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Mouse Tbc1d24 Knockout Project (CRISPR/Cas9)

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Mouse Tbc1d24 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Tbc1d24 Knockout Project (CRISPR/Cas9) Objective: To create a Tbc1d24 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Tbc1d24 gene (NCBI Reference Sequence: NM_001163850 ; Ensembl: ENSMUSG00000036473 ) is located on Mouse chromosome 17. 8 exons are identified, with the ATG start codon in exon 3 and the TGA stop codon in exon 8 (Transcript: ENSMUST00000168410). Exon 3~8 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: Mice heterozygous for a knock-out allele show altered primary neuron maturation and survival, impaired endocytosis and an enlarged endosomal compartment in neurons, and a decrease in spontaneous neurotransmission. Exon 3 starts from about 0.06% of the coding region. Exon 3~8 covers 100.0% of the coding region. The size of effective KO region: ~4923 bp. The KO region does not have any other known gene. Page 1 of 10 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 3 4 5 6 7 8 Legends Exon of mouse Tbc1d24 Knockout region Page 2 of 10 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 start 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. 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. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. Page 3 of 10 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(25.45% 509) | C(22.95% 459) | T(29.1% 582) | G(22.5% 450) Note: The 2000 bp section upstream of start 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. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(19.25% 385) | C(29.65% 593) | T(24.85% 497) | G(26.25% 525) 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 10 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% chr17 - 24186169 24188168 2000 browser details YourSeq 345 599 1609 2000 91.0% chr15 - 88766259 88767366 1108 browser details YourSeq 307 631 1376 2000 89.9% chr4 - 55393179 55393867 689 browser details YourSeq 292 631 1258 2000 89.0% chr7 + 128568705 128569115 411 browser details YourSeq 281 631 1258 2000 90.1% chr2 + 144576602 144577226 625 browser details YourSeq 273 623 1258 2000 87.5% chr7 + 127762829 127763196 368 browser details YourSeq 271 632 1258 2000 86.7% chr2 - 127002167 127002744 578 browser details YourSeq 269 623 1258 2000 88.6% chr2 - 26859072 26859631 560 browser details YourSeq 269 654 1260 2000 90.0% chr2 + 60162832 60163216 385 browser details YourSeq 268 654 1406 2000 93.9% chr13 + 97004495 97005307 813 browser details YourSeq 259 654 1258 2000 91.1% chr2 - 29878662 29879255 594 browser details YourSeq 259 623 1258 2000 93.7% chr19 - 45985837 45986513 677 browser details YourSeq 247 631 1260 2000 88.5% chr8 - 107027425 107027725 301 browser details YourSeq 243 845 1427 2000 87.0% chr17 - 56301389 56301929 541 browser details YourSeq 242 668 1280 2000 93.3% chr12 - 91797635 91798269 635 browser details YourSeq 241 931 1623 2000 86.3% chr11 - 95307078 95307605 528 browser details YourSeq 240 1071 1391 2000 92.9% chr10 + 61397071 61397403 333 browser details YourSeq 230 590 1583 2000 93.3% chr11 + 87419746 87420807 1062 browser details YourSeq 229 715 1350 2000 90.4% chr1 + 136702123 136702719 597 browser details YourSeq 228 1071 1623 2000 88.0% chr4 + 155372983 155373455 473 Note: The 2000 bp section upstream of start codon 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% chr17 - 24179244 24181243 2000 browser details YourSeq 92 1001 1180 2000 92.6% chr16 + 5483958 5484710 753 browser details YourSeq 67 998 1177 2000 92.5% chr8 + 106910324 106910611 288 browser details YourSeq 63 1001 1158 2000 89.5% chr2 + 80416008 80416163 156 browser details YourSeq 52 1770 1872 2000 90.8% chr12 + 36118256 36118865 610 browser details YourSeq 46 1670 1823 2000 94.3% chr10 + 41202489 41202698 210 browser details YourSeq 44 1043 1179 2000 69.9% chr15 - 6527212 6527315 104 browser details YourSeq 43 1768 1861 2000 73.5% chr19 + 29934873 29934943 71 browser details YourSeq 37 1764 1804 2000 95.2% chr5 - 117183899 117183939 41 browser details YourSeq 37 1787 1894 2000 88.4% chr14 + 17865775 17865881 107 browser