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Mouse Maats1 Conditional Knockout Project (CRISPR/Cas9)

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https://www.alphaknockout.com Mouse Maats1 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Maats1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Maats1 gene (NCBI Reference Sequence: NM_001081025 ; Ensembl: ENSMUSG00000022805 ) is located on Mouse chromosome 16. 17 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 17 (Transcript: ENSMUST00000023501). Exon 5~6 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Maats1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-351P21 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: Exon 5 starts from about 18.77% of the coding region. The knockout of Exon 5~6 will result in frameshift of the gene. The size of intron 4 for 5'-loxP site insertion: 931 bp, and the size of intron 6 for 3'-loxP site insertion: 3782 bp. The size of effective cKO region: ~1143 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 4 5 6 17 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Maats1 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(7643bp) | A(30.32% 2317) | C(19.6% 1498) | T(28.77% 2199) | G(21.31% 1629) 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% chr16 - 38333061 38336060 3000 browser details YourSeq 344 1155 1567 3000 93.1% chrX - 168511981 168512389 409 browser details YourSeq 341 1157 1568 3000 93.7% chrX + 36784572 36784988 417 browser details YourSeq 338 1157 1567 3000 92.6% chr3 - 31427885 31428293 409 browser details YourSeq 336 1157 1567 3000 92.8% chr17 + 82250375 82250782 408 browser details YourSeq 334 1157 1567 3000 92.3% chr4 - 147857153 147857561 409 browser details YourSeq 333 1156 1570 3000 92.6% chr9 - 105841486 105841901 416 browser details YourSeq 333 1157 1570 3000 94.2% chr10 - 99360713 99361126 414 browser details YourSeq 332 1157 1567 3000 92.5% chr15 - 60794520 60794928 409 browser details YourSeq 332 1157 1567 3000 93.1% chr13 - 119847415 119847851 437 browser details YourSeq 330 1157 1567 3000 92.8% chr13 + 120213416 120213862 447 browser details YourSeq 329 1156 1567 3000 91.5% chr14 + 15326873 15327282 410 browser details YourSeq 326 1157 1567 3000 91.5% chr12 - 44728749 44729157 409 browser details YourSeq 325 1151 1572 3000 91.1% chr10 - 10269008 10269404 397 browser details YourSeq 323 1155 1567 3000 90.5% chr12 - 79095234 79095636 403 browser details YourSeq 322 1157 1567 3000 91.8% chr9 - 36155729 36156139 411 browser details YourSeq 321 1153 1576 3000 90.6% chr9 + 12202125 12202521 397 browser details YourSeq 321 1157 1567 3000 90.5% chr8 + 18497381 18497789 409 browser details YourSeq 321 1157 1565 3000 93.1% chr12 + 60829301 60829759 459 browser details YourSeq 320 1147 1567 3000 90.6% chr1 - 95539355 95539789 435 Note: The 3000 bp section upstream of Exon 5 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% chr16 - 38328918 38331917 3000 browser details YourSeq 187 528 2436 3000 94.9% chr5 - 148244595 148630329 385735 browser details YourSeq 168 495 800 3000 91.8% chr4 - 136641271 136641845 575 browser details YourSeq 162 463 656 3000 93.2% chr3 + 105856640 105856845 206 browser details YourSeq 160 462 743 3000 94.0% chrX - 52869523 52870097 575 browser details YourSeq 154 468 684 3000 85.8% chr5 - 139530074 139530273 200 browser details YourSeq 151 463 656 3000 92.3% chr4 + 106605561 106609833 4273 browser details YourSeq 149 463 647 3000 92.7% chr3 + 122222154 122222355 202 browser details YourSeq 149 463 746 3000 92.7% chr11 + 115668869 115669208 340 browser details YourSeq 149 468 730 3000 92.7% chr11 + 74630266 74630898 633 browser details YourSeq 148 438 627 3000 90.2% chr4 - 107429010 107429222 213 browser details YourSeq 148 468 656 3000 88.8% chr11 - 68572341 68572525 185 browser details YourSeq 148 471 731 3000 90.4% chr10 - 40373434 40373686 253 browser details YourSeq 148 468 656 3000 90.2% chr4 + 57277362 57277546 185 browser details YourSeq 147 208 602 3000 81.9% chr7 + 81085770 81086054 285 browser details YourSeq 145 474 670 3000 88.0% chr8 - 34292570 34292757 188 browser details YourSeq 145 468 731 3000 93.0% chr4 - 150632109 150632440 332 browser details YourSeq 144 471 674 3000 89.4% chr5 + 105665057 105665259 203 browser details YourSeq 144 463 656 3000 89.5% chr2 + 130471276 130471468 193 browser details YourSeq 143 462 627 3000 93.4% chr14 - 52153816 52153988 173 Note: The 3000 bp section downstream of Exon 6 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 https://www.alphaknockout.com Gene and protein information: Maats1 MYCBP-associated, testis expressed 1 [ Mus musculus (house mouse) ] Gene ID: 320214, updated on 12-Aug-2019 Gene summary Official Symbol Maats1 provided by MGI Official Full Name MYCBP-associated, testis expressed 1 provided by MGI Primary source MGI:MGI:2443598 See related Ensembl:ENSMUSG00000022805 Gene type protein coding RefSeq status PROVISIONAL Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as Aat1; CFAP91; Spata26; 4932425I24Rik Expression Biased expression in testis adult (RPKM 9.6), placenta adult (RPKM 0.9) and 1 other tissue See more Orthologs human all Genomic context Location: 16; 16 B3 See Maats1 in Genome Data Viewer Exon count: 18 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (38297754..38341860, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 16 NC_000082.5 (38297840..38341946, complement) Chromosome 16 - NC_000082.6 Page 5 of 7 https://www.alphaknockout.com Transcript information: This gene has 2 transcripts Gene: Maats1 ENSMUSG00000022805 Description MYCBP-associated, testis expressed 1 [Source:MGI Symbol;Acc:MGI:2443598] Gene Synonyms 4932425I24Rik, Spata26 Location Chromosome 16: 38,297,754-38,342,143 reverse strand. GRCm38:CM001009.2 About this gene This gene has 2 transcripts (splice variants), 201 orthologues, is a member of 1 Ensembl protein family and is associated with 2 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Maats1-201 ENSMUST00000023501.15 3048 783aa ENSMUSP00000023501.8 Protein coding CCDS37341 Q8BRC6 TSL:1 GENCODE basic APPRIS P2 Maats1-202 ENSMUST00000114740.2 2529 345aa ENSMUSP00000110388.2 Protein coding - Q8BRC6 TSL:1 GENCODE basic APPRIS ALT2 64.39 kb Forward strand 38.30Mb 38.32Mb 38.34Mb Genes Maats1os-201 >lncRNA Cox17-204 >retained intron (Comprehensive set... Cox17-203 >retained intron Cox17-201 >protein coding Cox17-202 >protein coding Gm21987-201 >protein coding Cox17-205 >lncRNA Cox17-206 >lncRNA Contigs < AC154809.2 Genes (Comprehensive set... < Nr1i2-201protein coding < Maats1-201protein coding < Maats1-202protein coding Regulatory Build 38.30Mb 38.32Mb 38.34Mb Reverse strand 64.39 kb Regulation Legend CTCF Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding merged Ensembl/Havana Ensembl protein coding Non-Protein Coding RNA gene processed transcript Page 6 of 7 https://www.alphaknockout.com Transcript: ENSMUST00000023501 < Maats1-201protein coding Reverse strand 44.39 kb ENSMUSP00000023... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Pfam CFAP91 domain PANTHER Cilia- and flagella-associated protein 91 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant splice region variant synonymous variant Scale bar 0 80 160 240 320 400 480 560 640 783 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 7 of 7.
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    Structural Capacitance in Protein Evolution and Human Diseases Adrian Woolfson, Ashley Buckle, Natalie Borg, Geoffrey Webb, Itamar Kass, Malcolm Buckle, Jiangning Song, Chen Li, Liah Clark, Rory Zhang, et al. To cite this version: Adrian Woolfson, Ashley Buckle, Natalie Borg, Geoffrey Webb, Itamar Kass, et al.. Structural Ca- pacitance in Protein Evolution and Human Diseases. Journal of Molecular Biology, Elsevier, 2018, 10.1016/j.jmb.2018.06.051. hal-02368321 HAL Id: hal-02368321 https://hal.archives-ouvertes.fr/hal-02368321 Submitted on 20 Nov 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Structural Capacitance in Protein Evolution and Human Diseases Chen Li, Liah Clark, Rory Zhang, Benjamin Porebski, Julia Mccoey, Natalie Borg, Geoffrey Webb, Itamar Kass, Malcolm Buckle, Jiangning Song, etal. To cite this version: Chen Li, Liah Clark, Rory Zhang, Benjamin Porebski, Julia Mccoey, et al.. Structural Capaci- tance in Protein Evolution and Human Diseases. Journal of Molecular Biology, Elsevier, 2018, 10.1016/j.jmb.2018.06.051. hal-02368321 HAL Id: hal-02368321 https://hal.archives-ouvertes.fr/hal-02368321 Submitted on 20 Nov 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not.
  • Lncrna LUNAR1 Accelerates Colorectal Cancer Progression by Targeting the Mir‑495‑3P/MYCBP Axis

