https://www.alphaknockout.com

Mouse Sla2 Knockout Project (CRISPR/Cas9)

Objective: To create a Sla2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.

Strategy summary: The Sla2 gene (NCBI Reference Sequence: NM_029983 ; Ensembl: ENSMUSG00000027636 ) is located on Mouse chromosome 2. 8 exons are identified, with the ATG start codon in exon 2 and the TAG stop codon in exon 8 (Transcript: ENSMUST00000029164). Exon 2~6 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 a knock-out allele exhibit normal B and T cells.

Exon 2 starts from the coding region. Exon 2~6 covers 68.08% of the coding region. The size of effective KO region: ~7886 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 5 6 8

Legends Exon of mouse Sla2 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 812 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(28.0% 560) | C(24.1% 482) | T(21.45% 429) | G(26.45% 529)

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(812bp) | A(25.12% 204) | C(23.77% 193) | T(25.86% 210) | G(25.25% 205)

Note: The 812 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% chr2 - 156883677 156885676 2000 browser details YourSeq 609 1 1164 2000 93.3% chr2 - 156924115 156925276 1162 browser details YourSeq 268 1236 1757 2000 85.8% chr10 - 58467810 58468250 441 browser details YourSeq 251 1238 1750 2000 85.9% chr11 + 4811433 4811867 435 browser details YourSeq 250 1238 1742 2000 91.5% chr15 - 79652238 79652764 527 browser details YourSeq 240 1237 1747 2000 90.3% chr15 - 8089095 8089904 810 browser details YourSeq 234 1239 1746 2000 90.9% chr10 - 94016614 94017190 577 browser details YourSeq 233 1241 1738 2000 87.1% chr1 - 153759034 153759391 358 browser details YourSeq 227 1241 1747 2000 87.9% chr16 + 4040863 4041447 585 browser details YourSeq 207 1268 1747 2000 89.6% chr11 + 32633476 32683436 49961 browser details YourSeq 206 1272 1677 2000 92.0% chr10 - 45770062 45770641 580 browser details YourSeq 203 1328 1759 2000 93.2% chr7 + 116348716 116349400 685 browser details YourSeq 199 1265 1747 2000 81.6% chr8 + 106963806 106964119 314 browser details YourSeq 195 1263 1715 2000 86.5% chr4 - 126085604 126085929 326 browser details YourSeq 183 1263 1715 2000 91.1% chr7 - 105680012 105680468 457 browser details YourSeq 182 1241 1696 2000 91.5% chr7 + 75783401 75783857 457 browser details YourSeq 179 1264 1723 2000 81.3% chr17 - 32843234 32843497 264 browser details YourSeq 173 1263 1747 2000 82.5% chr8 + 120212094 120212469 376 browser details YourSeq 166 1280 1758 2000 82.9% chr9 - 55694113 55694414 302 browser details YourSeq 165 1263 1730 2000 82.3% chr3 + 90054247 90054610 364

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 812 1 812 812 100.0% chr2 - 156875010 156875821 812 browser details YourSeq 109 357 498 812 89.4% chr4 - 150557295 150557441 147 browser details YourSeq 106 357 498 812 91.0% chr6 + 88656605 88656744 140 browser details YourSeq 104 358 498 812 92.0% chr8 + 55882915 55883073 159 browser details YourSeq 103 357 498 812 86.0% chr10 + 81099574 81099713 140 browser details YourSeq 102 357 498 812 88.2% chr7 - 130829751 130829897 147 browser details YourSeq 101 344 481 812 92.5% chrX - 140459541 140459689 149 browser details YourSeq 101 361 498 812 86.3% chr17 - 23702892 23703027 136 browser details YourSeq 100 357 498 812 91.8% chr5 - 10728097 10728255 159 browser details YourSeq 100 357 482 812 90.4% chr18 - 68037119 68037248 130 browser details YourSeq 100 357 495 812 86.8% chr17 - 24551491 24551633 143 browser details YourSeq 100 357 499 812 89.6% chrX + 153098076 153098222 147 browser details YourSeq 100 361 498 812 92.6% chr1 + 195276507 195276652 146 browser details YourSeq 99 357 496 812 89.6% chr7 - 135690510 135690668 159 browser details YourSeq 99 361 485 812 90.4% chr7 - 102455684 102456170 487 browser details YourSeq 98 357 498 812 87.3% chr2 + 177800851 177800988 138 browser details YourSeq 98 356 498 812 84.8% chr1 + 171093745 171093884 140 browser details YourSeq 97 357 485 812 88.2% chr5 + 89437955 89438086 132 browser details YourSeq 97 361 485 812 93.9% chr11 + 104355250 104355378 129 browser details YourSeq 96 361 498 812 85.1% chr3 - 54428789 54428924 136

