https://www.alphaknockout.com
Mouse Zkscan5 Conditional Knockout Project (CRISPR/Cas9)
Objective: To create a Zkscan5 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Zkscan5 gene (NCBI Reference Sequence: NM_016683 ; Ensembl: ENSMUSG00000055991 ) is located on Mouse chromosome 5. 6 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 6 (Transcript: ENSMUST00000085671). Exon 2 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Zkscan5 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-119B21 as template. 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:
Exon 2 starts from about 16.89% of the coding region. The knockout of Exon 2 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 1867 bp, and the size of intron 2 for 3'-loxP site insertion: 4037 bp. The size of effective cKO region: ~633 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 2 6 Targeting vector
Targeted allele
Constitutive KO allele (After Cre recombination)
Legends Exon of mouse Zkscan5 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. 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 GC Content Distribution Window size: 300 bp
Sequence 12
Summary: Full Length(7133bp) | A(24.1% 1719) | C(21.09% 1504) | T(29.85% 2129) | G(24.97% 1781)
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% chr5 + 145204327 145207326 3000 browser details YourSeq 302 1736 2900 3000 92.0% chr3 + 104673103 104726618 53516 browser details YourSeq 252 1727 2299 3000 84.5% chr4 - 98939047 98939390 344 browser details YourSeq 245 1773 2299 3000 93.6% chr11 + 72239000 72432826 193827 browser details YourSeq 242 1748 2283 3000 93.0% chr10 + 59405865 59960601 554737 browser details YourSeq 241 1745 2281 3000 86.5% chr2 + 119205836 119206199 364 browser details YourSeq 228 1737 2283 3000 86.8% chr16 + 10996026 10996303 278 browser details YourSeq 223 1736 2284 3000 84.6% chr16 - 32182344 32182765 422 browser details YourSeq 211 1763 2298 3000 85.3% chr4 - 129728699 129729101 403 browser details YourSeq 211 1763 2302 3000 84.4% chr11 + 20609884 20610278 395 browser details YourSeq 192 1750 2280 3000 90.0% chr3 - 95552928 95553560 633 browser details YourSeq 166 1748 2280 3000 81.5% chr5 - 113750127 113750376 250 browser details YourSeq 155 1718 1906 3000 92.4% chr17 + 83579231 83579426 196 browser details YourSeq 153 1748 2141 3000 92.3% chr1 + 88535661 88536221 561 browser details YourSeq 151 1677 1904 3000 92.2% chr12 - 57256251 57256744 494 browser details YourSeq 151 1529 1905 3000 79.8% chr11 + 20143738 20144012 275 browser details YourSeq 147 1773 2273 3000 84.9% chr15 - 37380804 37381095 292 browser details YourSeq 147 2156 2677 3000 92.5% chr11 + 101868546 101869110 565 browser details YourSeq 146 1644 1907 3000 85.4% chr3 - 115644807 115644993 187 browser details YourSeq 146 1737 1904 3000 93.5% chr3 + 142914546 142914713 168
Note: The 3000 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 3000 1 3000 3000 100.0% chr5 + 145207960 145210959 3000 browser details YourSeq 329 60 600 3000 96.6% chr7 - 93280249 93280810 562 browser details YourSeq 328 278 966 3000 91.5% chr10 + 130555815 130556167 353 browser details YourSeq 319 278 951 3000 92.1% chr18 + 9894358 9894712 355 browser details YourSeq 317 86 600 3000 96.8% chr8 - 29381657 29382174 518 browser details YourSeq 315 90 600 3000 92.6% chr1 + 41462799 41463136 338 browser details YourSeq 315 278 600 3000 98.8% chr1 + 23971463 23971785 323 browser details YourSeq 313 83 600 3000 92.6% chr19 - 40957321 40957743 423 browser details YourSeq 313 278 600 3000 98.5% chr10 - 4491047 4491369 323 browser details YourSeq 313 277 602 3000 98.2% chr11 + 7048842 7049168 327 browser details YourSeq 312 276 601 3000 97.3% chr3 - 5978170 5978494 325 browser details YourSeq 312 277 600 3000 98.2% chr15 - 21966281 21966604 324 browser details YourSeq 311 273 605 3000 96.7% chr7 - 90735354 90735686 333 browser details YourSeq 311 278 601 3000 98.2% chr2 - 71908040 71908364 325 browser details YourSeq 311 278 601 3000 98.2% chr16 - 37128386 37128711 326 browser details YourSeq 311 278 600 3000 98.2% chr8 + 67677573 67677895 323 browser details YourSeq 311 277 601 3000 97.9% chr6 + 32597940 32598264 325 browser details YourSeq 310 278 601 3000 97.9% chr7 + 57641331 57641654 324 browser details YourSeq 310 278 601 3000 97.9% chr13 + 57045957 57046280 324 browser details YourSeq 310 278 601 3000 97.9% chr1 + 15794475 15794798 324