    Lncrna LUNAR1 Accelerates Colorectal Cancer Progression by Targeting the Mir‑495‑3P/MYCBP Axis

    INTERNATIONAL JOURNAL OF ONCOLOGY 57: 1157-1168, 2020 lncRNA LUNAR1 accelerates colorectal cancer progression by targeting the miR‑495‑3p/MYCBP axis JIAJIE QIAN1, ALOK GARG2, FUQIANG LI3, QIANYUN SHEN1 and KE XIAO4 1Department of Gastrointestinal Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China; 2Department of Surgery, City Hospital Braunschweig, D-38118 Braunschweig, Germany; 3Department of Thyroid Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China; 4Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, D-30625 Hannover, Lower Saxony, Germany Received April 16, 2020; Accepted September 14, 2020 DOI: 10.3892/ijo.2020.5128 Abstract. Colorectal cancer (CRC) is a tumor type and functional research showed that LUNAR1 accelerated characterized by high patient morbidity and mortality. It has CRC progression via the miR-495-3p/MYCBP axis. In been reported that long non-coding (lncRNA) LUNAR1 conclusion, LUNAR1 accelerates CRC progression via the (LUNAR1) participates in the regulation of tumor progression, miR-495-3p/MYCBP axis, indicating that LUNAR1 may such as diffuse large B-cell lymphoma. However, its role and serve as a prognostic biomarker for CRC patients. underlying mechanisms in CRC progression have not been elucidated. The present study was designed to investigate Introduction the underlying mechanisms by which LUNAR1 regulates CRC progression. RT-qPCR and Pearson's correlation Colorectal cancer (CRC) is a tumor type characterized by analysis revealed that LUNAR1 was highly expressed and high patient morbidity and mortality (1). At present, surgery, was negatively associated with the overall survival of CRC radiotherapy and chemotherapy are the primary strategies for patients.