https://www.alphaknockout.com
Mouse Cdc5l Knockout Project (CRISPR/Cas9)
Objective: To create a Cdc5l knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Cdc5l gene (NCBI Reference Sequence: NM_152810 ; Ensembl: ENSMUSG00000023932 ) is located on Mouse chromosome 17. 16 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 16 (Transcript: ENSMUST00000024727). Exon 3~7 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 3 starts from about 6.23% of the coding region. Exon 3~7 covers 31.34% of the coding region. The size of effective KO region: ~9737 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 16
Legends Exon of mouse Cdc5l Knockout region
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Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 1257 bp section upstream of Exon 3 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 1203 bp section downstream of Exon 7 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(1257bp) | A(30.63% 385) | C(20.05% 252) | T(26.33% 331) | G(22.99% 289)
Note: The 1257 bp section upstream of Exon 3 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(1203bp) | A(33.67% 405) | C(14.21% 171) | T(28.6% 344) | G(23.52% 283)
Note: The 1203 bp section downstream of Exon 7 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 1257 1 1257 1257 100.0% chr17 - 45426682 45427938 1257 browser details YourSeq 140 737 919 1257 91.8% chr10 + 77885733 78081626 195894 browser details YourSeq 129 702 964 1257 83.3% chr14 - 70228513 70228698 186 browser details YourSeq 127 752 946 1257 91.6% chr1 - 93921620 94045972 124353 browser details YourSeq 123 737 987 1257 89.0% chr11 + 115721217 115721584 368 browser details YourSeq 120 842 1022 1257 83.7% chr10 + 128609310 128609471 162 browser details YourSeq 118 716 949 1257 88.4% chr1 + 155512791 155513320 530 browser details YourSeq 116 734 956 1257 84.3% chr1 - 105665763 105665910 148 browser details YourSeq 113 737 956 1257 92.6% chr11 + 3454022 3868775 414754 browser details YourSeq 111 734 1006 1257 81.3% chr17 + 84780889 84781030 142 browser details YourSeq 110 734 1006 1257 81.0% chr2 + 32782014 32782169 156 browser details YourSeq 110 737 916 1257 92.4% chr18 + 77798192 77798512 321 browser details YourSeq 107 737 916 1257 92.4% chr1 - 74707505 74723575 16071 browser details YourSeq 105 734 947 1257 80.0% chr14 + 76184051 76184192 142 browser details YourSeq 103 734 960 1257 79.9% chrX + 93617650 93617792 143 browser details YourSeq 102 720 921 1257 79.3% chr10 + 43215033 43215164 132 browser details YourSeq 101 734 956 1257 81.9% chr9 - 92263448 92263597 150 browser details YourSeq 100 724 921 1257 82.4% chr14 + 20324721 20324845 125 browser details YourSeq 100 721 921 1257 79.9% chr1 + 57982174 57982304 131 browser details YourSeq 99 724 916 1257 82.5% chr2 - 145837951 145838070 120
Note: The 1257 bp section upstream of Exon 3 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 1203 1 1203 1203 100.0% chr17 - 45415742 45416944 1203 browser details YourSeq 218 528 843 1203 95.5% chr17 + 29781789 29782108 320 browser details YourSeq 199 523 795 1203 93.2% chr15 - 97653868 97654273 406 browser details YourSeq 179 515 816 1203 93.4% chr2 + 152961517 152962045 529 browser details YourSeq 163 512 718 1203 91.8% chr7 + 43268461 43268678 218 browser details YourSeq 156 510 969 1203 83.4% chr1 + 181217160 181217405 246 browser details YourSeq 148 523 716 1203 89.3% chr13 - 70737532 70737772 241 browser details YourSeq 147 524 718 1203 88.8% chr2 + 142531581 142531783 203 browser details YourSeq 147 528 701 1203 93.6% chr2 + 122622470 122622665 196 browser details YourSeq 145 516 689 1203 92.0% chr14 - 54429080 54429267 188 browser details