Note: The 3000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Zkscan5 zinc finger with KRAB and SCAN domains 5 [ Mus musculus (house mouse) ] Gene ID: 22757, updated on 12-Aug-2019
Gene summary
Official Symbol Zkscan5 provided by MGI Official Full Name zinc finger with KRAB and SCAN domains 5 provided by MGI Primary source MGI:MGI:107533 See related Ensembl:ENSMUSG00000055991 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 Zfp95; hKraba1; AI132486; AI326970 Expression Ubiquitous expression in CNS E11.5 (RPKM 3.5), testis adult (RPKM 3.4) and 28 other tissues See more Orthologs human all
Genomic context
Location: 5; 5 G2 See Zkscan5 in Genome Data Viewer
Exon count: 7
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (145204559..145221752)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (145965428..145982619)
Chromosome 5 - NC_000071.6
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Transcript information: This gene has 6 transcripts
Gene: Zkscan5 ENSMUSG00000055991
Description zinc finger with KRAB and SCAN domains 5 [Source:MGI Symbol;Acc:MGI:107533] Gene Synonyms Zfp95, hKraba1 Location Chromosome 5: 145,204,562-145,221,750 forward strand. GRCm38:CM000998.2 About this gene This gene has 6 transcripts (splice variants), 86 orthologues, 177 paralogues and is a member of 2 Ensembl protein families. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Zkscan5- ENSMUST00000085671.9 3794 819aa ENSMUSP00000082814.3 Protein coding CCDS39386 Q9Z1D8 TSL:1 202 GENCODE basic APPRIS P3
Zkscan5- ENSMUST00000031601.7 3469 746aa ENSMUSP00000031601.7 Protein coding CCDS51697 Q6PAK4 TSL:1 201 GENCODE basic APPRIS ALT2
Zkscan5- ENSMUST00000161881.1 443 148aa ENSMUSP00000124544.1 Protein coding - F6SSC9 CDS 5' and 3' 204 incomplete TSL:3
Zkscan5- ENSMUST00000161896.1 1227 219aa ENSMUSP00000124838.1 Nonsense mediated - E0CX87 TSL:3 205 decay
Zkscan5- ENSMUST00000162168.7 622 52aa ENSMUSP00000124171.1 Nonsense mediated - F6TRS7 CDS 5' incomplete 206 decay TSL:3
Zkscan5- ENSMUST00000160162.1 378 No - lncRNA - - TSL:3 203 protein
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37.19 kb Forward strand 145.20Mb 145.21Mb 145.22Mb 145.23Mb Genes (Comprehensive set... Zkscan5-202 >protein coding Zfp655-206 >protein coding
Zkscan5-201 >protein coding Zfp655-202 >protein coding
Zkscan5-205 >nonsense mediated decay Zfp655-203 >protein coding
Zkscan5-206 >nonsense mediated decay
Zkscan5-204 >protein coding
Zkscan5-203 >lncRNA
Contigs < AC127411.3 Genes < Zkscan14-201protein coding (Comprehensive set...
< Zkscan14-202protein coding
< Zkscan14-203protein coding
Regulatory Build
145.20Mb 145.21Mb 145.22Mb 145.23Mb Reverse strand 37.19 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
processed transcript RNA gene
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Transcript: ENSMUST00000085671
17.19 kb Forward strand
Zkscan5-202 >protein coding
ENSMUSP00000082... MobiDB lite Low complexity (Seg) Superfamily SSF47353 KRAB domain superfamily
Zinc finger C2H2 superfamily SMART SCAN domain Zinc finger C2H2-type
Krueppel-associated box Pfam SCAN domain Krueppel-associated box
Zinc finger C2H2-type PROSITE profiles SCAN domain Krueppel-associated box
Zinc finger C2H2-type PROSITE patterns Zinc finger C2H2-type PANTHER PTHR24377:SF214
PTHR24377 Gene3D SCAN domain superfamily 3.30.160.60
CDD SCAN domain Krueppel-associated box
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant splice region variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 819
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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