https://www.alphaknockout.com
Mouse Dcaf15 Knockout Project (CRISPR/Cas9)
Objective: To create a Dcaf15 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Dcaf15 gene (NCBI Reference Sequence: NM_172502 ; Ensembl: ENSMUSG00000037103 ) is located on Mouse chromosome 8. 13 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 13 (Transcript: ENSMUST00000041367). 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:
Exon 2 starts from about 6.95% of the coding region. Exon 2~6 covers 34.06% of the coding region. The size of effective KO region: ~1378 bp. The KO region does not have any other known gene.
Page 1 of 8 https://www.alphaknockout.com
Overview of the Targeting Strategy
Wildtype allele 5' gRNA region gRNA region 3'
1 2 3 4 5 6 13
Legends Exon of mouse Dcaf15 Knockout region
Page 2 of 8 https://www.alphaknockout.com
Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 1563 bp section upstream of Exon 2 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. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis.
Page 3 of 8 https://www.alphaknockout.com
Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(1563bp) | A(19.83% 310) | C(21.88% 342) | T(23.16% 362) | G(35.12% 549)
Note: The 1563 bp section upstream of Exon 2 is analyzed to determine the GC content. Significant high GC-content regions are found. The gRNA site is selected outside of these high GC-content regions.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(23.6% 472) | C(22.05% 441) | T(26.75% 535) | G(27.6% 552)
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.
Page 4 of 8 https://www.alphaknockout.com
BLAT Search Results (up)
QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ------browser details YourSeq 1563 1 1563 1563 100.0% chr8 - 84103054 84104616 1563 browser details YourSeq 43 1090 1180 1563 92.0% chr3 + 95871020 95871112 93 browser details YourSeq 32 40 73 1563 97.1% chr8 + 79029981 79030014 34 browser details YourSeq 31 843 974 1563 97.0% chr1 + 90725064 90725416 353 browser details YourSeq 29 1128 1177 1563 87.1% chr4 + 45115733 45115780 48 browser details YourSeq 25 1301 1329 1563 81.5% chr1 + 151216379 151216405 27 browser details YourSeq 23 1096 1118 1563 100.0% chr10 - 63810947 63810969 23 browser details YourSeq 23 1096 1120 1563 96.0% chr1 - 179920672 179920696 25 browser details YourSeq 21 1457 1477 1563 100.0% chr15 - 44075676 44075696 21 browser details YourSeq 20 1162 1181 1563 100.0% chr1 - 192747510 192747529 20 browser details YourSeq 20 1162 1181 1563 100.0% chr1 - 86672580 86672599 20 browser details YourSeq 20 1162 1181 1563 100.0% chr1 - 74341555 74341574 20 browser details YourSeq 20 1090 1111 1563 95.5% chr1 - 55007206 55007227 22 browser details YourSeq 20 1096 1117 1563 95.5% chr1 + 191665550 191665571 22 browser details YourSeq 20 1101 1120 1563 100.0% chr1 + 120669184 120669203 20 browser details YourSeq 20 1162 1181 1563 100.0% chr1 + 86549060 86549079 20 browser details YourSeq 20 1162 1181 1563 100.0% chr1 + 30778179 30778198 20
Note: The 1563 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 2000 1 2000 2000 100.0% chr8 - 84099676 84101675 2000 browser details YourSeq 176 727 945 2000 96.9% chr8 - 84100993 84101329 337 browser details YourSeq 149 765 945 2000 92.3% chr8 - 84101145 84101329 185 browser details YourSeq 148 357 528 2000 91.8% chr8 - 84100808 84100977 170 browser details YourSeq 147 341 505 2000 93.3% chr8 - 84100793 84100955 163 browser details YourSeq 112 582 705 2000 95.2% chr8 - 84100933 84101056 124 browser details YourSeq 111 341 467 2000 91.2% chr8 - 84100793 84100917 125 browser details YourSeq 80 522 799 2000 92.6% chr18 + 15055662 15055946 285 browser details YourSeq 70 484 722 2000 92.7% chr18 + 15055662 15055906 245 browser details YourSeq 69 675 917 2000 75.3% chr4 + 3614251 3614408 158 browser details YourSeq 54 789 917 2000 92.2% chr4 + 3614146 3614373 228 browser details YourSeq 52 560 723 2000 93.4% chr18 + 15055662 15055829 168 browser details YourSeq 50 392 554 2000 75.0% chr2 - 179636606 179636744 139 browser details YourSeq 47 396 790 2000 62.3% chr3 - 152964860 152964958 99 browser details YourSeq 42 826 917 2000 82.0% chr4 + 3613551 3613638 88 browser details YourSeq 42 1075 1121 2000 95.8% chr14 + 49098094 49098150 57 browser details YourSeq 41 1088 1135 2000 93.8% chr11 - 21952441 21952911 471 browser details YourSeq 40 791 880 2000 90.0% chr4 + 3613553 3613883 331 browser details YourSeq 40 789 880 2000 90.0% chr4 + 3613656 3613778 123 browser details YourSeq 38 1281 1338 2000 79.0% chr17 + 45791569 45791625 57
Note: The 2000 bp section downstream of Exon 6 is BLAT searched against the genome. No significant similarity is found.
