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Mouse Plxnb3 Knockout Project (CRISPR/Cas9)

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Mouse Plxnb3 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Plxnb3 Knockout Project (CRISPR/Cas9) Objective: To create a Plxnb3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Plxnb3 gene (NCBI Reference Sequence: NM_019587 ; Ensembl: ENSMUSG00000031385 ) is located on Mouse chromosome X. 35 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 35 (Transcript: ENSMUST00000002079). Exon 2~15 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 a knock-out allele exhibit normal retinal stratification. Exon 2 starts from the coding region. Exon 2~15 covers 48.05% of the coding region. The size of effective KO region: ~6850 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 35 Legends Exon of mouse Plxnb3 Knockout region Page 2 of 9 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 1372 bp section upstream of Exon 2 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 632 bp section downstream of Exon 15 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. Page 3 of 9 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(1372bp) | A(18.15% 249) | C(28.94% 397) | T(33.02% 453) | G(19.9% 273) Note: The 1372 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(632bp) | A(30.38% 192) | C(19.78% 125) | T(18.67% 118) | G(31.17% 197) Note: The 632 bp section downstream of Exon 15 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. Page 4 of 9 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 1372 1 1372 1372 100.0% chrX + 73757157 73758528 1372 browser details YourSeq 45 1207 1274 1372 77.8% chr2 - 117899229 117899286 58 browser details YourSeq 44 1128 1226 1372 90.6% chr10 - 11254267 11254422 156 browser details YourSeq 44 1163 1233 1372 78.0% chr1 + 149535353 149535413 61 browser details YourSeq 37 1213 1261 1372 92.7% chr10 + 89227258 89227307 50 browser details YourSeq 32 1188 1238 1372 69.5% chr15 + 25184076 25184111 36 browser details YourSeq 32 1202 1240 1372 83.8% chr14 + 79991247 79991283 37 browser details YourSeq 31 1207 1240 1372 97.1% chr19 + 41570591 41570626 36 browser details YourSeq 30 1209 1254 1372 71.9% chr1 + 99630970 99631003 34 browser details YourSeq 28 1208 1240 1372 83.9% chr2 + 157456203 157456233 31 browser details YourSeq 28 1211 1246 1372 85.3% chr11 + 117674076 117674110 35 browser details YourSeq 27 1209 1241 1372 93.6% chr8 + 114783669 114783702 34 browser details YourSeq 24 1207 1233 1372 84.0% chr8 + 34745131 34745155 25 browser details YourSeq 24 1209 1235 1372 84.0% chr6 + 101101222 101101246 25 browser details YourSeq 23 1208 1233 1372 83.4% chr16 + 76624544 76624567 24 browser details YourSeq 23 1208 1233 1372 83.4% chr13 + 111123477 111123500 24 browser details YourSeq 22 1209 1234 1372 84.0% chr7 + 135193577 135193601 25 browser details YourSeq 20 1209 1228 1372 100.0% chrX - 67229456 67229475 20 browser details YourSeq 20 1209 1228 1372 100.0% chr8 - 120623553 120623572 20 browser details YourSeq 20 1209 1228 1372 100.0% chr6 - 139771506 139771525 20 Note: The 1372 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 632 1 632 632 100.0% chrX + 73765374 73766005 632 browser details YourSeq 33 225 304 632 94.6% chr11 - 28639516 28639601 86 browser details YourSeq 28 511 539 632 100.0% chr11 - 82441084 82441452 369 browser details YourSeq 27 261 303 632 93.6% chr1 - 171709021 171709102 82 browser details YourSeq 23 492 514 632 100.0% chr12 + 53144119 53144141 23 browser details YourSeq 21 520 542 632 95.7% chr11 - 45687486 45687508 23 browser details YourSeq 21 480 500 632 100.0% chr1 - 14551238 14551258 21 browser details YourSeq 21 