https://www.alphaknockout.com
Mouse Nprl2 Knockout Project (CRISPR/Cas9)
Objective: To create a Nprl2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Nprl2 gene (NCBI Reference Sequence: NM_018879.2 ; Ensembl: ENSMUSG00000010057 ) is located on Mouse chromosome 9. 11 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 11 (Transcript: ENSMUST00000010201). Exon 5~10 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 reduced embryo size, microphthalmia, occaional anophthalmia, pale liver, reduced fetal liver hematopoiesis, impaired erythropoiesis and reduced methionine synthesis.
Exon 5 starts from about 39.39% of the coding region. Exon 5~10 covers 43.51% of the coding region. The size of effective KO region: ~1106 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 4 5 6 7 8 9 10 11
Legends Exon of mouse Nprl2 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 5 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 2000 bp section downstream of Exon 10 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(2000bp) | A(23.6% 472) | C(24.9% 498) | T(20.9% 418) | G(30.6% 612)
Note: The 2000 bp section upstream of Exon 5 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(25.9% 518) | C(21.4% 428) | T(23.75% 475) | G(28.95% 579)
Note: The 2000 bp section downstream of Exon 10 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 + 107542194 107544193 2000 browser details YourSeq 144 1664 1846 2000 93.4% chr10 - 62673331 62673571 241 browser details YourSeq 142 1682 1845 2000 94.4% chr5 + 104132482 104132646 165 browser details YourSeq 142 1680 1845 2000 93.4% chr19 + 10923310 10923481 172 browser details YourSeq 141 1682 1837 2000 95.5% chr6 - 4671477 4671632 156 browser details YourSeq 139 1676 1842 2000 92.1% chr6 + 49754767 49754934 168 browser details YourSeq 139 1682 1844 2000 93.2% chr13 + 112874178 112874341 164 browser details YourSeq 136 1691 1845 2000 92.8% chr12 + 109498023 109498176 154 browser details YourSeq 135 1686 1837 2000 94.7% chr10 - 43925741 43925892 152 browser details YourSeq 134 1686 1831 2000 94.5% chr3 + 34763503 34763647 145 browser details YourSeq 134 1682 1845 2000 88.2% chr10 + 59691628 59691788 161 browser details YourSeq 133 1691 1845 2000 91.6% chr9 - 107986235 107986388 154 browser details YourSeq 133 1682 1837 2000 93.6% chr7 - 126067311 126067472 162 browser details YourSeq 132 1691 1845 2000 93.5% chr17 - 74682161 74682368 208 browser details YourSeq 132 1691 1845 2000 91.4% chr17 + 29641743 29641895 153 browser details YourSeq 131 1691 1845 2000 94.0% chr10 - 94157417 94157582 166 browser details YourSeq 131 1691 1843 2000 91.5% chr1 - 93267976 93268127 152 browser details YourSeq 131 1691 1844 2000 92.8% chr5 + 3413920 3414073 154 browser details YourSeq 131 1686 1846 2000 91.2% chr2 + 128774995 128775156 162 browser details YourSeq 130 1691 1843 2000 92.9% chr13 - 11547626 11547787 162
Note: The 2000 bp section upstream of Exon 5 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 + 107545300 107547299 2000 browser details YourSeq 88 579 726 2000 85.6% chr7 - 101803778 101803926 149 browser details YourSeq 88 523 706 2000 81.3% chr11 - 119389308 119389468 161 browser details YourSeq 85 522 699 2000 86.0% chr1 - 10747475 10747651 177 browser details YourSeq 83 523 699 2000 81.2% chr3 - 138888516 138888662 147 browser details YourSeq 83 524 698 2000 86.5% chr10 + 40996463 40996634 172 browser details YourSeq 79 579 699 2000 88.5% chrX + 12841761 12841881 121 browser details YourSeq 78 537 701 2000 81.1% chr13 - 55731164 55731301 138 browser details YourSeq 78 579 707 2000 81.5% chr12 - 71103258 71103386 129 browser details YourSeq 78 585 740 2000 79.9% chr12 + 4657690 4657838 149 browser details YourSeq 76 579 699 2000 86.8% chr14 - 39793487 39793607 121 browser details YourSeq 74 523 698 2000 81.0% chr12 - 83669922 83670053 132 browser details YourSeq 74 538 699 2000 90.6% chr10 - 63242386 63242553 168 browser details YourSeq 71 594 771 2000 77.3% chr10 + 80885356 80885473 118 browser details YourSeq 69 603 701 2000 93.9% chr13 - 98281750 98281848 99 browser details YourSeq 68 603 701 2000 92.7% chr12 - 43474998 43475096 99 browser details YourSeq 68 605 699 2000 93.7% chr8 + 85103786 85103880 95 browser details YourSeq 67 603 707 2000 89.5% chr12 + 89409575 89409679 105 browser details YourSeq 67 594 700 2000 88.3% chr10 + 59538000 59538105 106 browser details YourSeq 66 603 698 2000 89.5% chr14 - 120866337 120866432 96