YourSeq 145 512 689 1203 92.5% chr2 + 29532453 29532644 192 browser details YourSeq 143 503 686 1203 90.9% chr6 + 108179699 108179897 199 browser details YourSeq 143 528 703 1203 92.4% chr4 + 140594449 140594641 193 browser details YourSeq 142 510 686 1203 91.4% chrX + 162835916 162836104 189 browser details YourSeq 142 514 701 1203 89.4% chr11 + 105171684 105171890 207 browser details YourSeq 142 528 700 1203 91.9% chr1 + 172840019 172840228 210 browser details YourSeq 140 512 689 1203 89.9% chr1 - 72555024 72555223 200 browser details YourSeq 139 522 689 1203 92.7% chr14 - 60725236 60725412 177 browser details YourSeq 139 525 697 1203 90.6% chr1 - 87352748 87353357 610 browser details YourSeq 138 524 686 1203 93.8% chr5 - 38253115 38253280 166
Note: The 1203 bp section downstream of Exon 7 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Cdc5l cell division cycle 5-like (S. pombe) [ Mus musculus (house mouse) ] Gene ID: 71702, updated on 12-Aug-2019
Gene summary
Official Symbol Cdc5l provided by MGI Official Full Name cell division cycle 5-like (S. pombe) provided by MGI Primary source MGI:MGI:1918952 See related Ensembl:ENSMUSG00000023932 Gene type protein coding RefSeq status PROVISIONAL Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as PCDC5RP; AA408004; 1200002I02Rik Expression Ubiquitous expression in CNS E11.5 (RPKM 14.3), CNS E14 (RPKM 10.2) and 28 other tissues See more Orthologs human all
Genomic context
Location: 17; 17 B3 See Cdc5l in Genome Data Viewer Exon count: 17
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (45391887..45433707, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 17 NC_000083.5 (45528836..45570656, complement)
Chromosome 17 - NC_000083.6
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Transcript information: This gene has 3 transcripts
Gene: Cdc5l ENSMUSG00000023932
Description cell division cycle 5-like (S. pombe) [Source:MGI Symbol;Acc:MGI:1918952] Gene Synonyms 1200002I02Rik, PCDC5RP Location Chromosome 17: 45,391,884-45,433,737 reverse strand. GRCm38:CM001010.2 About this gene This gene has 3 transcripts (splice variants), 207 orthologues, 15 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Cdc5l-201 ENSMUST00000024727.9 3027 802aa ENSMUSP00000024727.8 Protein coding CCDS37627 Q3UCF2 Q6A068 TSL:1 GENCODE basic APPRIS P1
Cdc5l-203 ENSMUST00000232910.1 418 No protein - Retained intron - - -
Cdc5l-202 ENSMUST00000232900.1 764 No protein - lncRNA - - -
61.85 kb Forward strand 45.39Mb 45.40Mb 45.41Mb 45.42Mb 45.43Mb 45.44Mb Genes B230354K17Rik-202 >lncRNA (Comprehensive set...
B230354K17Rik-204 >lncRNA
B230354K17Rik-201 >lncRNA
B230354K17Rik-203 >lncRNA
Contigs AC169676.2 > < AC163677.2 Genes (Comprehensive set... < Cdc5l-201protein coding < Spats1-202lncRNA
< Cdc5l-202lncRNA < Cdc5l-203retained intron
Regulatory Build
45.39Mb 45.40Mb 45.41Mb 45.42Mb 45.43Mb 45.44Mb Reverse strand 61.85 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana
Non-Protein Coding
RNA gene processed transcript
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Transcript: ENSMUST00000024727
< Cdc5l-201protein coding
Reverse strand 41.85 kb
ENSMUSP00000024... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily Homeobox-like domain superfamily SMART SANT/Myb domain Pfam PF13921 Pre-mRNA splicing factor component Cdc5p/Cef1
PROSITE profiles Myb domain PANTHER PTHR45885
Gene3D 1.10.10.60 CDD cd11659
SANT/Myb domain
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend stop gained missense variant splice region variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 802
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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