https://www.alphaknockout.com
Mouse Dlg2 Conditional Knockout Project (CRISPR/Cas9)
Objective: To create a Dlg2 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Dlg2 gene (NCBI Reference Sequence: NM_011807 ; Ensembl: ENSMUSG00000052572 ) is located on Mouse chromosome 7. 23 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 23 (Transcript: ENSMUST00000107196). Exon 13 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Dlg2 gene. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice homozygous for a knock-out allele display lower surface expression of NMDA receptor (NMDAR) subunits NR2A and NR2B in dorsal horn neurons and significantly reduced NMDAR-mediated excitatory synaptic currents and NMDAR-dependent persistent inflammatory or nerve injury-induced neuropathic pain.
Exon 13 starts from about 55.09% of the coding region. The knockout of Exon 13 will result in frameshift of the gene. The size of intron 12 for 5'-loxP site insertion: 37821 bp, and the size of intron 13 for 3'-loxP site insertion: 159848 bp. The size of effective cKO region: ~603 bp. The cKO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele gRNA region 5' gRNA region 3'
1 13 23 Targeting vector
Targeted allele
Constitutive KO allele (After Cre recombination)
Legends Exon of mouse Dlg2 Homology arm cKO region loxP site
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Overview of the Dot Plot Window size: 10 bp
Forward Reverse Complement
Sequence 12
Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. It may be difficult to construct this targeting vector.
Overview of the GC Content Distribution Window size: 300 bp
Sequence 12
Summary: Full Length(7103bp) | A(31.93% 2268) | C(18.74% 1331) | T(30.76% 2185) | G(18.57% 1319)
Note: The sequence of homologous arms and cKO region 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 3000 1 3000 3000 100.0% chr7 + 92123291 92126290 3000 browser details YourSeq 162 1375 1847 3000 91.0% chr19 + 4898482 5073011 174530 browser details YourSeq 145 1616 1864 3000 86.3% chr8 + 95029615 95030116 502 browser details YourSeq 138 1595 1847 3000 91.7% chr13 + 74852241 74852526 286 browser details YourSeq 138 1399 1839 3000 82.2% chr1 + 44541641 44541913 273 browser details YourSeq 135 1708 1866 3000 93.1% chr5 + 20977919 20978082 164 browser details YourSeq 133 1705 1864 3000 93.6% chr3 + 152388614 152388773 160 browser details YourSeq 131 1705 1865 3000 88.2% chrX - 140216856 140217008 153 browser details YourSeq 131 1405 1847 3000 83.1% chr6 - 122750449 122750808 360 browser details YourSeq 131 1696 1847 3000 93.5% chr1 + 161599036 161599190 155 browser details YourSeq 130 1705 1864 3000 91.2% chr11 - 106616439 106616618 180 browser details YourSeq 129 1704 1864 3000 88.4% chr2 - 120945448 120945604 157 browser details YourSeq 125 1704 1853 3000 91.9% chrX - 156047944 156048098 155 browser details YourSeq 125 1705 1862 3000 91.4% chr3 - 14634372 14634542 171 browser details YourSeq 124 1694 1859 3000 89.0% chr12 - 102799387 102799551 165 browser details YourSeq 123 1703 1848 3000 92.5% chr11 + 61806597 61806746 150 browser details YourSeq 122 1405 1839 3000 80.6% chr14 + 71981841 71982175 335 browser details YourSeq 121 1708 1863 3000 90.7% chr2 - 12755722 12755884 163 browser details YourSeq 121 1705 1864 3000 89.6% chr4 + 134078439 134078604 166 browser details YourSeq 121 1708 1864 3000 87.6% chr15 + 87527726 87527875 150
