https://www.alphaknockout.com
Mouse Dlgap2 Knockout Project (CRISPR/Cas9)
Objective: To create a Dlgap2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Dlgap2 gene (NCBI Reference Sequence: NM_172910 ; Ensembl: ENSMUSG00000047495 ) is located on Mouse chromosome 8. 16 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 16 (Transcript: ENSMUST00000133298). Exon 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 novelty-induced hyperactivity, increased aggression, impaired reverse learning, decreased dendritic spine density, synaptopathies, reduced mESPC amplitude and enhanced paired- pulse ratio.
Exon 6 starts from about 5.35% of the coding region. Exon 6 covers 33.68% of the coding region. The size of effective KO region: ~1070 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 6 16
Legends Exon of mouse Dlgap2 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 6 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 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(24.75% 495) | C(23.6% 472) | T(28.1% 562) | G(23.55% 471)
Note: The 2000 bp section upstream 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.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(23.15% 463) | C(25.25% 505) | T(30.65% 613) | G(20.95% 419)
Note: The 2000 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% chr8 + 14724930 14726929 2000 browser details YourSeq 28 1606 1647 2000 83.4% chr2 + 121392981 121393022 42 browser details YourSeq 27 1600 1628 2000 89.3% chr2 - 16537037 16537064 28 browser details YourSeq 23 1662 1688 2000 92.6% chr8 - 47565976 47566002 27 browser details YourSeq 23 1606 1646 2000 78.1% chr18 - 20655366 20655406 41 browser details YourSeq 23 951 975 2000 96.0% chr1 - 100103570 100103594 25 browser details YourSeq 23 293 318 2000 96.0% chr17 + 43347775 43347802 28 browser details YourSeq 22 715 736 2000 100.0% chrX + 64207121 64207142 22 browser details YourSeq 22 1629 1650 2000 100.0% chr13 + 92686850 92686871 22 browser details YourSeq 22 1764 1788 2000 95.9% chr1 + 184266351 184266381 31 browser details YourSeq 21 1626 1646 2000 100.0% chr1 - 121333052 121333072 21
Note: The 2000 bp section upstream of Exon 6 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% chr8 + 14728000 14729999 2000 browser details YourSeq 404 1318 1767 2000 96.8% chr8 + 14728961 14729475 515 browser details YourSeq 376 962 1449 2000 93.7% chr8 + 14729294 14729762 469 browser details YourSeq 309 1364 1767 2000 95.6% chr8 + 14728961 14729431 471 browser details YourSeq 293 962 1432 2000 90.8% chr8 + 14729409 14729766 358 browser details YourSeq 251 1145 1413 2000 97.1% chr8 + 14729302 14729614 313 browser details YourSeq 232 1403 1736 2000 96.1% chr8 + 14728975 14729375 401 browser details YourSeq 194 1513 1731 2000 95.4% chr8 + 14728975 14729301 327 browser details YourSeq 185 962 1406 2000 88.7% chr8 + 14729363 14729696 334 browser details YourSeq 181 1536 1771 2000 94.3% chr8 + 14728975 14729237 263 browser details YourSeq 172 1041 1703 2000 90.6% chr10 + 7173326 7174103 778 browser details YourSeq 167 1105 1746 2000 85.3% chr10 + 7173346 7173883 538 browser details YourSeq 155 1582 1771 2000 94.9% chr8 + 14728975 14729214 240 browser details YourSeq 149 1490 1721 2000 93.2% chr8 + 14728975 14729202 228 browser details YourSeq 141 1149 1637 2000 86.1% chr10 + 7173390 7173835 446 browser details YourSeq 134 962 1144 2000 93.6% chr8 + 14729565 14729750 186 browser details YourSeq 126 962 1213 2000 86.6% chr8 + 14729542 14729750 209 browser details YourSeq 123 962 1190 2000 85.5% chr8 + 14729588 14729750 163 browser details YourSeq 120 1195 1724 2000 92.9% chr10 + 7173486 7174073 588 browser details YourSeq 112 1307 1660 2000 93.1% chr10 + 7173438 7173835 398
