https://www.alphaknockout.com
Mouse Bcl2l12 Knockout Project (CRISPR/Cas9)
Objective: To create a Bcl2l12 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Bcl2l12 gene (NCBI Reference Sequence: NM_029410 ; Ensembl: ENSMUSG00000003190 ) is located on Mouse chromosome 7. 7 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 7 (Transcript: ENSMUST00000003290). Exon 4~6 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:
Exon 4 starts from about 32.81% of the coding region. Exon 4~6 covers 61.05% of the coding region. The size of effective KO region: ~1706 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 4 5 6 7
Legends Exon of mouse Bcl2l12 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 4 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 1289 bp section downstream of Exon 6 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(23.15% 463) | C(23.05% 461) | T(25.15% 503) | G(28.65% 573)
Note: The 2000 bp section upstream of Exon 4 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(1289bp) | A(24.05% 310) | C(23.74% 306) | T(22.73% 293) | G(29.48% 380)
Note: The 1289 bp section downstream of Exon 6 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% chr7 - 44994450 44996449 2000 browser details YourSeq 314 66 774 2000 84.7% chr18 + 47016318 47017305 988 browser details YourSeq 205 122 764 2000 87.4% chr9 - 53070889 53071569 681 browser details YourSeq 201 218 655 2000 91.9% chr7 - 43860195 43860916 722 browser details YourSeq 180 250 608 2000 85.8% chr5 + 33289812 33290322 511 browser details YourSeq 178 331 774 2000 84.8% chr10 + 81068701 81069141 441 browser details YourSeq 176 257 775 2000 83.6% chr4 - 133572608 133573104 497 browser details YourSeq 165 261 775 2000 86.4% chr9 + 121936800 121937466 667 browser details YourSeq 162 222 830 2000 87.4% chr10 - 117259805 117260419 615 browser details YourSeq 158 320 844 2000 87.3% chr7 - 128231763 128232426 664 browser details YourSeq 155 161 699 2000 88.3% chr7 - 66701314 66702051 738 browser details YourSeq 151 164 541 2000 85.3% chr6 + 95947980 95948577 598 browser details YourSeq 143 192 529 2000 86.1% chrX - 104120617 104120950 334 browser details YourSeq 143 348 763 2000 87.5% chr1 - 96554036 96554608 573 browser details YourSeq 139 220 730 2000 91.6% chr2 + 151171395 151172070 676 browser details YourSeq 136 218 519 2000 83.5% chr3 - 32984265 32984862 598 browser details YourSeq 135 128 604 2000 88.6% chr6 + 115582377 115582991 615 browser details YourSeq 131 182 473 2000 90.8% chr5 - 135565798 135566148 351 browser details YourSeq 128 268 730 2000 91.6% chr2 - 151240497 151241113 617 browser details YourSeq 127 218 731 2000 77.5% chr13 + 100210280 100210691 412
Note: The 2000 bp section upstream of Exon 4 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 1289 1 1289 1289 100.0% chr7 - 44991455 44992743 1289 browser details YourSeq 69 407 491 1289 89.8% chr10 + 98924867 98924949 83 browser details YourSeq 67 406 492 1289 88.2% chr2 - 3495273 3495356 84 browser details YourSeq 67 403 492 1289 84.9% chr3 + 129512069 129512154 86 browser details YourSeq 67 408 490 1289 88.2% chr2 + 165891923 165892002 80 browser details YourSeq 67 408 478 1289 98.6% chr11 + 96150391 96401213 250823 browser details YourSeq 66 394 492 1289 84.0% chr8 - 60543118 60543208 91 browser details YourSeq 66 409 492 1289 88.0% chr2 - 153769886 153769966 81 browser details YourSeq 66 409 492 1289 86.7% chr11 - 79294692 79294771 80 browser details YourSeq 66 404 798 1289 71.5% chr10 - 90741781 90741936 156 browser details YourSeq 66 408 492 1289 89.4% chrX + 73390468 73390550 83 browser details YourSeq 66 410 796 1289 74.3% chr13 + 98866716 98866878 163 browser details YourSeq 66 412 496 1289 86.5% chr12 + 76101388 76101468 81 browser details YourSeq 66 404 492 1289 84.7% chr11 + 104511636 104511720 85 browser details YourSeq 66 408 490 1289 89.1% chr11 + 86257943 86258022 80 browser details YourSeq 66 392 492 1289 88.7% chr10 + 77967450 77967549 100 browser details YourSeq 65 412 492 1289 87.9% chr3 - 95221293 95221370 78 browser details YourSeq 65 408 492 1289 85.9% chr11 - 113741772 113741853 82 browser details YourSeq 65 407 492 1289 86.5% chr13 + 51641008 51641088 81 browser details YourSeq 65 412 492 1289 86.4% chr11 + 95169782 95169858 77
Note: The 1289 bp section downstream of Exon 6 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Bcl2l12 BCL2-like 12 (proline rich) [ Mus musculus (house mouse) ] Gene ID: 75736, updated on 13-Aug-2019
Gene summary
