https://www.alphaknockout.com
Mouse Prx Knockout Project (CRISPR/Cas9)
Objective: To create a Prx knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Prx gene (NCBI Reference Sequence: NM_019412 ; Ensembl: ENSMUSG00000053198 ) is located on Mouse chromosome 7. 6 exons are identified, with the ATG start codon in exon 4 and the TAA stop codon in exon 6 (Transcript: ENSMUST00000108355). Exon 6 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: Mice homozygous for disruptions in this gene display locomotor problems as well as difficulty eating and breathing. Demyelination of peripheral nerves develops with age.
Exon 6 starts from about 41.67% of the coding region. Exon 6 covers 58.56% of the coding region. The size of effective KO region: ~4964 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
Legends Exon of mouse Prx 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 6 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 6 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(32.3% 646) | C(22.95% 459) | T(23.45% 469) | G(21.3% 426)
Note: The 2000 bp section upstream of Exon 6 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(22.9% 458) | C(29.65% 593) | T(26.15% 523) | G(21.3% 426)
Note: The 2000 bp section downstream of Exon 6 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% chr7 + 27513252 27515251 2000 browser details YourSeq 355 603 1216 2000 93.1% chrX - 129554551 129712878 158328 browser details YourSeq 348 569 1305 2000 91.5% chr11 + 120569043 120569827 785 browser details YourSeq 331 569 1240 2000 92.4% chr4 - 115105369 115106950 1582 browser details YourSeq 321 569 1200 2000 93.6% chr8 + 111232257 111519470 287214 browser details YourSeq 292 569 1328 2000 87.2% chr9 - 110058243 110058727 485 browser details YourSeq 291 804 1237 2000 94.3% chr4 - 44304951 44305576 626 browser details YourSeq 281 569 1241 2000 88.8% chr19 + 5978532 5978904 373 browser details YourSeq 278 826 1312 2000 90.4% chr15 - 81000934 81001349 416 browser details YourSeq 273 569 1240 2000 90.0% chr18 - 75066230 75066782 553 browser details YourSeq 271 592 1305 2000 89.1% chr10 + 128449923 128450506 584 browser details YourSeq 267 569 1236 2000 88.5% chr17 - 70810332 70810744 413 browser details YourSeq 262 843 1240 2000 94.6% chr4 + 135836658 135837212 555 browser details YourSeq 261 569 1200 2000 88.0% chr2 + 170081908 170082276 369 browser details YourSeq 258 815 1192 2000 96.1% chr6 - 29577349 29577760 412 browser details YourSeq 257 569 1191 2000 87.3% chr11 + 104428323 104428668 346 browser details YourSeq 256 581 1200 2000 88.9% chr10 - 62982935 62983340 406 browser details YourSeq 255 806 1215 2000 92.4% chr2 - 71410298 71410703 406 browser details YourSeq 252 826 1216 2000 94.7% chr4 - 48406015 48406508 494 browser details YourSeq 251 603 1200 2000 92.0% chr3 - 95090255 95090891 637
Note: The 2000 bp section upstream of Exon 6 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% chr7 + 27520216 27522215 2000 browser details YourSeq 139 1402 1911 2000 81.2% chr8 + 70326442 70326815 374 browser details YourSeq 114 1352 1911 2000 80.8% chr4 + 136036602 136036858 257 browser details YourSeq 112 1402 2000 2000 79.3% chr5 + 31051339 31051805 467 browser details YourSeq 89 4 114 2000 92.5% chr10 - 67347918 67348340 423 browser details YourSeq 88 1 123 2000 92.4% chr2 - 155832033 155832312 280 browser details YourSeq 88 1796 1911 2000 89.9% chrX + 20296245 20296361 117 browser details YourSeq 83 1784 1911 2000 83.2% chr1 + 62941485 62941599 115 browser details YourSeq 81 1 91 2000 94.6% chr18 - 71181247 71181337 91 browser details YourSeq 81 1699 1903 2000 87.7% chr2 + 160005851 160006087 237 browser details YourSeq 78 1784 1911 2000 84.5% chr11 - 53377024 53377136 113 browser details YourSeq 78 1801 1911 2000 89.6% chr2 + 172534496 