https://www.alphaknockout.com
Mouse Cntrob Knockout Project (CRISPR/Cas9)
Objective: To create a Cntrob knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Cntrob gene (NCBI Reference Sequence: NM_172560 ; Ensembl: ENSMUSG00000032782 ) is located on Mouse chromosome 11. 19 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 19 (Transcript: ENSMUST00000092973). Exon 3~9 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 13.49% of the coding region. Exon 3~9 covers 35.25% of the coding region. The size of effective KO region: ~6709 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 8 9 19
Legends Exon of mouse Cntrob Knockout region
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Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 429 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 9 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(429bp) | A(30.3% 130) | C(18.41% 79) | T(26.11% 112) | G(25.17% 108)
Note: The 429 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(26.75% 535) | C(19.5% 390) | T(29.9% 598) | G(23.85% 477)
Note: The 2000 bp section downstream of Exon 9 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 429 1 429 429 100.0% chr11 - 69321420 69321848 429 browser details YourSeq 156 78 273 429 90.4% chr12 - 65126236 65126462 227 browser details YourSeq 145 83 279 429 91.6% chr11 + 5812780 5813014 235 browser details YourSeq 140 83 373 429 86.0% chr11 - 116883248 116884093 846 browser details YourSeq 139 85 279 429 91.2% chr18 + 76291793 76291988 196 browser details YourSeq 139 83 295 429 84.4% chr13 + 95235692 95235891 200 browser details YourSeq 139 83 299 429 85.2% chr13 + 55519956 55520168 213 browser details YourSeq 138 81 281 429 86.1% chr6 - 35222142 35222332 191 browser details YourSeq 138 79 270 429 84.9% chr11 + 94304806 94304996 191 browser details YourSeq 137 78 260 429 88.3% chr4 - 134910328 134910532 205 browser details YourSeq 137 83 280 429 88.3% chr18 + 31740735 31741124 390 browser details YourSeq 134 79 271 429 90.0% chr19 - 21564690 21564882 193 browser details YourSeq 132 81 269 429 87.9% chr14 - 103678928 103679113 186 browser details YourSeq 131 78 281 429 88.9% chr10 + 111461606 111461801 196 browser details YourSeq 130 82 270 429 90.3% chr2 - 127081975 127082167 193 browser details YourSeq 130 85 371 429 88.4% chr16 - 32240092 32240415 324 browser details YourSeq 130 83 274 429 89.3% chr15 - 99836198 99836397 200 browser details YourSeq 129 84 269 429 87.5% chr19 + 46848036 46848216 181 browser details YourSeq 129 84 276 429 82.3% chr11 + 75954448 75954639 192 browser details YourSeq 128 83 278 429 84.0% chr13 + 16132496 16132690 195
Note: The 429 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% chr11 - 69312711 69314710 2000 browser details YourSeq 98 824 1056 2000 75.0% chr12 + 102298597 102298739 143 browser details YourSeq 91 928 1236 2000 71.1% chr15 + 13131923 13132099 177 browser details YourSeq 91 928 1055 2000 88.4% chr11 + 94584056 94584186 131 browser details YourSeq 90 937 1055 2000 88.3% chr9 - 96475324 96475443 120 browser details YourSeq 90 1890 2000 2000 92.6% chr4 - 94541447 94541565 119 browser details YourSeq 89 929 1236 2000 69.5% chr1 - 82841582 82841757 176 browser details YourSeq 86 928 1055 2000 83.6% chr9 + 31103143 31103270 128 browser details YourSeq 85 928 1062 2000 79.9% chr11 - 74616810 74616943 134 browser details YourSeq 85 928 1055 2000 83.6% chr10 - 59833429 60020177 186749 browser details YourSeq 84 928 1055 2000 82.9% chr11 - 104028161 104028288 128 browser details YourSeq 83 930 1052 2000 83.8% chr11 - 34894055 34894177 123 browser details YourSeq 81 927 1051 2000 82.4% chr4 - 126767896 126768020 125 browser details YourSeq 81 931 1055 2000 88.6% chr4 - 116711564 116711688 125 browser details YourSeq 81 938 1058 2000 84.3% chr10 - 93873092 93873216 125 browser details YourSeq 80 938 1215 2000 73.2% chr17 - 11260180 11260321 142 browser details YourSeq 80 933 1103 2000 89.2% chr14 + 61539691 61540221 531 browser details YourSeq 79 928 1052 2000 81.6% chr6 - 71952224 71952348 125 browser details YourSeq 79 928 1052 2000 85.6% chr12 - 84683114 84683238 125 browser details YourSeq 79 938 1234 2000 74.3% chr10 - 7208085 7208270 186