Note: The 2000 bp section downstream of Exon 10 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Nprl2 NPR2 like, GATOR1 complex subunit [ Mus musculus (house mouse) ] Gene ID: 56032, updated on 26-Jun-2020
Gene summary
Official Symbol Nprl2 provided by MGI Official Full Name NPR2 like, GATOR1 complex subunit provided by MGI Primary source MGI:MGI:1914482 See related Ensembl:ENSMUSG00000010057 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 G21; NPR2L; Tusc4; 2810446G01Rik Expression Ubiquitous expression in CNS E18 (RPKM 22.0), whole brain E14.5 (RPKM 21.6) and 28 other tissues See more Orthologs human all
Genomic context
Location: 9; 9 F1 See Nprl2 in Genome Data Viewer Exon count: 11
Annotation release Status Assembly Chr Location
108.20200622 current GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (107542177..107545706)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (107444540..107448037)
Chromosome 9 - NC_000075.6
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Transcript information: This gene has 5 transcripts
Gene: Nprl2 ENSMUSG00000010057
Description NPR2 like, GATOR1 complex subunit [Source:MGI Symbol;Acc:MGI:1914482] Gene Synonyms 2810446G01Rik, G21, NPR2L, NPRL2, Tusc4 Location Chromosome 9: 107,542,226-107,545,706 forward strand. GRCm38:CM001002.2 About this gene This gene has 5 transcripts (splice variants), 259 orthologues, is a member of 1 Ensembl protein family and is associated with 9 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Nprl2- ENSMUST00000010201.8 1441 380aa ENSMUSP00000010201.3 Protein coding CCDS23492 Q9WUE4 TSL:1 201 GENCODE basic APPRIS P1
Nprl2- ENSMUST00000195370.5 829 163aa ENSMUSP00000141746.1 Nonsense mediated - A0A0A6YWX8 TSL:3 205 decay
Nprl2- ENSMUST00000193628.5 1736 No - Retained intron - - TSL:2 203 protein
Nprl2- ENSMUST00000194848.1 637 No - Retained intron - - TSL:2 204 protein
Nprl2- ENSMUST00000192951.1 391 No - Retained intron - - TSL:3 202 protein
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23.48 kb Forward strand 107.535Mb 107.540Mb 107.545Mb 107.550Mb 107.555Mb Genes (Comprehensive set... Tmem115-201 >protein coding Nprl2-201 >protein coding Zmynd10-201 >protein coding Rassf1-210 >processed transcript
Nprl2-205 >nonsense mediated decay Zmynd10-205 >processed transcript Rassf1-201 >protein coding
Nprl2-203 >retained intron Zmynd10-203 >nonsense mediated decay
Nprl2-204 >retained intron Zmynd10-204 >retained intron
Nprl2-202 >retained intron Zmynd10-202 >retained intron
Rassf1-209 >nonsense mediated decay
Rassf1-202 >protein coding
Rassf1-205 >retained intron
Rassf1-204 >protein coding
Contigs AL672219.7 >
Genes < Cyb561d2-201protein coding < Gm34106-201antisense (Comprehensive set...
< Cyb561d2-205protein coding
< Cyb561d2-202protein coding
< Cyb561d2-203processed transcript
< Cyb561d2-204nonsense mediated decay
Regulatory Build
107.535Mb 107.540Mb 107.545Mb 107.550Mb 107.555Mb Reverse strand 23.48 kb
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript
Regulation Legend CTCF Promoter Promoter Flank
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Transcript: ENSMUST00000010201
3.48 kb Forward strand
Nprl2-201 >protein coding
ENSMUSP00000010... Pfam Nitrogen permease regulator 2 PANTHER Nitrogen permease regulator 2
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant splice region variant synonymous variant
Scale bar 0 40 80 120 160 200 240 280 320 380
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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