Page 5 of 8 https://www.alphaknockout.com
Gene and protein information: Dcaf15 DDB1 and CUL4 associated factor 15 [ Mus musculus (house mouse) ] Gene ID: 212123, updated on 24-Oct-2019
Gene summary
Official Symbol Dcaf15 provided by MGI Official Full Name DDB1 and CUL4 associated factor 15 provided by MGI Primary source MGI:MGI:2684420 See related Ensembl:ENSMUSG00000037103 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 6720484B16 Expression Ubiquitous expression in testis adult (RPKM 77.9), thymus adult (RPKM 65.5) and 28 other tissues See more Orthologs human all
Genomic context
Location: 8; 8 C2 See Dcaf15 in Genome Data Viewer Exon count: 14
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (84097069..84104797, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 8 NC_000074.5 (86620971..86628661, complement)
Chromosome 8 - NC_000074.6
Page 6 of 8 https://www.alphaknockout.com
Transcript information: This gene has 3 transcripts
Gene: Dcaf15 ENSMUSG00000037103
Description DDB1 and CUL4 associated factor 15 [Source:MGI Symbol;Acc:MGI:2684420] Location Chromosome 8: 84,097,072-84,104,768 reverse strand. GRCm38:CM001001.2 About this gene This gene has 3 transcripts (splice variants), 160 orthologues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Dcaf15- ENSMUST00000041367.8 2312 638aa ENSMUSP00000038568.7 Protein coding CCDS40406 Q6PFH3 TSL:1 201 GENCODE basic
Dcaf15- ENSMUST00000210279.1 2199 600aa ENSMUSP00000147690.1 Protein coding - Q6PFH3 TSL:1 202 GENCODE basic APPRIS P1
Dcaf15- ENSMUST00000210625.1 432 51aa ENSMUSP00000147657.1 Nonsense mediated - A0A1B0GRT7 TSL:2 203 decay
27.70 kb Forward strand
84.09Mb 84.10Mb 84.11Mb Genes Rfx1-204 >protein coding (Comprehensive set...
Rfx1-201 >protein coding
Rfx1-203 >retained intron
Contigs AC159266.3 >
Genes (Comprehensive set... < Dcaf15-202protein coding
< Dcaf15-201protein coding
< Dcaf15-203nonsense mediated decay
Regulatory Build
84.09Mb 84.10Mb 84.11Mb Reverse strand 27.70 kb
Regulation Legend
CTCF Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript
Page 7 of 8 https://www.alphaknockout.com
Transcript: ENSMUST00000041367
< Dcaf15-201protein coding
Reverse strand 7.69 kb
ENSMUSP00000038... MobiDB lite Low complexity (Seg) Pfam DDB1- and CUL4-associated factor 15, WD40 repeat-containing domain PANTHER DDB1- and CUL4-associated factor 15
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 60 120 180 240 300 360 420 480 540 638
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
Page 8 of 8