Note: The 812 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: Sla2 Src-like-adaptor 2 [ Mus musculus (house mouse) ] Gene ID: 77799, updated on 24-Oct-2019

Gene summary

Official Symbol Sla2 provided by MGI Official Full Name Src-like-adaptor 2 provided by MGI Primary source MGI:MGI:1925049 See related Ensembl:ENSMUSG00000027636 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 SLAP2; SLAP-2; AI430952; A930009E21Rik Expression Ubiquitous expression in thymus adult (RPKM 36.8), placenta adult (RPKM 10.3) and 27 other tissues See more Orthologs human all

Genomic context

Location: 2; 2 H1 See Sla2 in Genome Data Viewer Exon count: 8

Annotation release Status Assembly Chr Location

108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (156874151..156887250, complement)

Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (156698658..156712814, complement)

Chromosome 2 - NC_000068.7

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Transcript information: This gene has 2 transcripts

Gene: Sla2 ENSMUSG00000027636

Description Src-like-adaptor 2 [Source:MGI Symbol;Acc:MGI:1925049] Gene Synonyms A930009E21Rik, SLAP-2, SLAP2 Location Chromosome 2: 156,872,457-156,887,192 reverse strand. GRCm38:CM000995.2 About this gene This gene has 2 transcripts (splice variants), 186 orthologues, 8 paralogues and is a member of 1 Ensembl protein family. Transcripts

Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags

Sla2-201 ENSMUST00000029164.8 2973 259aa ENSMUSP00000029164.2 Protein coding CCDS38302 Q8R4L0 TSL:1 GENCODE basic APPRIS P1

Sla2-202 ENSMUST00000109561.3 2634 259aa ENSMUSP00000105189.3 Protein coding CCDS38302 Q8R4L0 TSL:1 GENCODE basic APPRIS P1

34.74 kb Forward strand 156.87Mb 156.88Mb 156.89Mb Genes Rab5if-201 >protein coding Gm14248-201 >processed pseudogene (Comprehensive set...

Rab5if-203 >lncRNA

Rab5if-204 >retained intron Rab5if-202 >lncRNA

Contigs AL935150.10 > Genes (Comprehensive set... < 5430405H02Rik-203lncRNA < Sla2-201protein coding < Gm14278-201unprocessed pseudogene

< 5430405H02Rik-202lncRNA < Sla2-202protein coding < Gm14247-201processed pseudogene

< 5430405H02Rik-201lncRNA

Regulatory Build

156.87Mb 156.88Mb 156.89Mb Reverse strand 34.74 kb

Regulation Legend CTCF Enhancer Promoter Promoter Flank

Gene Legend Protein Coding

merged Ensembl/Havana Ensembl protein coding

Non-Protein Coding

processed transcript RNA gene pseudogene

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Transcript: ENSMUST00000029164

< Sla2-201protein coding

Reverse strand 14.62 kb

ENSMUSP00000029... MobiDB lite Low complexity (Seg) Superfamily SH3-like domain superfamily SH2 domain superfamily

SMART SH3 domain SH2 domain

Prints SH2 domain Pfam SH3 domain SH2 domain

PROSITE profiles SH3 domain SH2 domain

PANTHER Src-like-adapter 2

PTHR10155 Gene3D 2.30.30.40 SH2 domain superfamily

CDD SLAP, SH2 domain

All sequence SNPs/i... Sequence variants (dbSNP and all other sources)

Variant Legend inframe insertion missense variant splice region variant synonymous variant

Scale bar 0 40 80 120 160 200 259

We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.

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