Note: The 2000 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: Dlgap2 DLG associated protein 2 [ Mus musculus (house mouse) ] Gene ID: 244310, updated on 14-Aug-2019
Gene summary
Official Symbol Dlgap2 provided by MGI Official Full Name DLG associated protein 2 provided by MGI Primary source MGI:MGI:2443181 See related Ensembl:ENSMUSG00000047495 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 Dap2; Dap-2; Sapap2; 6430596N04Rik Expression Biased expression in cortex adult (RPKM 4.2), frontal lobe adult (RPKM 3.8) and 6 other tissues See more Orthologs human all
Genomic context
Location: 8; 8 A1.1 See Dlgap2 in Genome Data Viewer Exon count: 20
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (14095776..14853426)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 8 NC_000074.5 (14095875..14847687)
Chromosome 8 - NC_000074.6
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Transcript information: This gene has 9 transcripts
Gene: Dlgap2 ENSMUSG00000047495
Description DLG associated protein 2 [Source:MGI Symbol;Acc:MGI:2443181] Gene Synonyms 6430596N04Rik, DAP2, PSD-95/SAP90-binding protein 2, SAP90/PSD-95-associated protein 2, Sapap2 Location Chromosome 8: 14,095,865-14,847,680 forward strand. GRCm38:CM001001.2 About this gene This gene has 9 transcripts (splice variants), 194 orthologues, 4 paralogues, is a member of 1 Ensembl protein family and is associated with 14 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Dlgap2-203 ENSMUST00000133298.7 4503 1059aa ENSMUSP00000119613.1 Protein coding CCDS52492 Q8BJ42 TSL:1 GENCODE basic APPRIS ALT2
Dlgap2-209 ENSMUST00000152652.7 3842 1060aa ENSMUSP00000123078.1 Protein coding CCDS52491 Q0VF59 TSL:1 GENCODE basic APPRIS P4
Dlgap2-201 ENSMUST00000043279.8 3580 1059aa ENSMUSP00000039647.8 Protein coding CCDS52492 Q8BJ42 TSL:5 GENCODE basic APPRIS ALT2
Dlgap2-208 ENSMUST00000150247.7 3138 1045aa ENSMUSP00000123104.1 Protein coding - Q8BJ42 TSL:5 GENCODE basic APPRIS ALT2
Dlgap2-207 ENSMUST00000141214.7 2949 No protein - Retained intron - - TSL:1
Dlgap2-202 ENSMUST00000129119.1 2271 No protein - lncRNA - - TSL:1
Dlgap2-206 ENSMUST00000141155.1 1156 No protein - lncRNA - - TSL:1
Dlgap2-205 ENSMUST00000137130.1 414 No protein - lncRNA - - TSL:1
Dlgap2-204 ENSMUST00000136000.7 400 No protein - lncRNA - - TSL:3
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771.82 kb Forward strand
Genes (Comprehensive set... Gm10699-201 >TEC Gm44347-201 >miRNA Dlgap2-205 >lncRNA
Dlgap2-209 >protein coding
Dlgap2-203 >protein coding
Gm3160-201 >processed pseudogene Dlgap2-206 >lncRNA Dlgap2-202 >lncRNA
Dlgap2-201 >protein coding
Dlgap2-208 >protein coding
Dlgap2-204 >lncRNA
Dlgap2-207 >retained intron
Contigs < AC129599.3 < AC130213.3 AC127363.3 > AC125467.4 > < AC153015.4 Genes < Erich1-201protein coding < Gm26184-201snoRNA < C030037F17Rik-201lncRNA (Comprehensive set...
< Erich1-202protein coding
Regulatory Build
Reverse strand 771.82 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
pseudogene processed transcript RNA gene
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Transcript: ENSMUST00000133298
751.81 kb Forward strand
Dlgap2-203 >protein coding
ENSMUSP00000119... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Pfam SAPAP family
PANTHER SAPAP family
Disks large-associated protein 2
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant synonymous variant
Scale bar 0 100 200 300 400 500 600 700 800 900 1059
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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