Note: The 3000 bp section upstream of Exon 13 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 3000 1 3000 3000 100.0% chr7 + 92126894 92129893 3000 browser details YourSeq 63 349 415 3000 97.1% chr15 - 27792260 27792326 67 browser details YourSeq 47 1895 2082 3000 92.8% chr16 - 28805298 28805589 292 browser details YourSeq 35 1742 1905 3000 92.7% chr18 + 46386796 46387166 371 browser details YourSeq 32 1737 1772 3000 94.5% chr14 - 121925082 121925117 36 browser details YourSeq 32 2070 2177 3000 97.2% chr10 - 52727740 52727849 110 browser details YourSeq 31 1903 1947 3000 94.6% chr17 - 69122640 69122698 59 browser details YourSeq 31 1734 1768 3000 94.3% chr1 - 128468980 128469014 35 browser details YourSeq 29 1805 1890 3000 87.1% chr4 - 151914528 151914611 84 browser details YourSeq 29 1789 1826 3000 80.6% chr4 - 66255576 66255611 36 browser details YourSeq 28 1736 1767 3000 93.8% chr17 - 6372254 6372285 32 browser details YourSeq 28 1736 1767 3000 93.8% chr17 - 6539129 6539160 32 browser details YourSeq 28 1736 1767 3000 93.8% chr17 + 6712300 6712331 32 browser details YourSeq 28 1735 1768 3000 91.2% chr11 + 107284729 107284762 34 browser details YourSeq 27 1798 1826 3000 96.6% chr3 - 68621346 68621374 29 browser details YourSeq 27 1738 1766 3000 96.6% chr11 - 96509145 96509173 29 browser details YourSeq 24 2718 2749 3000 84.7% chr2 + 11114135 11114164 30 browser details YourSeq 24 1899 1927 3000 76.0% chr14 + 103898132 103898156 25 browser details YourSeq 23 2957 2984 3000 96.0% chr3 + 125570935 125570963 29
Note: The 3000 bp section downstream of Exon 13 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Dlg2 discs large MAGUK scaffold protein 2 [ Mus musculus (house mouse) ] Gene ID: 23859, updated on 10-Oct-2019
Gene summary
Official Symbol Dlg2 provided by MGI Official Full Name discs large MAGUK scaffold protein 2 provided by MGI Primary source MGI:MGI:1344351 See related Ensembl:ENSMUSG00000052572 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 Dlgh2; PSD93; Gm1197; Gm21505; A330103J02Rik; B230218P12Rik; B330007M19Rik Expression Biased expression in frontal lobe adult (RPKM 12.3), cortex adult (RPKM 11.4) and 5 other tissues See more Orthologs human all
Genomic context
Location: 7 E1; 7 51.07 cM See Dlg2 in Genome Data Viewer
Exon count: 40
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (90476188..92449246)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 7 NC_000073.5 (98239296..99597599)
Chromosome 7 - NC_000073.6
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Transcript information: This gene has 22 transcripts
Gene: Dlg2 ENSMUSG00000052572
Description discs large MAGUK scaffold protein 2 [Source:MGI Symbol;Acc:MGI:1344351] Gene Synonyms A330103J02Rik, B230218P12Rik, B330007M19Rik, Chapsyn-110, Dlgh2, Gm21505, LOC382816, PSD93 Location Chromosome 7: 90,476,672-92,449,247 forward strand. GRCm38:CM001000.2 About this gene This gene has 22 transcripts (splice variants), 180 orthologues, 3 paralogues, is a member of 1 Ensembl protein family and is associated with 12 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Dlg2-204 ENSMUST00000107196.9 7490 852aa ENSMUSP00000102814.2 Protein coding CCDS40021 Q91XM9 TSL:1 GENCODE basic APPRIS P2
