http://www.alphaknockout.com/
Mouse Homer1 Knockout Project (CRISPR/Cas9)
Objective: To create a Homer1 knockout mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Homer1 gene ( NCBI Reference Sequence: NM_152134 ; Ensembl: ENSMUSG00000007617 ) is located on mouse chromosome 13. 9 exons are identified , with the ATG start codon in exon 1 and the TAA stop codon in exon 9 (Transcript: ENSMUST00000079086). Exon 2 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: Homozygous mutants exhibit an increase in spontaneous calcium influx in pancreatic acinar cells. Mice homozygous for a knock-out allele exhibit decreased response to formalin-induced pain.
Exon 2 starts from about 4.86% of the coding region. Exon 2 covers 14.14% of the coding region. The size of effective KO region: ~1306 bp.
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Overview of the Targeting Strategy
Wildtype allele gRNA region 5' gRNA region 3'
1 2 9
Legends Exon of mouse Homer1 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 2 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(26.8% 536) | C(20.0% 400) | G(17.65% 353) | T(35.55% 711)
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(29.4% 588) | C(19.1% 382) | G(17.95% 359) | T(33.55% 671)
Note: The 2000 bp section downstream 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.
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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% chr13 + 93339757 93341756 2000 browser details YourSeq 134 684 859 2000 90.0% chr10 - 92645028 92645204 177 browser details YourSeq 64 651 814 2000 77.7% chr1 - 152373672 152373776 105 browser details YourSeq 63 757 824 2000 97.1% chr10 - 62821871 62821939 69 browser details YourSeq 63 1436 1762 2000 91.0% chr12 + 32425919 32426287 369 browser details YourSeq 61 1192 1474 2000 77.7% chr11 + 60839787 60840019 233 browser details YourSeq 59 763 822 2000 100.0% chr7 - 135724857 135724938 82 browser details YourSeq 55 764 824 2000 89.7% chr14 - 21971107 21971164 58 browser details YourSeq 55 763 823 2000 89.7% chr11 - 14803166 14803223 58 browser details YourSeq 55 1435 1747 2000 92.5% chr17 + 44414546 44414871 326 browser details YourSeq 54 763 816 2000 100.0% chr11 - 5116952 5117005 54 browser details YourSeq 54 752 818 2000 84.3% chr1 + 11192055 11192111 57 browser details YourSeq 53 763 816 2000 100.0% chr5 - 46564236 46564298 63 browser details YourSeq 52 763 817 2000 92.5% chr9 - 113108746 113108798 53 browser details YourSeq 52 767 823 2000 96.5% chr11 - 121230025 121230090 66 browser details YourSeq 51 773 844 2000 94.8% chr17 - 57050380 57050467 88 browser details YourSeq 51 766 816 2000 100.0% chr16 - 85164697 85164747 51 browser details YourSeq 51 766 816 2000 100.0% chr2 + 169183792 169183842 51 browser details YourSeq 51 756 816 2000 84.3% chr13 + 37853797 37853853 57 browser details YourSeq 50 763 821 2000 85.5% chr10 + 79114025 79114079 55
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% chr13 + 93341914 93343913 2000 browser details YourSeq 41 691 769 2000 84.8% chr11 - 6295485 6295565 81 browser details YourSeq 41 729 824 2000 86.0% chr3 + 88658029 88658460 432 browser details YourSeq 41 683 770 2000 90.2% chr1 + 131078465 131078553 89 browser details YourSeq 39 683 774 2000 91.5% chr15 - 77394280 77394377 98 browser details YourSeq 37 731 773 2000 93.1% chr9 + 107206105 107206147 43 browser details YourSeq 36 731 778 2000 87.5% chr5 - 125458239 125458286 48 browser details YourSeq 36 683 774 2000 87.5% chr12 - 74184112 74184222 111 browser details YourSeq 36 729 785 2000 82.5% chr11 - 4407690 4407749 60 browser details YourSeq 36 729 778 2000 86.0% chr2 + 130239568 130239617 50 browser details YourSeq 35 729 771 2000 90.7% chr15 - 76821551 76821593 43 browser details YourSeq 35 729 773 2000 88.9% chr4 + 47676185 47676229 45 browser details YourSeq 34 729 780 2000 82.7% chr6 - 145094146 145094197 52 browser details YourSeq 33 683 763 2000 86.9% chr11 - 62526324 62526402 79 browser details YourSeq 32 729 774 2000 84.8% chr2 - 148715397 148715442 46 browser details YourSeq 32 729 774 2000 84.8% chr19 - 4031431 4031476 46 browser details YourSeq 31 741 774 2000 97.1% chr2 + 126669684 126669718 35 browser details YourSeq 31 729 773 2000 80.5% chr13 + 65201373 65201415 43 browser details YourSeq 31 729 769 2000 87.9% chr1 + 139166795 139166835 41 browser details YourSeq 30 729 770 2000 85.8% chr14 + 63017004 63017045 42
Note: The 2000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found.
