https://www.alphaknockout.com
Mouse Olfm3 Knockout Project (CRISPR/Cas9)
Objective: To create a Olfm3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Olfm3 gene (NCBI Reference Sequence: NM_153458 ; Ensembl: ENSMUSG00000027965 ) is located on Mouse chromosome 3. 6 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 6 (Transcript: ENSMUST00000081752). 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:
Exon 3 starts from about 15.79% of the coding region. Exon 3~4 covers 27.37% of the coding region. The size of effective KO region: ~5148 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 6
Legends Exon of mouse Olfm3 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(27.6% 552) | C(18.15% 363) | T(34.95% 699) | G(19.3% 386)
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(33.15% 663) | C(15.3% 306) | T(34.4% 688) | G(17.15% 343)
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% chr3 + 115094877 115096876 2000 browser details YourSeq 117 1 147 2000 94.1% chr13 + 75483273 75488861 5589 browser details YourSeq 115 1 125 2000 96.8% chr19 + 20744031 20744180 150 browser details YourSeq 113 4 153 2000 92.6% chr15 - 6016402 6016773 372 browser details YourSeq 113 1 125 2000 96.0% chr13 + 24965604 24965751 148 browser details YourSeq 110 1 126 2000 94.5% chr5 + 108987651 108987794 144 browser details YourSeq 110 1 126 2000 94.5% chr5 + 108993513 108993661 149 browser details YourSeq 108 1 126 2000 94.4% chr17 - 18144437 18144585 149 browser details YourSeq 108 1 125 2000 94.4% chr1 - 81893712 81893866 155 browser details YourSeq 107 1 125 2000 92.8% chr13 + 19965503 19965627 125 browser details YourSeq 106 1 125 2000 93.6% chr9 - 92514583 92520954 6372 browser details YourSeq 106 1 125 2000 92.7% chr18 - 65386850 65386995 146 browser details YourSeq 105 1 127 2000 92.8% chr17 - 18076283 18076431 149 browser details YourSeq 105 1 125 2000 92.8% chr14 - 53118032 53118179 148 browser details YourSeq 105 1 126 2000 95.7% chr18 + 10269345 10269492 148 browser details YourSeq 104 1 126 2000 92.1% chr3 - 106252629 106252777 149 browser details YourSeq 104 1 125 2000 96.5% chr18 + 10276047 10276192 146 browser details YourSeq 104 1 125 2000 92.8% chr17 + 79466201 79466366 166 browser details YourSeq 103 10 126 2000 94.9% chr5 - 138006848 138006987 140 browser details YourSeq 103 1 125 2000 92.0% chrX + 80463477 80463624 148
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% chr3 + 115102025 115104024 2000 browser details YourSeq 128 1814 2000 2000 83.7% chr10 + 100408402 100408580 179 browser details YourSeq 57 342 413 2000 92.4% chrX - 77814193 77814275 83 browser details YourSeq 57 340 409 2000 93.9% chr15 - 49261292 49261366 75 browser details YourSeq 55 348 417 2000 98.3% chr5 + 72417577 72417653 77 browser details YourSeq 51 350 413 2000 96.5% chrX - 69858764 69858833 70 browser details YourSeq 50 335 413 2000 77.6% chr12 - 72414484 72414548 65 browser details YourSeq 50 335 393 2000 87.3% chr10 - 103124509 103124564 56 browser details YourSeq 50 354 417 2000 96.3% chr17 + 62252703 62253135 433 browser details YourSeq 47 337 385 2000 98.0% chr2 + 81418326 81418374 49 browser details YourSeq 47 357 418 2000 82.0% chr10 + 94175139 94175189 51 browser details YourSeq 43 323 385 2000 78.8% chr10 - 15852485 15852532 48 browser details YourSeq 42 1645 1710 2000 75.5% chr13 - 105300393 105300447 55 browser details YourSeq 42 1649 1716 2000 77.1% chr13 - 51051475 51051531 57 browser details YourSeq 42 1668 1738 2000 77.4% chr1 - 47395065 47395129 65 browser details YourSeq 41 348 394 2000 97.7% chr18 + 75180792 75180842 51 browser details YourSeq 41 360 413 2000 93.5% chr11 + 74622876 74622930 55 browser details YourSeq 39 336 396 2000 75.0% chr7 + 5545227 5545273 47 browser details YourSeq 39 343 385 2000 97.7% chr18 + 74189337 74189385 49 browser details YourSeq 38 328 382 2000 83.0% chr15 - 83248906 83248953 48
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: Olfm3 olfactomedin 3 [ Mus musculus (house mouse) ] Gene ID: 229759, updated on 12-Aug-2019
Gene summary
Official Symbol Olfm3 provided by MGI Official Full Name olfactomedin 3 provided by MGI Primary source MGI:MGI:2387329 See related Ensembl:ENSMUSG00000027965 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 B230206G02Rik Expression Biased expression in cerebellum adult (RPKM 12.6), cortex adult (RPKM 2.5) and 5 other tissues See more Orthologs human all
Genomic context
Location: 3; 3 F3 See Olfm3 in Genome Data Viewer Exon count: 9
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (114904078..115125764)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (114607281..114828174)
Chromosome 3 - NC_000069.6
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Transcript information: This gene has 3 transcripts
Gene: Olfm3 ENSMUSG00000027965
Description olfactomedin 3 [Source:MGI Symbol;Acc:MGI:2387329] Gene Synonyms B230206G02Rik, optimedin Location Chromosome 3: 114,904,078-115,125,722 forward strand. GRCm38:CM000996.2 About this gene This gene has 3 transcripts (splice variants), 247 orthologues, 10 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Olfm3-202 ENSMUST00000081752.12 4647 458aa ENSMUSP00000080448.6 Protein coding CCDS17779 P63056 Q3UVC5 TSL:1 GENCODE basic APPRIS ALT1
Olfm3-201 ENSMUST00000051309.8 3928 478aa ENSMUSP00000060985.8 Protein coding CCDS17780 P63056 TSL:1 GENCODE basic APPRIS P4
Olfm3-203 ENSMUST00000149158.7 674 211aa ENSMUSP00000121097.1 Protein coding - D3YTM3 CDS 3' incomplete TSL:2
241.65 kb Forward strand 114.9Mb 115.0Mb 115.1Mb Genes (Comprehensive set... Olfm3-202 >protein coding
Olfm3-203 >protein coding
Olfm3-201 >protein coding
Contigs AC116411.7 > AC161527.18 > Regulatory Build
114.9Mb 115.0Mb 115.1Mb Reverse strand 241.65 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
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Transcript: ENSMUST00000081752
221.65 kb Forward strand
Olfm3-202 >protein coding
ENSMUSP00000080... Low complexity (Seg) Coiled-coils (Ncoils) Cleavage site (Sign... Superfamily Quinoprotein amine dehydrogenase, beta chain-like
SMART Olfactomedin-like domain
Pfam Noelin domain Olfactomedin-like domain
PROSITE profiles Olfactomedin-like domain
PANTHER Noelin-3
PTHR23192 CDD cd08985
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
synonymous variant
Scale bar 0 40 80 120 160 200 240 280 320 360 400 458
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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