https://www.alphaknockout.com
Mouse Lims2 Knockout Project (CRISPR/Cas9)
Objective: To create a Lims2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Lims2 gene (NCBI Reference Sequence: NM_144862 ; Ensembl: ENSMUSG00000024395 ) is located on Mouse chromosome 18. 10 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 10 (Transcript: ENSMUST00000025254). 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 null mice are viable and fertile with no gross abnormalities. Mice homozygous for a different targeted allele exhibit decreased fractional shortening and increased area affected following myocardial infarct.
Exon 2 starts from about 1.17% of the coding region. Exon 2 covers 15.64% of the coding region. The size of effective KO region: ~160 bp. The KO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele 5' gRNA region gRNA region 3'
1 2 10
Legends Exon of mouse Lims2 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. 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 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(24.8% 496) | C(24.4% 488) | T(24.05% 481) | G(26.75% 535)
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(27.15% 543) | C(24.5% 490) | T(23.3% 466) | G(25.05% 501)
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% chr18 + 31939741 31941740 2000 browser details YourSeq 331 1184 1766 2000 90.4% chrX - 151306765 151764682 457918 browser details YourSeq 283 1184 1752 2000 87.2% chr9 - 87643141 88187507 544367 browser details YourSeq 256 1184 1764 2000 85.4% chr10 + 74870845 74871302 458 browser details YourSeq 249 1184 1757 2000 82.4% chr9 - 118763602 118764026 425 browser details YourSeq 230 1200 1759 2000 84.0% chr5 + 73764245 73764772 528 browser details YourSeq 230 1396 1751 2000 88.2% chr18 + 16480193 16480563 371 browser details YourSeq 224 1261 1757 2000 88.6% chr13 - 16361084 16361829 746 browser details YourSeq 224 1412 1757 2000 86.6% chr16 + 34680478 34680854 377 browser details YourSeq 202 1415 1753 2000 89.9% chr8 + 87542139 87542486 348 browser details YourSeq 195 1402 1745 2000 87.7% chr7 + 13480070 13480638 569 browser details YourSeq 192 1413 1750 2000 81.3% chr1 - 184164824 184165171 348 browser details YourSeq 190 1184 1705 2000 88.2% chr5 + 67956061 67956606 546 browser details YourSeq 190 1414 1760 2000 83.7% chr10 + 17939143 17939485 343 browser details YourSeq 189 1477 1756 2000 92.0% chr2 - 155161697 155161981 285 browser details YourSeq 188 1403 1737 2000 87.6% chr3 + 15121078 15121427 350 browser details YourSeq 181 1410 1766 2000 84.2% chr14 - 65414318 65414664 347 browser details YourSeq 178 1396 1694 2000 88.8% chr16 + 96959725 96960039 315 browser details YourSeq 170 1379 1756 2000 91.8% chr10 + 81309451 81309878 428 browser details YourSeq 169 1403 1735 2000 85.0% chr7 - 91905308 91905644 337
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% chr18 + 31941901 31943900 2000 browser details YourSeq 111 338 578 2000 92.4% chr12 + 54082422 54082719 298 browser details YourSeq 98 340 576 2000 90.0% chr3 - 137711109 137711483 375 browser details YourSeq 97 395 588 2000 91.6% chr10 - 20138424 20139084 661 browser details YourSeq 96 424 578 2000 90.6% chr10 + 40547235 40547390 156 browser details YourSeq 96 424 571 2000 94.6% chr1 + 185988430 185988880 451 browser details YourSeq 94 395 571 2000 83.1% chr4 - 150641460 150641713 254 browser details YourSeq 94 340 578 2000 92.1% chr10 + 8962100 8962468 369 browser details YourSeq 92 403 574 2000 90.6% chr10 - 68610439 68640989 30551 browser details YourSeq 88 340 534 2000 94.2% chr11 - 114590035 114590372 338 browser details YourSeq 88 362 559 2000 84.1% chr10 - 123952456 123953108 653 browser details YourSeq 87 352 578 2000 93.3% chr10 - 120159217 120159473 257 browser details YourSeq 86 340 577 2000 94.0% chr10 + 21794939 21795185 247 browser details YourSeq 84 400 575 2000 87.4% chr11 - 87784437 87784640 204 browser details YourSeq 83 432 573 2000 91.9% chr10 + 125750765 125751063 299 browser details YourSeq 82 395 557 2000 92.8% chr10 - 69747171 69747394 224 browser details YourSeq 80 402 578 2000 93.6% chr2 + 118523922 118524108 187 browser details YourSeq 79 448 578 2000 94.5% chr18 + 82819523 82819659 137 browser details YourSeq 77 402 578 2000 94.4% chr10 + 60746127 60746480 354 browser details YourSeq 77 448 578 2000 80.5% chr10 + 59963420 59963525 106
