https://www.alphaknockout.com
Mouse Nbeal2 Knockout Project (CRISPR/Cas9)
Objective: To create a Nbeal2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Nbeal2 gene (NCBI Reference Sequence: NM_183276 ; Ensembl: ENSMUSG00000056724 ) is located on Mouse chromosome 9. 54 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 54 (Transcript: ENSMUST00000167320). Exon 7~27 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: Homozygous null mice exhibit megakaryocyte and platelet abnormalities resulting in impaired arterial thrombus formation and protection from infarction following cerebral ischemia. Wound repair is impaired. These abnormalities result in a bleeding disorder similiar to Gray Platelet Syndrome.
Exon 7 starts from about 6.72% of the coding region. Exon 7~27 covers 45.59% of the coding region. The size of effective KO region: ~8789 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' 15 18
1 7 8 9 10 11 12 13 14 16 17 1920 21 22 23 24 25 26 27 54
Legends Exon of mouse Nbeal2 Knockout region
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Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 1241 bp section upstream of Exon 7 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 526 bp section downstream of Exon 27 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(1241bp) | A(19.26% 239) | C(31.67% 393) | T(24.66% 306) | G(24.42% 303)
Note: The 1241 bp section upstream of Exon 7 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(526bp) | A(21.29% 112) | C(27.76% 146) | T(24.33% 128) | G(26.62% 140)
Note: The 526 bp section downstream of Exon 27 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 1241 1 1241 1241 100.0% chr9 - 110642471 110643711 1241 browser details YourSeq 27 578 606 1241 96.6% chr1 - 51913979 51914007 29 browser details YourSeq 26 584 610 1241 100.0% chr11 - 121520026 121520054 29 browser details YourSeq 25 334 364 1241 96.3% chr19 - 4622186 4622218 33 browser details YourSeq 24 729 756 1241 96.2% chr1 - 87258024 87258056 33 browser details YourSeq 22 722 743 1241 100.0% chr2 - 150131060 150131081 22 browser details YourSeq 21 587 607 1241 100.0% chr1 - 180621686 180621706 21 browser details YourSeq 21 586 606 1241 100.0% chr1 - 64256372 64256392 21 browser details YourSeq 21 587 607 1241 100.0% chr1 - 34077411 34077431 21 browser details YourSeq 21 586 606 1241 100.0% chr1 - 15179472 15179492 21 browser details YourSeq 20 416 437 1241 95.5% chr1 - 132153761 132153782 22
Note: The 1241 bp section upstream of Exon 7 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 526 1 526 526 100.0% chr9 - 110633156 110633681 526 browser details YourSeq 41 209 262 526 90.0% chr1 + 89955805 89955860 56 browser details YourSeq 40 209 257 526 91.7% chr2 + 157132852 157132903 52 browser details YourSeq 39 209 268 526 84.4% chr10 + 70966439 70966497 59 browser details YourSeq 38 209 256 526 91.5% chr10 + 30460329 30460381 53 browser details YourSeq 37 209 253 526 93.4% chr1 - 37228416 37228464 49 browser details YourSeq 37 209 252 526 93.1% chr9 + 117635454 117635500 47 browser details YourSeq 37 210 251 526 95.2% chr1 + 16015814 16015858 45 browser details YourSeq 36 210 252 526 92.9% chr7 + 102027500 102027545 46 browser details YourSeq 36 202 252 526 89.2% chr10 + 92627242 92627765 524 browser details YourSeq 36 209 253 526 91.0% chr10 + 75527038 75527085 48 browser details YourSeq 35 209 252 526 90.7% chr1 + 16602982 16603028 47 browser details YourSeq 34 209 253 526 88.7% chr18 - 5927648 5927692 45 browser details YourSeq 34 208 250 526 90.5% chr1 - 153316574 153316619 46 browser details YourSeq 34 209 253 526 88.7% chr8 + 106570274 106570321 48 browser details YourSeq 33 222 264 526 81.1% chr7 - 116464041 116464078 38 browser details YourSeq 33 209 251 526 90.3% chr11 + 72944422 72944467 46 browser details YourSeq 33 209 249 526 92.4% chr10 + 95922152 95922195 44 browser details YourSeq 33 218 255 526 94.8% chr1 + 133454703 133454747 45 browser details YourSeq 32 209 253 526 86.4% chrX - 103289721 103289768 48
Note: The 526 bp section downstream of Exon 27 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Nbeal2 neurobeachin-like 2 [ Mus musculus (house mouse) ] Gene ID: 235627, updated on 13-Aug-2019
Gene summary