Dlg2-202 ENSMUST00000098308.3 2329 481aa ENSMUSP00000095910.2 Protein coding CCDS57562 D3YWU0 TSL:1 GENCODE basic
Dlg2-217 ENSMUST00000231777.2 7801 994aa ENSMUSP00000155862.2 Protein coding - A0A338P6J0 GENCODE basic APPRIS ALT2
Dlg2-218 ENSMUST00000238467.1 7573 919aa ENSMUSP00000158695.1 Protein coding - - GENCODE basic
Dlg2-220 ENSMUST00000238619.1 7559 887aa ENSMUSP00000158731.1 Protein coding - - GENCODE basic
Dlg2-219 ENSMUST00000238608.1 7401 901aa ENSMUSP00000158616.1 Protein coding - - GENCODE basic
Dlg2-201 ENSMUST00000074273.9 5278 870aa ENSMUSP00000073885.3 Protein coding - E9Q2L2 TSL:5 GENCODE basic APPRIS ALT2
Dlg2-203 ENSMUST00000107193.7 4910 755aa ENSMUSP00000102811.1 Protein coding - D3YUZ8 TSL:5 GENCODE basic
Dlg2-222 ENSMUST00000239136.1 540 78aa ENSMUSP00000159135.1 Protein coding - - CDS 3' incomplete
Dlg2-215 ENSMUST00000208919.1 396 47aa ENSMUSP00000159178.1 Protein coding - - CDS 3' incomplete TSL:3
Dlg2-209 ENSMUST00000146563.8 4236 No protein - Retained intron - - TSL:5
Dlg2-210 ENSMUST00000152139.7 2934 No protein - Retained intron - - TSL:1
Dlg2-211 ENSMUST00000207095.1 2397 No protein - Retained intron - - TSL:NA
Dlg2-206 ENSMUST00000129818.1 2218 No protein - Retained intron - - TSL:1
Dlg2-221 ENSMUST00000238788.1 1216 No protein - Retained intron - - -
Dlg2-213 ENSMUST00000207891.1 448 No protein - Retained intron - - TSL:3
Dlg2-208 ENSMUST00000138389.7 3218 No protein - lncRNA - - TSL:1
Dlg2-216 ENSMUST00000209170.1 1057 No protein - lncRNA - - TSL:2
Dlg2-207 ENSMUST00000135581.2 964 No protein - lncRNA - - TSL:3
Dlg2-205 ENSMUST00000128592.2 922 No protein - lncRNA - - TSL:5
Dlg2-212 ENSMUST00000207798.1 842 No protein - lncRNA - - TSL:5
Dlg2-214 ENSMUST00000208377.1 672 No protein - lncRNA - - TSL:5
1.99 Mb Forward strand 90.5Mb 91.0Mb 91.5Mb 92.0Mb Genes (Comprehensive set... Dlg2-211 >retained intron A930002H02Rik-201 >TEC Gm24552-201 >snRNA Gm44679-201 >TEC Gm45130-201 >TEC Dlg2-202 >protein coding
Dlg2-215 >protein coding Gm45159-201 >lncRNGAm45176-201 >TEC Dlg2-222 >protein coding Gm45129-201 >TEC Dlg2-206 >retained intron
Dlg2-216 >lncRNA Gm45178-201 >TEC Gm45183-201 >TEC Gm44675-201 >TEC Gm45131-201 >TEC
Dlg2-217 >protein coding Page 6 of 8
Gm45179-201 >TEC Gm44678-201 >TEC Gm44676-201 >TEC B230206I08Rik-201 >TEC
Dlg2-204 >protein coding
Dlg2-209 >retained intron
Dlg2-201 >protein coding
Gm45177-201 >TEC Dlg2-221 >retained intron Dlg2-212 >lncRNA
Gm45182-201 >TEC Gm44677-201 >TEC Dlg2-213 >retained intron
Gm44680-201 >TEC Gm45201-201 >TEC
Gm44681-201 >TEC Dlg2-208 >lncRNA
Dlg2-220 >protein coding
Dlg2-218 >protein coding
Dlg2-219 >protein coding
Dlg2-210 >retained intron Dlg2-207 >lncRNA
C030038I04Rik-201 >TEC Dlg2-214 >lncRNA
Dlg2-203 >protein coding
Dlg2-205 >lncRNA
Contigs Genes < Tmem126b-201protein coding< Gm45162-201processed pseudogene < Gm22080-201snRNA < Gm23928-201snRNA < 4931412I15Rik-201TEC (Comprehensive set...