172534605 110 browser details YourSeq 77 1 91 2000 92.4% chr8 - 124823643 124823733 91 browser details YourSeq 77 1 91 2000 92.4% chr5 - 66653228 66653318 91 browser details YourSeq 77 1 91 2000 92.4% chrX + 85287008 85287098 91 browser details YourSeq 77 1 91 2000 92.4% chr12 + 83934754 83934844 91 browser details YourSeq 76 1 92 2000 91.4% chr14 + 51963430 51963521 92 browser details YourSeq 76 1 80 2000 97.5% chr1 + 39352898 39352977 80 browser details YourSeq 75 1 91 2000 91.3% chr7 - 133684273 133684363 91 browser details YourSeq 75 1 91 2000 91.3% chr5 - 123199052 123199142 91
Note: The 2000 bp section downstream of Exon 6 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Prx periaxin [ Mus musculus (house mouse) ] Gene ID: 19153, updated on 12-Aug-2019
Gene summary
Official Symbol Prx provided by MGI Official Full Name periaxin provided by MGI Primary source MGI:MGI:108176 See related Ensembl:ENSMUSG00000053198 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 L-Periaxin Expression Biased expression in lung adult (RPKM 29.1), mammary gland adult (RPKM 3.3) and 3 other tissues See more Orthologs human all
Genomic context
Location: 7 A3; 7 15.91 cM See Prx in Genome Data Viewer Exon count: 8
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (27499305..27520041)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 7 NC_000073.5 (28284343..28305060)
Chromosome 7 - NC_000073.6
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Transcript information: This gene has 6 transcripts
Gene: Prx ENSMUSG00000053198
Description periaxin [Source:MGI Symbol;Acc:MGI:108176] Gene Synonyms L-Periaxin Location Chromosome 7: 27,497,388-27,520,214 forward strand. GRCm38:CM001000.2 About this gene This gene has 6 transcripts (splice variants), 143 orthologues, 2 paralogues, is a member of 1 Ensembl protein family and is associated with 18 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Prx-203 ENSMUST00000108355.1 5433 148aa ENSMUSP00000103992.1 Protein coding CCDS39849 O55103 TSL:1 GENCODE basic APPRIS ALT2
Prx-202 ENSMUST00000098644.8 4841 1391aa ENSMUSP00000096241.2 Protein coding CCDS21023 E9QQ57 TSL:1 GENCODE basic APPRIS P3
Prx-205 ENSMUST00000238936.1 4841 1391aa ENSMUSP00000158878.1 Protein coding CCDS21023 - GENCODE basic APPRIS P3
Prx-206 ENSMUST00000238964.1 4575 1525aa ENSMUSP00000159082.1 Protein coding - - CDS 3' incomplete
Prx-201 ENSMUST00000065487.6 4497 1391aa ENSMUSP00000066110.6 Protein coding - Q6NVF7 TSL:1 GENCODE basic APPRIS ALT2
Prx-204 ENSMUST00000125990.1 4298 1252aa ENSMUSP00000145598.1 Protein coding - A0A0U1RNK1 TSL:1 GENCODE basic
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42.83 kb Forward strand 27.49Mb 27.50Mb 27.51Mb 27.52Mb 27.53Mb Genes (Comprehensive set... Sertad1-201 >protein coding Prx-206 >protein coding Hipk4-202 >protein coding
Sertad1-202 >protein coding Prx-205 >protein coding Hipk4-201 >protein coding
Prx-203 >protein coding
Prx-202 >protein coding
Prx-204 >protein coding
Prx-201 >protein coding
Contigs < AC158304.11
Genes < Gm15541-201lncRNA (Comprehensive set...
Regulatory Build
27.49Mb 27.50Mb 27.51Mb 27.52Mb 27.53Mb Reverse strand 42.83 kb
Regulation Legend
CTCF Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
RNA gene
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Transcript: ENSMUST00000108355
20.89 kb Forward strand
Prx-203 >protein coding
ENSMUSP00000103... Low complexity (Seg) Superfamily PDZ superfamily SMART PDZ domain Pfam PDZ domain PROSITE profiles PDZ domain PANTHER PTHR23348
PTHR23348:SF42 Gene3D 2.30.42.10 CDD cd00992
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant splice region variant synonymous variant
Scale bar 0 20 40 60 80 100 120 148
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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