Page 5 of 9 http://www.alphaknockout.com/ Gene and protein information: Homer1 homer scaffolding protein 1 [ Mus musculus (house mouse) ] Gene ID: 26556, updated on 10-Oct-2019
Gene summary
Official Symbol Homer1 provided by MGI Official Full Name homer scaffolding protein 1 provided by MGI Primary source MGI:MGI:1347345 See related Ensembl:ENSMUSG00000007617 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 SYN47; Ves-1; vesl-1; homer-1; PSD-Zip45 Expression Broad expression in cortex adult (RPKM 6.9), frontal lobe adult (RPKM 5.3) and 24 other tissues See more Orthologs human all
Genomic context
Location: 13; 13 C3 See Homer1 in Genome Data Viewer
Exon count: 12
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (93303757..93405129)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 13 NC_000079.5 (94074450..94174917)
Chromosome 13 - NC_000079.6
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Transcript information: This gene has 12 transcripts
Gene: Homer1 ENSMUSG00000007617
Description homer scaffolding protein 1 [Source:MGI Symbol;Acc:MGI:1347345] Gene Synonyms PSD-Zip45, Ves-1 Location Chromosome 13: 93,299,635-93,405,129 forward strand. GRCm38:CM001006.2 About this gene This gene has 12 transcripts (splice variants), 254 orthologues, 2 paralogues, is a member of 1 Ensembl protein family and is associated with 11 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Homer1- ENSMUST00000102752.9 5713 186aa ENSMUSP00000099813.3 Protein CCDS26687 Q5D052 TSL:1 204 coding Q9Z2Y3 GENCODE basic
Homer1- ENSMUST00000079086.7 4287 370aa ENSMUSP00000078093.6 Protein CCDS36746 Q9Z2Y3 TSL:1 202 coding GENCODE basic
Homer1- ENSMUST00000080127.11 3052 366aa ENSMUSP00000079026.5 Protein CCDS36745 Q9Z2Y3 TSL:1 203 coding GENCODE basic
Homer1- ENSMUST00000060490.10 2765 354aa ENSMUSP00000050471.4 Protein CCDS70484 Q9Z2Y3 TSL:1 201 coding GENCODE basic APPRIS P1
Homer1- ENSMUST00000109492.8 1533 203aa ENSMUSP00000105118.1 Protein CCDS84048 Q9Z2Y3 TSL:1 205 coding GENCODE basic
Homer1- ENSMUST00000109493.8 2580 233aa ENSMUSP00000105119.1 Protein - D3Z6A9 TSL:5 206 coding GENCODE basic
Homer1- ENSMUST00000109494.7 2468 193aa ENSMUSP00000105120.1 Protein - Q3UVL6 TSL:1 207 coding GENCODE basic
Homer1- ENSMUST00000109498.7 815 192aa ENSMUSP00000105124.1 Protein - E9Q0I7 TSL:5 211 coding GENCODE basic
Homer1- ENSMUST00000109495.7 813 191aa ENSMUSP00000105121.1 Protein - D3Z6A8 TSL:5 208 coding GENCODE basic
Homer1- ENSMUST00000109497.7 779 180aa ENSMUSP00000105123.1 Protein - E9Q0I8 TSL:5 210 coding GENCODE basic
Homer1- ENSMUST00000109496.7 772 224aa ENSMUSP00000105122.1 Protein - D3Z6A7 TSL:5 209 coding GENCODE basic
Homer1- ENSMUST00000220609.1 625 No - lncRNA - - TSL:3 212 protein
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125.50 kb Forward strand 93.44Mb 93.46Mb 93.48Mb 93.50Mb 93.52Mb 93.54Mb Genes Gm2076-201 >processed pseudogGenme47088-201 >TEC Gm47155-201 >TEC (Comprehensive set...
Homer1-212 >processed transcript
Homer1-207 >protein coding
Homer1-206 >protein coding
Homer1-204 >protein coding
Homer1-203 >protein coding
Homer1-211 >protein coding
Homer1-210 >protein coding
Homer1-201 >protein coding
Homer1-205 >protein coding
Homer1-208 >protein coding
Homer1-209 >protein coding
Homer1-202 >protein coding
Gm47075-201 >TEC
Contigs AC120347.7 > AC154231.2 > Regulatory Build
93.44Mb 93.46Mb 93.48Mb 93.50Mb 93.52Mb 93.54Mb Reverse strand 125.50 kb
Regulation Legend CTCF Enhancer Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript pseudogene
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Transcript: ENSMUST00000079086
97.10 kb Forward strand
Homer1-202 >protein coding
ENSMUSP00000078... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SSF50729 SSF57997
SMART WH1/EVH1 domain Pfam WH1/EVH1 domain PROSITE profiles WH1/EVH1 domain PANTHER PTHR10918:SF3
PTHR10918 Gene3D PH-like domain superfamily CDD cd01206
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 40 80 120 160 200 240 280 320 370
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC, VectorBuilder.
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