224 244 632 100.0% chr13 + 80624618 80624638 21 browser details YourSeq 20 111 130 632 100.0% chr14 - 66786966 66786985 20 browser details YourSeq 20 486 505 632 100.0% chr12 - 35707487 35707506 20 Note: The 632 bp section downstream of Exon 15 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Plxnb3 plexin B3 [ Mus musculus (house mouse) ] Gene ID: 140571, updated on 11-Sep-2019 Gene summary Official Symbol Plxnb3 provided by MGI Official Full Name plexin B3 provided by MGI Primary source MGI:MGI:2154240 See related Ensembl:ENSMUSG00000031385 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 Plxn6; AI451018 Expression Biased expression in cerebellum adult (RPKM 6.4), cortex adult (RPKM 3.8) and 10 other tissues See more Orthologs human all Genomic context Location: X; X A7.3 See Plxnb3 in Genome Data Viewer Exon count: 37 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (73756556..73772510) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) X NC_000086.6 (71002442..71017849) Chromosome X - NC_000086.7 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 5 transcripts Gene: Plxnb3 ENSMUSG00000031385 Description plexin B3 [Source:MGI Symbol;Acc:MGI:2154240] Gene Synonyms Plxn6 Location Chromosome X: 73,757,090-73,772,514 forward strand. GRCm38:CM001013.2 About this gene This gene has 5 transcripts (splice variants), 166 orthologues, 8 paralogues, is a member of 1 Ensembl protein family and is associated with 2 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Plxnb3-201 ENSMUST00000002079.6 6030 1902aa ENSMUSP00000002079.6 Protein coding CCDS41013 Q9QY40 TSL:5 GENCODE basic APPRIS P1 Plxnb3-204 ENSMUST00000149478.7 6217 No protein - Retained intron - - TSL:1 Plxnb3-203 ENSMUST00000147127.7 5212 No protein - Retained intron - - TSL:2 Plxnb3-202 ENSMUST00000146812.7 5030 No protein - Retained intron - - TSL:1 Plxnb3-205 ENSMUST00000155096.1 2296 No protein - Retained intron - - TSL:1 Page 7 of 9 https://www.alphaknockout.com 35.42 kb Forward strand 73.75Mb 73.76Mb 73.77Mb 73.78Mb Genes Gm25226-201 >snoRNPAlxnb3-203 >retained intron Srpk3-202 >retained intron (Comprehensive set... Plxnb3-202 >retained intron Srpk3-201 >protein coding Plxnb3-204 >retained intron Srpk3-203 >retained intron Plxnb3-201 >protein coding Srpk3-204 >retained intron Plxnb3-205 >retained intron Contigs AL672094.11 > Genes < Idh3g-209retained intron (Comprehensive set... < Idh3g-202retained intron < Idh3g-208retained intron < Idh3g-204retained intron < Idh3g-206retained intron < Idh3g-203retained intron < Idh3g-201protein coding < Idh3g-205lncRNA < Idh3g-207lncRNA Regulatory Build 73.75Mb 73.76Mb 73.77Mb 73.78Mb Reverse strand 35.42 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding merged Ensembl/Havana Non-Protein Coding RNA gene processed transcript Page 8 of 9 https://www.alphaknockout.com Transcript: ENSMUST00000002079 15.42 kb Forward strand Plxnb3-201 >protein coding ENSMUSP00000002... Transmembrane heli... Low complexity (Seg) Coiled-coils (Ncoils) Cleavage site (Sign... Superfamily Sema domain superfamily SSF103575 Immunoglobulin E-set Rho GTPase activation protein SMART Sema domain PSI domain IPT domain Pfam Sema domain Plexin repeat IPT domain Plexin, cytoplasmic RasGAP domain Plexin, TIG domain 1 Plexin, TIG domain 2 PROSITE profiles Sema domain PANTHER Plexin family PTHR22625:SF33 Gene3D WD40/YVTN repeat-like-containing domain superfamily 1.10.506.10 Immunoglobulin-like fold 3.10.20.90 CDD cd11277 cd01180 cd00603 cd12791 cd01179 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 200 400 600 800 1000 1200 1400 1600 1902 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 9 of 9.
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