Official Symbol Nbeal2 provided by MGI Official Full Name neurobeachin-like 2 provided by MGI Primary source MGI:MGI:2448554 See related Ensembl:ENSMUSG00000056724 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 BC042396; mKIAA0540; 1110014F23Rik Expression Broad expression in thymus adult (RPKM 58.1), colon adult (RPKM 27.1) and 15 other tissues See more Orthologs human all
Genomic context
Location: 9; 9 F2 See Nbeal2 in Genome Data Viewer Exon count: 54
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (110624789..110654161, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (110527293..110556665, complement)
Chromosome 9 - NC_000075.6
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Transcript information: This gene has 11 transcripts
Gene: Nbeal2 ENSMUSG00000056724
Description neurobeachin-like 2 [Source:MGI Symbol;Acc:MGI:2448554] Gene Synonyms 1110014F23Rik Location Chromosome 9: 110,624,789-110,654,161 reverse strand. GRCm38:CM001002.2 About this gene This gene has 11 transcripts (splice variants), 191 orthologues, 7 paralogues, is a member of 1 Ensembl protein family and is associated with 32 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Nbeal2- ENSMUST00000167320.7 8803 2750aa ENSMUSP00000128586.1 Protein coding CCDS52939 E9Q9L6 TSL:1 210 GENCODE basic APPRIS P2
Nbeal2- ENSMUST00000133191.7 8782 2743aa ENSMUSP00000121373.1 Protein coding - Q6ZQA0 TSL:5 206 GENCODE basic APPRIS ALT2
Nbeal2- ENSMUST00000196488.4 8599 2716aa ENSMUSP00000143265.1 Protein coding - A0A0G2JFQ4 TSL:5 211 GENCODE basic APPRIS ALT2
Nbeal2- ENSMUST00000130024.1 6180 2032aa ENSMUSP00000118061.1 Protein coding - F6VTL9 CDS 5' 204 incomplete TSL:5
Nbeal2- ENSMUST00000131017.7 3303 1073aa ENSMUSP00000114660.1 Protein coding - F6ZZB1 CDS 5' 205 incomplete TSL:5
Nbeal2- ENSMUST00000149089.1 1869 593aa ENSMUSP00000119254.1 Protein coding - D3Z2K6 CDS 3' 208 incomplete TSL:5
Nbeal2- ENSMUST00000123996.1 457 96aa ENSMUSP00000122014.1 Nonsense mediated - F7CGQ9 CDS 5' 201 decay incomplete TSL:5
Nbeal2- ENSMUST00000129095.1 664 No - Retained intron - - TSL:2 203 protein
Nbeal2- ENSMUST00000138072.1 479 No - Retained intron - - TSL:2 207 protein
Nbeal2- ENSMUST00000126088.3 432 No - Retained intron - - TSL:2 202 protein
Nbeal2- ENSMUST00000153960.1 295 No - Retained intron - - TSL:5 209 protein
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49.37 kb Forward strand 110.62Mb 110.63Mb 110.64Mb 110.65Mb 110.66Mb Genes Setd2-201 >protein coding Gm42470-201 >lncRNA (Comprehensive set...
Setd2-203 >nonsense mediated decay Ccdc12-201 >protein coding
Setd2-210 >protein coding Ccdc12-206 >retained intron
Setd2-205 >nonsense mediated decay Ccdc12-203 >retained intron
Setd2-204 >retained intron Ccdc12-204 >protein coding
Ccdc12-208 >retained intron
Ccdc12-207 >lncRNA
Contigs < AC132103.3 < AC123811.3 Genes (Comprehensive set... < Nradd-201protein coding< Nbeal2-202retained intron < Mir8107-201miRNA
< Nradd-202protein coding < Nbeal2-203retained intron < Nbeal2-208protein coding
< Nradd-203protein coding < Nbeal2-201nonsense mediated decay
< Nradd-204retained intron < Nbeal2-207retained intron
< Nbeal2-210protein coding
< Nbeal2-206protein coding
< Nbeal2-211protein coding
< Nbeal2-204protein coding
< Nbeal2-205protein coding < Nbeal2-209retained intron
Regulatory Build
110.62Mb 110.63Mb 110.64Mb 110.65Mb 110.66Mb Reverse strand 49.37 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
RNA gene processed transcript
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Transcript: ENSMUST00000167320
< Nbeal2-210protein coding
Reverse strand 29.37 kb
ENSMUSP00000128... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily Concanavalin A-like lectin/glucanase domain superfamily SSF50729 WD40-repeat-containing domain superfamily
Armadillo-type fold BEACH domain superfamily SMART BEACH domain WD40 repeat
Pfam PF16057 PH-BEACH domain WD40 repeat
Domain of unknown function DUF4704 BEACH domain PROSITE profiles BEACH domain WD40 repeat
PH-BEACH domain WD40-repeat-containing domain PANTHER Neurobeachin-like protein 2
PTHR13743 Gene3D BEACH domain superfamily
2.30.29.40 CDD PH-BEACH domain
BEACH domain
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
stop gained inframe insertion missense variant splice region variant synonymous variant
Scale bar 0 400 800 1200 1600 2000 2750
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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