https://www.alphaknockout.com
Mouse Cfap53 Knockout Project (CRISPR/Cas9)
Objective: To create a Cfap53 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Cfap53 gene (NCBI Reference Sequence: NM_028948 ; Ensembl: ENSMUSG00000035394 ) is located on Mouse chromosome 18. 8 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 8 (Transcript: ENSMUST00000114895). 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 4.54% of the coding region. Exon 2~6 covers 74.19% of the coding region. The size of effective KO region: ~8263 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 2 3 4 5 6 8
Legends Exon of mouse Cfap53 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 2 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.
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(29.1% 582) | C(20.35% 407) | T(29.85% 597) | G(20.7% 414)
Note: The 2000 bp section upstream of Exon 2 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(25.35% 507) | C(24.3% 486) | T(33.0% 660) | G(17.35% 347)
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% chr18 + 74297113 74299112 2000 browser details YourSeq 469 285 1193 2000 90.9% chr2 - 29597058 29597846 789 browser details YourSeq 410 770 1214 2000 97.1% chr17 + 33082672 33083125 454 browser details YourSeq 401 768 1193 2000 97.7% chr17 + 48490309 48490734 426 browser details YourSeq 399 779 1193 2000 98.1% chr1 + 154186997 154187411 415 browser details YourSeq 398 770 1194 2000 97.0% chr12 - 111958993 111959418 426 browser details YourSeq 397 770 1216 2000 95.5% chr12 + 38931014 38931596 583 browser details YourSeq 395 770 1201 2000 96.1% chr10 - 82566916 82567348 433 browser details YourSeq 395 768 1194 2000 96.3% chr9 + 124096533 124096959 427 browser details YourSeq 395 770 1193 2000 96.7% chr8 + 126314489 126314914 426 browser details YourSeq 395 770 1193 2000 96.7% chr4 + 82721772 82722197 426 browser details YourSeq 395 770 1193 2000 96.7% chr17 + 80926831 80927256 426 browser details YourSeq 395 781 1193 2000 97.9% chr13 + 113177283 113177695 413 browser details YourSeq 395 770 1193 2000 96.7% chr10 + 65725157 65725582 426 browser details YourSeq 395 765 1198 2000 95.7% chr1 + 67566878 67567311 434 browser details YourSeq 394 770 1193 2000 96.5% chr8 - 67387718 67388141 424 browser details YourSeq 394 768 1193 2000 96.3% chr2 - 84178289 84178714 426 browser details YourSeq 394 770 1195 2000 96.5% chr10 - 7976024 7976467 444 browser details YourSeq 394 758 1195 2000 94.7% chr14 + 75161690 75162125 436 browser details YourSeq 393 770 1194 2000 96.3% chr9 - 8174120 8174544 425
Note: The 2000 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% chr18 + 74307376 74309375 2000 browser details YourSeq 235 1487 1772 2000 96.5% chr12 - 78221232 78543830 322599 browser details YourSeq 228 1505 1774 2000 94.3% chr1 + 135275591 135276024 434 browser details YourSeq 226 1505 1765 2000 97.1% chr15 + 82816296 83184509 368214 browser details YourSeq 216 1514 1771 2000 96.2% chr17 - 88051603 88052238 636 browser details YourSeq 216 1505 1766 2000 94.0% chr10 - 128864997 128865521 525 browser details YourSeq 215 1464 1774 2000 93.9% chr10 + 120611478 120611871 394 browser details YourSeq 213 1516 1766 2000 97.4% chr2 + 75713358 76061784 348427 browser details YourSeq 210 1505 1756 2000 94.6% chr1 - 155046726 155047016 291 browser details YourSeq 201 1513 1766 2000 94.3% chr7 - 27177273 27177741 469 browser details YourSeq 201 1505 1766 2000 96.4% chr4 + 80930722 80931140 419 browser details YourSeq 189 1513 1773 2000 91.3% chr11 - 59808080 59808380 301 browser details YourSeq 188 