https://www.alphaknockout.com
Mouse Ppp2r3a Knockout Project (CRISPR/Cas9)
Objective: To create a Ppp2r3a knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Ppp2r3a gene (NCBI Reference Sequence: NM_001161362 ; Ensembl: ENSMUSG00000043154 ) is located on Mouse chromosome 9. 14 exons are identified, with the ATG start codon in exon 2 and the TAG stop codon in exon 14 (Transcript: ENSMUST00000075941). Exon 3 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 3 starts from about 57.77% of the coding region. Exon 3 covers 7.74% of the coding region. The size of effective KO region: ~267 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 3 14
Legends Exon of mouse Ppp2r3a 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 3 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 3 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(31.45% 629) | C(20.25% 405) | T(32.05% 641) | G(16.25% 325)
Note: The 2000 bp section upstream of Exon 3 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(29.15% 583) | C(22.25% 445) | T(32.65% 653) | G(15.95% 319)
Note: The 2000 bp section downstream of Exon 3 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% chr9 - 101194426 101196425 2000 browser details YourSeq 114 1460 1661 2000 82.3% chr1 + 86530508 86530700 193 browser details YourSeq 102 1471 1653 2000 88.7% chr16 + 3927248 3927453 206 browser details YourSeq 67 1460 1568 2000 88.0% chr14 - 8799392 8799499 108 browser details YourSeq 46 1148 1231 2000 76.8% chr16 + 32470314 32470388 75 browser details YourSeq 43 432 587 2000 81.0% chrX + 101049132 101049286 155 browser details YourSeq 43 526 585 2000 87.8% chr17 + 57037815 57037875 61 browser details YourSeq 39 1445 1497 2000 82.7% chr13 + 20749328 20749379 52 browser details YourSeq 38 1079 1209 2000 79.6% chr15 + 99358278 99358402 125 browser details YourSeq 35 525 571 2000 90.0% chr6 - 88065728 88065773 46 browser details YourSeq 34 1109 1202 2000 87.5% chr8 + 104343160 104343252 93 browser details YourSeq 32 529 571 2000 88.1% chr16 - 31239125 31239168 44 browser details YourSeq 31 1186 1216 2000 100.0% chr17 - 43070098 43070128 31 browser details YourSeq 31 559 595 2000 91.9% chr10 + 42605116 42605152 37 browser details YourSeq 30 1181 1212 2000 96.9% chr9 + 67102495 67102526 32 browser details YourSeq 30 1186 1215 2000 100.0% chr15 + 80454195 80454224 30 browser details YourSeq 30 1181 1212 2000 90.4% chr1 + 71521354 71521384 31 browser details YourSeq 29 1186 1214 2000 100.0% chr12 + 21377000 21377028 29 browser details YourSeq 28 1460 1497 2000 86.9% chr8 - 89146210 89146247 38 browser details YourSeq 28 1181 1212 2000 83.4% chr15 - 76544383 76544412 30
Note: The 2000 bp section upstream of Exon 3 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% chr9 - 101192159 101194158 2000 browser details YourSeq 277 198 524 2000 95.7% chrX - 140038558 140038940 383 browser details YourSeq 65 142 453 2000 93.4% chr15 + 38280938 38281446 509 browser details YourSeq 57 371 436 2000 95.4% chr1 + 185340683 185340758 76 browser details YourSeq 54 534 599 2000 88.6% chr5 + 116343640 116343702 63 browser details YourSeq 53 394 453 2000 95.0% chr1 + 189559898 189560005 108 browser details YourSeq 49 398 446 2000 100.0% chr7 - 108987935 108987983 49 browser details YourSeq 48 127 190 2000 82.0% chr15 - 54800725 54800776 52 browser details YourSeq 45 385 433 2000 96.0% chrX - 140038691 140038739 49 browser details YourSeq 38 536 841 2000 97.6% chr1 + 138190200 138190656 457 browser details YourSeq 35 311 361 2000 75.0% chr4 + 126069294 126069337 44 browser details YourSeq 33 142 182 2000 91.9% chr18 - 90290839 90290880 42 browser details YourSeq 28 670 699 2000 96.7% chr11 - 121413096 121413125 30 browser details YourSeq 28 670 701 2000 93.8% chr8 + 110870990 110871021 32 browser details YourSeq 27 142 172 2000 89.7% chr16 + 33942150 33942179 30 browser details YourSeq 23 537 566 2000 90.0% chr6 - 133069015 133069045 31 browser details YourSeq 23 370 395 2000 96.0% chr11 - 93810730 93810775 46 browser details YourSeq 22 677 698 2000 100.0% chr10 + 18424231 18424252 22