Note: The 2000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Lims2 LIM and senescent cell antigen like domains 2 [ Mus musculus (house mouse) ] Gene ID: 225341, updated on 12-Aug-2019
Gene summary
Official Symbol Lims2 provided by MGI Official Full Name LIM and senescent cell antigen like domains 2 provided by MGI Primary source MGI:MGI:2385067 See related Ensembl:ENSMUSG00000024395 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 PINCH2 Expression Broad expression in bladder adult (RPKM 69.7), lung adult (RPKM 57.8) and 20 other tissues See more Orthologs human all
Genomic context
Location: 18; 18 B1 See Lims2 in Genome Data Viewer Exon count: 12
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (31922293..31958620)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 18 NC_000084.5 (32091161..32118273)
Chromosome 18 - NC_000084.6
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Transcript information: This gene has 12 transcripts
Gene: Lims2 ENSMUSG00000024395
Description LIM and senescent cell antigen like domains 2 [Source:MGI Symbol;Acc:MGI:2385067] Gene Synonyms PINCH2 Location Chromosome 18: 31,922,290-31,958,619 forward strand. GRCm38:CM001011.2 About this gene This gene has 12 transcripts (splice variants), 135 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 4 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Lims2- ENSMUST00000025254.8 1870 341aa ENSMUSP00000025254.7 Protein coding CCDS29113 Q91XD2 TSL:1 201 GENCODE basic APPRIS P1
Lims2- ENSMUST00000233994.1 685 164aa ENSMUSP00000157357.1 Protein coding - A0A3Q4EC95 CDS 3' 210 incomplete
Lims2- ENSMUST00000223753.1 627 206aa ENSMUSP00000153122.1 Protein coding - A0A286YCS7 CDS 3' 202 incomplete
Lims2- ENSMUST00000224383.1 557 153aa ENSMUSP00000152960.1 Protein coding - A0A286YCF2 CDS 3' 204 incomplete
Lims2- ENSMUST00000224328.1 450 59aa ENSMUSP00000153433.1 Protein coding - A0A286YDH9 CDS 5' 203 incomplete
Lims2- ENSMUST00000225404.1 805 37aa ENSMUSP00000153218.1 Nonsense mediated - A0A286YD07 - 207 decay
Lims2- ENSMUST00000225400.1 415 No - Retained intron - - - 206 protein
Lims2- ENSMUST00000225125.1 491 No - lncRNA - - - 205 protein
Lims2- ENSMUST00000225470.1 436 No - lncRNA - - - 208 protein
Lims2- ENSMUST00000234549.1 430 No - lncRNA - - - 211 protein
Lims2- ENSMUST00000234678.1 410 No - lncRNA - - - 212 protein
Lims2- ENSMUST00000226112.1 175 No - lncRNA - - - 209 protein
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56.33 kb Forward strand 31.92Mb 31.93Mb 31.94Mb 31.95Mb 31.96Mb Genes (Comprehensive set... Lims2-210 >protein coding Lims2-202 >protein coding
Lims2-211 >lncRNA Lims2-203 >protein coding
Lims2-201 >protein coding
Lims2-207 >nonsense mediated decay Lims2-205 >lncRNA
Lims2-208 >lncRNA
Lims2-212 >lncRNA Lims2-209 >lncRNA
Lims2-204 >protein coding
Lims2-206 >retained intron
Contigs < AC131761.4
Genes < Gpr17-201protein coding < Myo7b-201protein coding (Comprehensive set...
Regulatory Build
31.92Mb 31.93Mb 31.94Mb 31.95Mb 31.96Mb Reverse strand 56.33 kb
Regulation Legend
CTCF Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
RNA gene processed transcript
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Transcript: ENSMUST00000025254
27.30 kb Forward strand
Lims2-201 >protein coding
ENSMUSP00000025... Low complexity (Seg) Superfamily SSF57716 SMART Zinc finger, LIM-type Pfam Zinc finger, LIM-type PROSITE profiles Zinc finger, LIM-type PROSITE patterns Zinc finger, LIM-type PIRSF LIM and senescent cell antigen-like-containing domain protein 1 PANTHER LIM and senescent cell antigen-like-containing domain protein 1
PTHR24210:SF10 Gene3D 2.10.110.10 CDD cd09331 cd09332 cd09333 cd09334 cd09335
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant splice region variant synonymous variant
Scale bar 0 40 80 120 160 200 240 280 341
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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