Note: The 2000 bp section downstream of Exon 9 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Cntrob centrobin, centrosomal BRCA2 interacting protein [ Mus musculus (house mouse) ] Gene ID: 216846, updated on 8-Oct-2019
Gene summary
Official Symbol Cntrob provided by MGI Official Full Name centrobin, centrosomal BRCA2 interacting protein provided by MGI Primary source MGI:MGI:2443290 See related Ensembl:ENSMUSG00000032782 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 Lip8; Nip2; 9830165K03Rik Expression Ubiquitous expression in CNS E11.5 (RPKM 14.8), thymus adult (RPKM 11.8) and 28 other tissues See more Orthologs human all
Genomic context
Location: 11; 11 B3 See Cntrob in Genome Data Viewer Exon count: 19
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (69297909..69323898, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (69112998..69137375, complement)
Chromosome 11 - NC_000077.6
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Transcript information: This gene has 10 transcripts
Gene: Cntrob ENSMUSG00000032782
Description centrobin, centrosomal BRCA2 interacting protein [Source:MGI Symbol;Acc:MGI:2443290] Gene Synonyms 9830165K03Rik, Lip8, Nip2 Location Chromosome 11: 69,299,487-69,323,775 reverse strand. GRCm38:CM001004.2 About this gene This gene has 10 transcripts (splice variants), 110 orthologues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Cntrob- ENSMUST00000092973.5 3861 887aa ENSMUSP00000090651.5 Protein coding CCDS24888 Q8CB62 TSL:1 201 GENCODE basic APPRIS P1
Cntrob- ENSMUST00000176938.1 450 51aa ENSMUSP00000135258.1 Protein coding - H3BK55 CDS 5' 210 incomplete TSL:2
Cntrob- ENSMUST00000130780.1 424 75aa ENSMUSP00000134842.1 Protein coding - H3BJ47 CDS 5' 204 incomplete TSL:3
Cntrob- ENSMUST00000135979.1 334 32aa ENSMUSP00000115422.1 Protein coding - F6TUD4 CDS 5' 205 incomplete TSL:3
Cntrob- ENSMUST00000123176.7 3776 152aa ENSMUSP00000122205.1 Nonsense mediated - D6RGB4 TSL:1 202 decay
Cntrob- ENSMUST00000156175.1 2341 No - Retained intron - - TSL:1 207 protein
Cntrob- ENSMUST00000156671.7 752 No - Retained intron - - TSL:2 208 protein
Cntrob- ENSMUST00000125777.7 750 No - Retained intron - - TSL:3 203 protein
Cntrob- ENSMUST00000148490.1 622 No - Retained intron - - TSL:3 206 protein
Cntrob- ENSMUST00000176111.1 467 No - Retained intron - - TSL:3 209 protein
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44.29 kb Forward strand 69.29Mb 69.30Mb 69.31Mb 69.32Mb 69.33Mb Genes Cntrobos-201 >lncRNA Trappc1-203 >protein coding (Comprehensive set...
Trappc1-202 >protein coding
Trappc1-201 >protein coding
Trappc1-204 >protein coding
Trappc1-205 >lncRNA
Kcnab3-201 >protein coding
Kcnab3-203 >retained intron
Kcnab3-202 >retained intron
Contigs AL645527.20 >
Genes < Cntrob-201protein coding < Kcnab3os-201lncRNA (Comprehensive set...
< Cntrob-202nonsense mediated decay
< Cntrob-208retained intron < Cntrob-205protein coding< Cntrob-203retained intron
< Cntrob-210protein coding
< Cntrob-204protein coding < Cntrob-206retained intron
< Cntrob-207retained intron < Cntrob-209retained intron
Regulatory Build
69.29Mb 69.30Mb 69.31Mb 69.32Mb 69.33Mb Reverse strand 44.29 kb
Regulation Legend CTCF Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript RNA gene
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Transcript: ENSMUST00000092973
< Cntrob-201protein coding
Reverse strand 24.29 kb
ENSMUSP00000090... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) PANTHER Centrobin
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant splice region variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 800 887
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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