Note: The 2000 bp section downstream of Exon 3 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Ppp2r3a protein phosphatase 2, regulatory subunit B'', alpha [ Mus musculus (house mouse) ] Gene ID: 235542, updated on 12-Aug-2019
Gene summary
Official Symbol Ppp2r3a provided by MGI Official Full Name protein phosphatase 2, regulatory subunit B'', alpha provided by MGI Primary source MGI:MGI:2442104 See related Ensembl:ENSMUSG00000043154 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 A730042E07; 3222402P14Rik; C530025M11Rik Expression Broad expression in heart adult (RPKM 13.2), CNS E18 (RPKM 5.5) and 20 other tissues See more Orthologs human all
Genomic context
Location: 9; 9 E4 See Ppp2r3a in Genome Data Viewer Exon count: 17
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (101104989..101251832, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (101007319..101154162, complement)
Chromosome 9 - NC_000075.6
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Transcript information: This gene has 7 transcripts
Gene: Ppp2r3a ENSMUSG00000043154
Description protein phosphatase 2, regulatory subunit B'', alpha [Source:MGI Symbol;Acc:MGI:2442104] Gene Synonyms 3222402P14Rik Location Chromosome 9: 101,105,084-101,251,795 reverse strand. GRCm38:CM001002.2 About this gene This gene has 7 transcripts (splice variants), 208 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 14 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Ppp2r3a-202 ENSMUST00000075941.11 6786 1150aa ENSMUSP00000075327.5 Protein coding CCDS52900 B2RXC8 TSL:5 GENCODE basic
Ppp2r3a-201 ENSMUST00000066773.8 4461 530aa ENSMUSP00000069688.7 Protein coding CCDS52899 G3X9E8 TSL:1 GENCODE basic APPRIS P1
Ppp2r3a-204 ENSMUST00000185735.1 3079 No protein - Retained intron - - TSL:NA
Ppp2r3a-206 ENSMUST00000188612.1 2333 No protein - Retained intron - - TSL:1
Ppp2r3a-205 ENSMUST00000185887.1 2227 No protein - Retained intron - - TSL:1
Ppp2r3a-207 ENSMUST00000191226.1 807 No protein - lncRNA - - TSL:1
Ppp2r3a-203 ENSMUST00000185719.1 317 No protein - lncRNA - - TSL:5
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166.71 kb Forward strand 101.10Mb 101.15Mb 101.20Mb 101.25Mb Genes Msl2-202 >protein coding Gm37953-201 >TEC Gm24338-201 >snoRNA (Comprehensive set...
Msl2-201 >protein coding
Gm37962-201 >TEC
Gm37621-201 >TEC
Contigs AC242670.3 > < AC120390.12 < AC138288.13 Genes (Comprehensive set... < Ppp2r3a-202protein coding
< Ppp2r3a-201protein coding < Ppp2r3a-207lncRNA
< Ppp2r3a-203lncRNA < Gm38344-201TEC
< Ppp2r3a-206retained intron
< Gm37314-201TEC
< Ppp2r3a-205retained intron
< Ppp2r3a-204retained intron
Regulatory Build
101.10Mb 101.15Mb 101.20Mb 101.25Mb Reverse strand 166.71 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript RNA gene
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Transcript: ENSMUST00000075941
< Ppp2r3a-202protein coding
Reverse strand 146.71 kb
ENSMUSP00000075... MobiDB lite Low complexity (Seg) Superfamily EF-hand domain pair Pfam PP2A regulatory subunit B'', EF-hand domain
EF-hand domain PROSITE profiles EF-hand domain PROSITE patterns EF-Hand 1, calcium-binding site PANTHER PTHR14095:SF3
PTHR14095 Gene3D 1.10.238.230 1.10.238.10
1.10.238.220
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 100 200 300 400 500 600 700 800 900 1000 1150
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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