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Mouse Tmem43 Knockout Project (CRISPR/Cas9)

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Mouse Tmem43 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Tmem43 Knockout Project (CRISPR/Cas9) Objective: To create a Tmem43 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Tmem43 gene (NCBI Reference Sequence: NM_028766 ; Ensembl: ENSMUSG00000030095 ) is located on Mouse chromosome 6. 12 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 12 (Transcript: ENSMUST00000032183). Exon 2~12 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: In a high-throughput screen, female homozygous mutant mice exhibited an increased anxiety-like response during open field activity testing when compared with their gender-matched wild-type littermates and the historical mean. Homozygous KO or certain codon substitution mutants don't affect heart function. Exon 2 starts from about 1.08% of the coding region. Exon 2~12 covers 99.0% of the coding region. The size of effective KO region: ~9700 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 11 12 Legends Exon of mouse Tmem43 Knockout region Page 2 of 8 https://www.alphaknockout.com 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. 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 stop codon 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. Page 3 of 8 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(24.6% 492) | C(24.95% 499) | T(27.4% 548) | G(23.05% 461) 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(23.3% 466) | C(25.15% 503) | T(28.65% 573) | G(22.9% 458) Note: The 2000 bp section downstream of stop codon 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. Page 4 of 8 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr6 + 91475246 91477245 2000 browser details YourSeq 22 429 450 2000 100.0% chr3 + 36694660 36694681 22 browser details YourSeq 21 1536 1556 2000 100.0% chr8 + 89011976 89011996 21 browser details YourSeq 20 319 338 2000 100.0% chr1 - 135637676 135637695 20 browser details YourSeq 20 879 898 2000 100.0% chr1 + 58952629 58952648 20 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% chr6 + 91486946 91488945 2000 browser details YourSeq 29 735 765 2000 90.0% chr3 - 37137579 37137608 30 browser details YourSeq 24 1370 1393 2000 100.0% chr9 - 70172938 70172961 24 browser details YourSeq 23 55 77 2000 100.0% chr14 - 22766559 22766581 23 browser details YourSeq 21 354 374 2000 100.0% chr2 - 162092386 162092406 21 browser details YourSeq 21 736 756 2000 100.0% chr13 - 103262361 103262381 21 browser details YourSeq 21 1787 1807 2000 100.0% chr2 + 35435366 35435386 21 browser details YourSeq 20 25 44 2000 100.0% chr1 - 51995833 51995852 20 browser details YourSeq 20 946 967 2000 95.5% chr1 + 123734231 123734252 22 Note: The 2000 bp section downstream of stop codon is BLAT searched against the genome. No significant similarity is found. Page 5 of 8 https://www.alphaknockout.com Gene and protein information: Tmem43 transmembrane protein 43 [ Mus musculus (house mouse) ] Gene ID: 74122, updated on 10-Sep-2019 Gene summary Official Symbol Tmem43 provided by MGI Official Full Name transmembrane protein 43 provided by MGI Primary source MGI:MGI:1921372 See related Ensembl:ENSMUSG00000030095 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 LUMA; 1200015A22Rik Expression Ubiquitous expression in subcutaneous fat pad adult (RPKM 68.5), mammary gland adult (RPKM 49.0) and 26 other Orthologs tissues See more human all Genomic context Location: 6; 6 D1 See Tmem43 in Genome Data Viewer Exon count: 12 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (91473707..91488463) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (91423745..91438452) Chromosome 6 - NC_000072.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 5 transcripts Gene: Tmem43 ENSMUSG00000030095 Description transmembrane protein 43 [Source:MGI Symbol;Acc:MGI:1921372] Gene Synonyms 1200015A22Rik, LUMA Location Chromosome 6: 91,473,703-91,488,463 forward strand. GRCm38:CM000999.2 About this gene This gene has 5 transcripts (splice variants), 195 orthologues, is a member of 1 Ensembl protein family and is associated with 1 phenotype. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Tmem43-201 ENSMUST00000032183.5 2903 400aa ENSMUSP00000032183.4 Protein coding CCDS20368 Q9DBS1 TSL:1 GENCODE basic APPRIS P1 Tmem43-202 ENSMUST00000140246.7 860 No protein - Retained intron - - TSL:2 Tmem43-204 ENSMUST00000153179.1 561 No protein - Retained intron - - TSL:2 Tmem43-203 ENSMUST00000144246.1 465 No protein - lncRNA - - TSL:3 Tmem43-205 ENSMUST00000205954.1 376 No protein - lncRNA - - TSL:5 34.76 kb Forward strand 91.47Mb 91.48Mb 91.49Mb Genes (Comprehensive set... Tmem43-201 >protein coding Tmem43-204 >retained intron Tmem43-205 >lncRNA Tmem43-202 >retained intron Tmem43-203 >lncRNA Contigs < AC161456.3 Genes < Chchd4-201protein coding < Xpc-201protein coding (Comprehensive set... < Chchd4-202retained intron < Xpc-202nonsense mediated decay Regulatory Build 91.47Mb 91.48Mb 91.49Mb Reverse strand 34.76 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding merged Ensembl/Havana Non-Protein Coding processed transcript RNA gene Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000032183 14.76 kb Forward strand Tmem43-201 >protein coding ENSMUSP00000032... Transmembrane heli... Pfam Transmembrane protein 43 family PANTHER PTHR13416:SF2 Transmembrane protein 43 family 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 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
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