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Mouse Tmem43 Conditional Knockout Project (CRISPR/Cas9)

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Mouse Tmem43 Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Tmem43 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Tmem43 conditional 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 2~4 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Tmem43 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-53E13 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO 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. The knockout of Exon 2~4 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 3346 bp, and the size of intron 4 for 3'-loxP site insertion: 772 bp. The size of effective cKO region: ~2056 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 12 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Tmem43 Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region 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 GC Content Distribution Window size: 300 bp Sequence 12 Summary: Full Length(8556bp) | A(23.31% 1994) | C(25.58% 2189) | T(24.26% 2076) | G(26.85% 2297) Note: The sequence of homologous arms and cKO region 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 3 of 7 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr6 + 91473996 91476995 3000 browser details YourSeq 32 826 969 3000 97.2% chr5 - 121378425 121378570 146 browser details YourSeq 22 1679 1700 3000 100.0% chr3 + 36694660 36694681 22 browser details YourSeq 21 2786 2806 3000 100.0% chr8 + 89011976 89011996 21 Note: The 3000 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 3000 1 3000 3000 100.0% chr6 + 91479052 91482051 3000 browser details YourSeq 61 2475 2704 3000 80.2% chr2 + 155987671 155987927 257 browser details YourSeq 51 2483 2626 3000 86.8% chr10 + 127112218 127112448 231 browser details YourSeq 45 2641 2720 3000 76.8% chr2 + 31330544 31330621 78 browser details YourSeq 45 2641 2745 3000 79.3% chr11 + 28847031 28847168 138 browser details YourSeq 43 2475 2544 3000 83.1% chr19 + 46748829 46748899 71 browser details YourSeq 42 2475 2656 3000 62.3% chr4 + 103165360 103165424 65 browser details YourSeq 41 2641 2705 3000 81.6% chr15 - 31377282 31377346 65 browser details YourSeq 38 2637 2705 3000 97.6% chr5 - 134178127 134178195 69 browser details YourSeq 37 2489 2540 3000 86.3% chr5 - 134707376 134707427 52 browser details YourSeq 37 2638 2702 3000 78.5% chr5 - 122063375 122063439 65 browser details YourSeq 37 2468 2536 3000 93.2% chr4 - 132501016 132501090 75 browser details YourSeq 37 2508 2704 3000 95.2% chr7 + 101332010 101332324 315 browser details YourSeq 35 2613 2665 3000 94.9% chr11 - 52228024 52228076 53 browser details YourSeq 35 2611 2705 3000 87.9% chr2 + 118705145 118705238 94 browser details YourSeq 35 2479 2530 3000 84.7% chr10 + 37296621 37296673 53 browser details YourSeq 34 2475 2657 3000 57.5% chr2 - 18070723 18070787 65 browser details YourSeq 34 2642 2705 3000 76.6% chr15 + 99956466 99956529 64 browser details YourSeq 33 2648 2705 3000 83.8% chr5 - 122335280 122335336 57 browser details YourSeq 33 2641 2705 3000 75.4% chr4 - 8571040 8571104 65 Note: The 3000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 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 5 of 7 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 6 of 7 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 7 of 7.
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