< Tmem126b-202retained intron < Gm45161-201TEC < 4930567K12Rik-201lncRNA
< Gm27470-201misc RNA
< Gm27660-201misc RNA
Regulatory Build
90.5Mb 91.0Mb 91.5Mb 92.0Mb Reverse strand 1.99 Mb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
pseudogene processed transcript RNA gene 1.99 Mb Forward strand 90.5Mb 91.0Mb 91.5Mb 92.0Mb Genes (Comprehensive set... Dlg2-211 >retained intron A930002H02Rik-201 >TEC Gm24552-201 >snRNA Gm44679-201 >TEC Gm45130-201 >TEC Dlg2-202 >protein coding
Dlg2-215 >protein coding Gm45159-201 >lncRNGAm45176-201 >TEC Dlg2-222 >protein coding Gm45129-201 >TEC Dlg2-206 >retained intron
Dlg2-216 >lncRNA Gm45178-201 >TEC Gm45183-201 >TEC Gm44675-201 >TEC Gm45131-201 >TEC https://www.alphaknockout.com
Dlg2-217 >protein coding
Gm45179-201 >TEC Gm44678-201 >TEC Gm44676-201 >TEC B230206I08Rik-201 >TEC
Dlg2-204 >protein coding
Dlg2-209 >retained intron
Dlg2-201 >protein coding
Gm45177-201 >TEC Dlg2-221 >retained intron Dlg2-212 >lncRNA
Gm45182-201 >TEC Gm44677-201 >TEC Dlg2-213 >retained intron
Gm44680-201 >TEC Gm45201-201 >TEC
Gm44681-201 >TEC Dlg2-208 >lncRNA
Dlg2-220 >protein coding
Dlg2-218 >protein coding
Dlg2-219 >protein coding
Dlg2-210 >retained intron Dlg2-207 >lncRNA
C030038I04Rik-201 >TEC Dlg2-214 >lncRNA
Dlg2-203 >protein coding
Dlg2-205 >lncRNA
Contigs Genes < Tmem126b-201protein coding< Gm45162-201processed pseudogene < Gm22080-201snRNA < Gm23928-201snRNA < 4931412I15Rik-201TEC (Comprehensive set...
< Tmem126b-202retained intron < Gm45161-201TEC < 4930567K12Rik-201lncRNA
< Gm27470-201misc RNA
< Gm27660-201misc RNA
Regulatory Build
90.5Mb 91.0Mb 91.5Mb 92.0Mb Reverse strand 1.99 Mb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
pseudogene processed transcript RNA gene
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Transcript: ENSMUST00000107196
1.36 Mb Forward strand
Dlg2-204 >protein coding
ENSMUSP00000102... PDB-ENSP mappings Low complexity (Seg) Coiled-coils (Ncoils) Superfamily PDZ superfamily P-loop containing nucleoside triphosphate hydrolase
SH3-like domain superfamily SMART Disks large homologue 1, N-terminal PEST domain SH3 domain Guanylate kinase/L-type calcium channel beta subunit
PDZ domain Pfam Disks large homologue 1, N-terminal PEST domain SH3 domain Guanylate kinase/L-type calcium channel beta subunit
PDZ-associated domain of NMDA receptors
PDZ domain PROSITE profiles PDZ domain SH3 domain Guanylate kinase-like domain
PROSITE patterns Guanylate kinase, conserved site
PIRSF Disks large 1-like PANTHER PTHR23122
PTHR23122:SF67 Gene3D 2.30.42.10 2.30.30.40
3.30.63.10
3.40.50.300 CDD cd00992 cd00071
Disks Large homologue 2, SH3 domain
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 852
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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