM000998.2 About this gene This gene has 3 transcripts (splice variants), 228 orthologues, 3 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Ppp2r2c-201 ENSMUST00000031003.10 4088 447aa ENSMUSP00000031003.7 Protein coding CCDS19244 Q8BG02 TSL:1 GENCODE basic APPRIS P1
Ppp2r2c-203 ENSMUST00000201156.1 461 76aa ENSMUSP00000144342.1 Protein coding - A0A0J9YUU0 TSL:5 GENCODE basic
Ppp2r2c-202 ENSMUST00000138124.1 453 No protein - lncRNA - - TSL:3
106.57 kb Forward strand 36.86Mb 36.88Mb 36.90Mb 36.92Mb 36.94Mb 36.96Mb Genes (Comprehensive set... Ppp2r2c-201 >protein coding
Ppp2r2c-203 >protein coding Ppp2r2c-202 >lncRNA
Gm42506-201 >TEC
Contigs AC169036.3 > < AC114605.11 < AC115722.12 Genes < Ppp2r2cos-201lncRNA (Comprehensive set...
Regulatory Build
36.86Mb 36.88Mb 36.90Mb 36.92Mb 36.94Mb 36.96Mb Reverse strand 106.57 kb
Regulation Legend
CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
RNA gene processed transcript
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Transcript: ENSMUST00000031003
86.57 kb Forward strand
Ppp2r2c-201 >protein coding
ENSMUSP00000031... Low complexity (Seg) Superfamily WD40-repeat-containing domain superfamily SMART WD40 repeat Prints Protein phosphatase 2A regulatory subunit PR55 PROSITE patterns Protein phosphatase 2A regulatory subunit PR55, conserved site
Protein phosphatase 2A regulatory subunit PR55, conserved site PIRSF Protein phosphatase 2A regulatory subunit PR55
PANTHER Protein phosphatase 2A regulatory subunit PR55
PTHR11871:SF5 Gene3D WD40/YVTN repeat-like-containing domain superfamily
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant synonymous variant
Scale bar 0 40 80 120 160 200 240 280 320 360 400 447
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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