1516 1746 2000 92.4% chr17 - 46785062 46785558 497 browser details YourSeq 182 1538 1766 2000 95.6% chr1 - 167206491 167206946 456 browser details YourSeq 178 1618 1817 2000 95.0% chr12 + 116291707 116518577 226871 browser details YourSeq 175 1611 1824 2000 96.8% chr12 - 11606500 11606953 454 browser details YourSeq 171 1611 1808 2000 95.8% chr16 - 3996584 3997157 574 browser details YourSeq 165 1619 1808 2000 96.1% chrX - 74050552 74050891 340 browser details YourSeq 164 1463 1773 2000 88.1% chr1 + 16722067 16722243 177 browser details YourSeq 161 1612 1810 2000 94.1% chrX + 160141821 160142156 336
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: Cfap53 cilia and flagella associated protein 53 [ Mus musculus (house mouse) ] Gene ID: 74453, updated on 12-Aug-2019
Gene summary
Official Symbol Cfap53 provided by MGI Official Full Name cilia and flagella associated protein 53 provided by MGI Primary source MGI:MGI:1921703 See related Ensembl:ENSMUSG00000035394 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 Ccdc11; 4933415I03Rik Expression Biased expression in testis adult (RPKM 7.8) and genital fat pad adult (RPKM 0.6) See more Orthologs human all
Genomic context
Location: 18; 18 E2 See Cfap53 in Genome Data Viewer Exon count: 10
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (74283100..74359984)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 18 NC_000084.5 (74442754..74519638)
Chromosome 18 - NC_000084.6
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Transcript information: This gene has 5 transcripts
Gene: Cfap53 ENSMUSG00000035394
Description cilia and flagella associated protein 53 [Source:MGI Symbol;Acc:MGI:1921703] Gene Synonyms 4933415I03Rik, Ccdc11 Location Chromosome 18: 74,283,090-74,359,986 forward strand. GRCm38:CM001011.2 About this gene This gene has 5 transcripts (splice variants), 8 orthologues, is a member of 1 Ensembl protein family and is associated with 40 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Cfap53- ENSMUST00000114895.3 1888 514aa ENSMUSP00000110545.3 Protein coding CCDS37857 Q9D439 TSL:1 201 GENCODE basic APPRIS P1
Cfap53- ENSMUST00000176435.7 2086 38aa ENSMUSP00000134908.1 Nonsense mediated - H3BJA5 TSL:1 202 decay
Cfap53- ENSMUST00000177101.7 943 38aa ENSMUSP00000135452.1 Nonsense mediated - H3BJA5 TSL:5 204 decay
Cfap53- ENSMUST00000177407.1 562 No - lncRNA - - TSL:2 205 protein
Cfap53- ENSMUST00000176766.1 487 No - lncRNA - - TSL:3 203 protein
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96.90 kb Forward strand 74.28Mb 74.30Mb 74.32Mb 74.34Mb 74.36Mb Genes (Comprehensive set... Mbd1-201 >protein coding Cfap53-203 >lncRNA Cfap53-205 >lncRNA
Mbd1-207 >protein coding
Mbd1-203 >retained intron
Mbd1-202 >protein coding
Mbd1-204 >protein coding
Mbd1-206 >retained intron
Cfap53-201 >protein coding
Cfap53-202 >nonsense mediated decay
Cfap53-204 >nonsense mediated decay
Contigs < AC147367.3 < AC147992.3
Genes < Gm14328-201processed pseudogene (Comprehensive set...
Regulatory Build
74.28Mb 74.30Mb 74.32Mb 74.34Mb 74.36Mb Reverse strand 96.90 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: ENSMUST00000114895
76.90 kb Forward strand
Cfap53-201 >protein coding
ENSMUSP00000110... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Pfam PF13868
PANTHER Cilia- and flagella-associated protein 53
PTHR31183
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant splice region variant synonymous variant
Scale bar 0 60 120 180 240 300 360 420 514
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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