https://www.alphaknockout.com
Mouse Capzb Knockout Project (CRISPR/Cas9)
Objective: To create a Capzb knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Capzb gene (NCBI Reference Sequence: NM_001037761 ; Ensembl: ENSMUSG00000028745 ) is located on Mouse chromosome 4. 10 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 9 (Transcript: ENSMUST00000102507). Exon 3~4 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 conditional allele activated in the ear exhibit increased ABR threshold, absent DPOE, reduced vestibular function, head shaking and abnormal stereocilia length and width in the cochlea and utricle.
Exon 3 starts from about 11.31% of the coding region. Exon 3~4 covers 28.4% of the coding region. The size of effective KO region: ~4837 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 10
Legends Exon of mouse Capzb 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 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 2000 bp section downstream of Exon 4 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(25.6% 512) | C(23.95% 479) | T(24.65% 493) | G(25.8% 516)
Note: The 2000 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(2000bp) | A(23.5% 470) | C(24.35% 487) | T(27.0% 540) | G(25.15% 503)
Note: The 2000 bp section downstream of Exon 4 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% chr4 + 139255262 139257261 2000 browser details YourSeq 55 1276 1455 2000 93.7% chr1 - 6741447 6741626 180 browser details YourSeq 49 1 59 2000 91.6% chr13 - 97616622 97616680 59 browser details YourSeq 46 1 52 2000 94.3% chr12 + 73001026 73001077 52 browser details YourSeq 45 1 49 2000 96.0% chr6 + 120759206 120759254 49 browser details YourSeq 44 1 49 2000 96.0% chr17 - 46439043 46439095 53 browser details YourSeq 44 1 51 2000 94.0% chr13 - 9001020 9001081 62 browser details YourSeq 43 1 52 2000 95.8% chr17 - 29076718 29076895 178 browser details YourSeq 42 1 46 2000 95.7% chr16 - 18407336 18407381 46 browser details YourSeq 42 1 52 2000 80.5% chr17 + 45480175 45480220 46 browser details YourSeq 42 1 49 2000 93.8% chr16 + 33316955 33317004 50 browser details YourSeq 41 1 48 2000 88.9% chr5 - 143813172 143813217 46 browser details YourSeq 41 1 52 2000 84.8% chr14 - 99219017 99219065 49 browser details YourSeq 40 1 46 2000 88.9% chr2 - 120622284 120622328 45 browser details YourSeq 40 1 46 2000 91.0% chr3 + 100158926 100158970 45 browser details YourSeq 39 1 41 2000 97.6% chr9 - 106164469 106164509 41 browser details YourSeq 39 1 46 2000 93.4% chr1 - 17950845 17950890 46 browser details YourSeq 39 1 43 2000 95.4% chr18 + 34478471 34478513 43 browser details YourSeq 39 1 46 2000 93.4% chr12 + 68611386 68611431 46 browser details YourSeq 38 1 46 2000 83.0% chr12 - 28830890 28830930 41
Note: The 2000 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 2000 1 2000 2000 100.0% chr4 + 139262099 139264098 2000 browser details YourSeq 50 579 653 2000 91.3% chr4 - 151488834 151488976 143 browser details YourSeq 45 579 754 2000 92.5% chr5 + 38396481 38396660 180 browser details YourSeq 44 789 850 2000 85.5% chrX - 144169290 144169351 62 browser details YourSeq 37 582 642 2000 81.0% chr13 - 7573295 7573348 54 browser details YourSeq 35 581 652 2000 68.0% chr17 - 29210809 29210867 59 browser details YourSeq 33 565 619 2000 75.0% chr10 + 125894516 125894563 48 browser details YourSeq 30 614 667 2000 96.9% chr5 - 136070121 136070175 55 browser details YourSeq 30 795 852 2000 90.7% chr9 + 72234011 72234067 57 browser details YourSeq 29 579 625 2000 72.8% chr6 + 142574358 142574393 36 browser details YourSeq 28 1448 1475 2000 100.0% chr10 - 127243774 127243801 28 browser details YourSeq 27 1448 1474 2000 100.0% chr6 - 59534386 59534412 27 browser details YourSeq 27 1429 1472 2000 96.6% chr1 + 87088011 87088131 121 browser details YourSeq 26 1448 1473 2000 100.0% chr4 - 148811371 148811396 26 browser details YourSeq 26 1448 1473 2000 100.0% chr2 - 116640201 116640226 26 browser details YourSeq 26 609 635 2000 100.0% chr10 - 92395061 92395088 28 browser details YourSeq 26 411 441 2000 93.4% chr14 + 7986519 7986551 33 browser details YourSeq 25 597 624 2000 96.5% chr18 - 82719004 82719033 30 browser details YourSeq 25 647 671 2000 100.0% chr4 + 135928502 135928526 25 browser details YourSeq 24 597 625 2000 84.7% chr10 - 66043955 66043981 27
Note: The 2000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Capzb capping protein (actin filament) muscle Z-line, beta [ Mus musculus (house mouse) ] Gene ID: 12345, updated on 21-Aug-2019
Gene summary