Official Symbol Bcl2l12 provided by MGI Official Full Name BCL2-like 12 (proline rich) provided by MGI Primary source MGI:MGI:1922986 See related Ensembl:ENSMUSG00000003190 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 Bcl-L12; Bcl2-L12; 2810475P17Rik; 5430429M05Rik Expression Ubiquitous expression in testis adult (RPKM 30.0), limb E14.5 (RPKM 23.2) and 25 other tissues See more Orthologs human all
Genomic context
Location: 7; 7 B3 See Bcl2l12 in Genome Data Viewer Exon count: 7
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (44991222..44997638, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 7 NC_000073.5 (52246592..52252949, complement)
Chromosome 7 - NC_000073.6
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Transcript information: This gene has 6 transcripts
Gene: Bcl2l12 ENSMUSG00000003190
Description BCL2-like 12 (proline rich) [Source:MGI Symbol;Acc:MGI:1922986] Gene Synonyms 2810475P17Rik, 5430429M05Rik, Bcl-L12, Bcl2-L12 Location Chromosome 7: 44,991,222-44,998,712 reverse strand. GRCm38:CM001000.2 About this gene This gene has 6 transcripts (splice variants), 141 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 15 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Bcl2l12-201 ENSMUST00000003290.11 1075 255aa ENSMUSP00000003290.4 Protein coding CCDS21223 Q9D3J3 TSL:1 GENCODE basic APPRIS P2
Bcl2l12-205 ENSMUST00000207755.1 605 115aa ENSMUSP00000146542.1 Protein coding - A0A140LHT8 TSL:2 GENCODE basic APPRIS ALT2
Bcl2l12-204 ENSMUST00000207443.1 537 148aa ENSMUSP00000146945.1 Protein coding - A0A140LIT0 CDS 3' incomplete TSL:3
Bcl2l12-203 ENSMUST00000207342.1 520 83aa ENSMUSP00000146355.1 Protein coding - A0A140LHC2 CDS 3' incomplete TSL:2
Bcl2l12-206 ENSMUST00000208128.1 1596 No protein - Retained intron - - TSL:2
Bcl2l12-202 ENSMUST00000207213.1 949 No protein - Retained intron - - TSL:1
27.49 kb Forward strand 44.985Mb 44.990Mb 44.995Mb 45.000Mb 45.005Mb Genes Gm15545-202 >lncRNA Irf3-201 >protein coding (Comprehensive set...
Gm15545-203 >lncRNA Irf3-213 >protein coding
Gm15545-201 >lncRNA Irf3-205 >retained intron
Gm15545-204 >lncRNA Irf3-212 >retained intron
Irf3-207 >retained intron
Irf3-202 >protein coding
Irf3-206 >protein coding
Irf3-209 >retained intron
Irf3-203 >protein coding
Irf3-208 >retained intron
Irf3-204 >protein coding
Irf3-211 >protein coding
Irf3-210 >retained intron
Contigs AC155806.3 > AC126256.4 > Genes (Comprehensive set... < Prmt1-203protein coding < Bcl2l12-206retained intron < Scaf1-201protein coding
< Prmt1-202protein coding < Bcl2l12-201protein coding < Scaf1-206protein coding
< Prmt1-205protein coding Page 7 of <9 Bcl2l12-205protein coding
< Prmt1-210protein coding < Bcl2l12-202retained intron
< Prmt1-201protein coding < Bcl2l12-204protein coding
< Prmt1-214protein coding < Bcl2l12-203protein coding
< Prmt1-208protein coding
< Prmt1-212protein coding
< Prmt1-213protein coding
< Prmt1-204nonsense mediated decay
< Prmt1-206retained intron
Regulatory Build
44.985Mb 44.990Mb 44.995Mb 45.000Mb 45.005Mb Reverse strand 27.49 kb
Regulation Legend CTCF Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript RNA gene 27.49 kb Forward strand 44.985Mb 44.990Mb 44.995Mb 45.000Mb 45.005Mb Genes Gm15545-202 >lncRNA Irf3-201 >protein coding (Comprehensive set...
Gm15545-203 >lncRNA Irf3-213 >protein coding
Gm15545-201 >lncRNA Irf3-205 >retained intron
Gm15545-204 >lncRNA Irf3-212 >retained intron
Irf3-207 >retained intron
Irf3-202 >protein coding
Irf3-206 >protein coding
Irf3-209 >retained intron
Irf3-203 >protein coding
Irf3-208 >retained intron
Irf3-204 >protein coding
Irf3-211 >protein coding
Irf3-210 >retained intron
Contigs AC155806.3 > AC126256.4 > Genes < Prmt1-203protein coding < Bcl2l12-206retained intron < Scaf1-201protein coding (Comprehensive set...
< Prmt1-202protein coding < Bcl2l12-201protein coding h < Prmt1-205protein coding < Bcl2l12-205protein coding < Prmt1-210protein coding < Bcl2l12-202retained intron < Prmt1-201protein coding < Bcl2l12-204protein coding < Prmt1-214protein coding < Bcl2l12-203protein coding < Prmt1-208protein coding < Prmt1-212protein coding < Prmt1-213protein coding < Prmt1-204nonsense mediated decay < Prmt1-206retained intron Regulatory Build 44.985Mb 44.990Mb 44.995Mb 45.000Mb 45.005Mb Reverse strand 27.49 kb Regulation Legend CTCF Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding merged Ensembl/Havana Ensembl protein coding Non-Protein Coding processed transcript RNA gene Page 8 of 9 https://www.alphaknockout.com Transcript: ENSMUST00000003290 < Bcl2l12-201protein coding Reverse strand 6.36 kb ENSMUSP00000003... MobiDB lite Low complexity (Seg) PANTHER PTHR14965:SF2 PTHR14965 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 40 80 120 160 200 255 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 9 of 9