details YourSeq 36 1773 1808 2000 100.0% chr6 - 39483997 39484032 36 browser details YourSeq 36 1785 1826 2000 92.9% chr15 - 83256916 83256957 42 browser details YourSeq 36 1787 1826 2000 95.0% chr5 + 123608602 123608641 40 browser details YourSeq 33 1770 1804 2000 97.2% chr9 + 49698305 49698339 35 browser details YourSeq 33 1780 1820 2000 86.5% chr1 + 58830206 58830244 39 browser details YourSeq 32 1766 1799 2000 97.1% chr7 - 19722259 19722292 34 browser details YourSeq 32 1773 1808 2000 94.5% chr10 - 42985603 42985638 36 browser details YourSeq 32 1784 1823 2000 90.0% chr1 - 156430130 156430169 40 browser details YourSeq 31 1787 1821 2000 94.3% chr1 - 178585171 178585205 35 browser details YourSeq 31 1786 1822 2000 91.9% chr8 + 121254251 121254287 37 Note: The 2000 bp section downstream of stop codon is BLAT searched against the genome. No significant similarity is found. Page 5 of 10 https://www.alphaknockout.com Gene and protein information: Tbc1d24 TBC1 domain family, member 24 [ Mus musculus (house mouse) ] Gene ID: 224617, updated on 10-Oct-2019 Gene summary Official Symbol Tbc1d24 provided by MGI Official Full Name TBC1 domain family, member 24 provided by MGI Primary source MGI:MGI:2443456 See related Ensembl:ENSMUSG00000036473 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 mKIAA1171; 9630033P11; C530046L02Rik Expression Ubiquitous expression in CNS E18 (RPKM 17.3), whole brain E14.5 (RPKM 14.4) and 28 other tissues See more Orthologs human all Genomic context Location: 17; 17 A3.3 See Tbc1d24 in Genome Data Viewer Exon count: 12 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (24175431..24205562, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 17 NC_000083.5 (24312376..24342507, complement) Chromosome 17 - NC_000083.6 Page 6 of 10 https://www.alphaknockout.com Transcript information: This gene has 15 transcripts Gene: Tbc1d24 ENSMUSG00000036473 Description TBC1 domain family, member 24 [Source:MGI Symbol;Acc:MGI:2443456] Gene Synonyms C530046L02Rik Location Chromosome 17: 24,175,431-24,205,562 reverse strand. GRCm38:CM001010.2 About this gene This gene has 15 transcripts (splice variants), 203 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 Tbc1d24- ENSMUST00000168410.8 7683 555aa ENSMUSP00000128868.2 Protein coding CCDS28477 Q3UUG6 TSL:1 205 GENCODE basic APPRIS P3 Tbc1d24- ENSMUST00000097376.9 7265 561aa ENSMUSP00000094989.3 Protein coding CCDS50012 Q3UUG6 TSL:1 202 GENCODE basic APPRIS ALT2 Tbc1d24- ENSMUST00000040474.10 6269 555aa ENSMUSP00000036458.7 Protein coding CCDS28477 Q3UUG6 TSL:1 201 GENCODE basic APPRIS P3 Tbc1d24- ENSMUST00000171189.7 4592 555aa ENSMUSP00000128001.1 Protein coding CCDS28477 Q3UUG6 TSL:1 206 GENCODE basic APPRIS P3 Tbc1d24- ENSMUST00000167791.8 4383 561aa ENSMUSP00000127005.2 Protein coding CCDS50012 Q3UUG6 TSL:1 203 GENCODE basic APPRIS ALT2 Tbc1d24- ENSMUST00000168378.7 4350 555aa ENSMUSP00000126107.1 Protein coding CCDS28477 Q3UUG6 TSL:1 204 GENCODE basic APPRIS P3 Tbc1d24- ENSMUST00000201960.3 4305 555aa ENSMUSP00000144208.1 Protein coding CCDS28477 Q3UUG6 TSL:5 213 GENCODE basic APPRIS P3 Tbc1d24- ENSMUST00000201301.3 4261 561aa ENSMUSP00000143949.1 Protein coding CCDS50012 Q3UUG6 TSL:5 208 GENCODE basic APPRIS ALT2 Tbc1d24- ENSMUST00000202925.3 4216 555aa ENSMUSP00000144575.1 Protein coding CCDS28477 Q3UUG6 TSL:5 215 GENCODE basic APPRIS P3 Tbc1d24- ENSMUST00000201089.3 4081 555aa ENSMUSP00000144250.1 Protein coding CCDS28477 Q3UUG6 TSL:1 207 GENCODE basic APPRIS P3 Tbc1d24- ENSMUST00000201805.3 3806 561aa ENSMUSP00000143883.1 Protein coding CCDS50012 Q3UUG6 TSL:1 212 GENCODE basic APPRIS Page 7 of 10 https://www.alphaknockout.com ALT2 Tbc1d24- ENSMUST00000201583.1 893 182aa ENSMUSP00000144097.1 Protein coding - A0A0J9YUB2 TSL:5 210 GENCODE basic Tbc1d24- ENSMUST00000201359.3 4098 325aa ENSMUSP00000144026.1 Nonsense mediated - Q8BRB6 TSL:1 209 decay Tbc1d24- ENSMUST00000201716.1 434 No - lncRNA - - TSL:2 211 protein Tbc1d24- ENSMUST00000202018.1 370 No - lncRNA - - TSL:3 214 protein Page 8 of 10 https://www.alphaknockout.com 50.13 kb Forward strand 24.17Mb 24.18Mb 24.19Mb 24.20Mb 24.21Mb Genes BC028777-203 >lncRNA (Comprehensive set..
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