Official Symbol Capzb provided by MGI Official Full Name capping protein (actin filament) muscle Z-line, beta provided by MGI Primary source MGI:MGI:104652 See related Ensembl:ENSMUSG00000028745 Gene type protein coding RefSeq status REVIEWED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as CPB1; CPB2; Cappb1; CPbeat2; CPbeta1; CPbeta2; AI325129; 1700120C01Rik Summary This gene encodes the beta subunit of a highly conserved filamentous actin capping protein that binds the barbed end of Expression filamentous actin to stabilize it and terminate elongation. Interaction of this protein with the barbed end of the actin filament occurs through binding of the amphipathic helix at the C-terminus to the hydrophobic cleft on the actin molecule. This gene is required for a variety of dynamic actin-mediated processes including organization of lamellipodia and filopodia, growth cone morphology and neurite outgrowth in hippocampal neurons, and asymmetric spindle migration and polar body extrusion during oocyte maturation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015] Orthologs Ubiquitous expression in bladder adult (RPKM 93.6), large intestine adult (RPKM 76.5) and 28 other tissues See more human all
Genomic context
Location: 4 D3; 4 70.59 cM See Capzb in Genome Data Viewer
Exon count: 11
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (139192899..139291820)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 4 NC_000070.5 (138748846..138847727)
Chromosome 4 - NC_000070.6
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Transcript information: This gene has 11 transcripts
Gene: Capzb ENSMUSG00000028745
Description capping protein (actin filament) muscle Z-line, beta [Source:MGI Symbol;Acc:MGI:104652] Gene Synonyms 1700120C01Rik, CPB1, CPB2, CPbeta1, CPbeta2, Cappb1 Location Chromosome 4: 139,192,899-139,291,818 forward strand. GRCm38:CM000997.2 About this gene This gene has 11 transcripts (splice variants), 202 orthologues, is a member of 1 Ensembl protein family and is associated with 2 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Capzb- ENSMUST00000102507.9 1702 277aa ENSMUSP00000099565.3 Protein coding CCDS18842 P47757 TSL:1 203 GENCODE basic APPRIS P4
Capzb- ENSMUST00000102508.9 1674 272aa ENSMUSP00000099566.3 Protein coding CCDS18841 P47757 TSL:1 204 Q923G3 GENCODE basic APPRIS ALT1
Capzb- ENSMUST00000030518.15 1390 301aa ENSMUSP00000030518.9 Protein coding CCDS71503 P47757 TSL:1 201 GENCODE basic APPRIS ALT1
Capzb- ENSMUST00000042675.8 1604 260aa ENSMUSP00000038011.7 Protein coding - A2AMW0 TSL:1 202 GENCODE basic
Capzb- ENSMUST00000138045.7 730 204aa ENSMUSP00000122077.1 Protein coding - F7CAZ6 CDS 3' 208 incomplete TSL:3
Capzb- ENSMUST00000131912.7 669 188aa ENSMUSP00000114973.1 Protein coding - F6YHZ8 CDS 3' 206 incomplete TSL:2
Capzb- ENSMUST00000145368.7 388 109aa ENSMUSP00000119252.1 Protein coding - A0A0A0MQI9 CDS 3' 209 incomplete TSL:5
Capzb- ENSMUST00000156760.1 632 No - Retained - - TSL:1 211 protein intron
Capzb- ENSMUST00000131793.1 353 No - Retained - - TSL:2 205 protein intron
Capzb- ENSMUST00000150077.1 1559 No - lncRNA - - TSL:1 210 protein
Capzb- ENSMUST00000132385.1 498 No - lncRNA - - TSL:5 207 protein
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118.92 kb Forward strand 139.20Mb 139.25Mb 139.30Mb Genes (Comprehensive set... Capzb-204 >protein coding
Capzb-206 >protein coding Capzb-207 >lncRNA
Capzb-203 >protein coding
Capzb-205 >retained intron
Capzb-210 >lncRNA
Capzb-201 >protein coding
Capzb-211 >retained intron
Capzb-209 >protein coding
Capzb-208 >protein coding
Capzb-202 >protein coding
Contigs AL807811.9 > Genes < Pqlc2-203nonsense mediated decay (Comprehensive set...
< Pqlc2-204nonsense mediated decay
< Pqlc2-201protein coding
< Pqlc2-202protein coding
< Pqlc2-205protein coding
Regulatory Build
139.20Mb 139.25Mb 139.30Mb Reverse strand 118.92 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
RNA gene processed transcript
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Transcript: ENSMUST00000102507
97.44 kb Forward strand
Capzb-201 >protein coding
ENSMUSP00000030... Coiled-coils (Ncoils) Superfamily F-actin-capping protein subunit alpha/beta Prints F-actin-capping protein subunit beta Pfam F-actin-capping protein subunit beta
PROSITE patterns F-actin capping protein, beta subunit, conserved site PANTHER PTHR10619:SF1
F-actin-capping protein subunit beta Gene3D 1.20.58.570 F-actin-capping protein subunit alpha/beta, domain 2
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
synonymous variant
Scale bar 0 40 80 120 160 200 240 301
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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