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Mouse Lancl1 Conditional Knockout Project (CRISPR/Cas9)
Objective: To create a Lancl1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Lancl1 gene (NCBI Reference Sequence: NM_001190985 ; Ensembl: ENSMUSG00000026000 ) is located on Mouse chromosome 1. 9 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 9 (Transcript: ENSMUST00000113979). Exon 2 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Lancl1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-343K22 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: Mice homozygous for a null mutation display postnatal neurodegeneration with increased oxidative stress and mitochondrial impairment.
Exon 2 starts from about 6.85% of the coding region. The knockout of Exon 2 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 4253 bp, and the size of intron 2 for 3'-loxP site insertion: 13058 bp. The size of effective cKO region: ~618 bp. The cKO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele gRNA region 5' gRNA region 3'
1 2 9 Targeting vector
Targeted allele
Constitutive KO allele (After Cre recombination)
Legends Exon of mouse Lancl1 Homology arm cKO region loxP site
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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(7118bp) | A(26.76% 1905) | C(22.27% 1585) | T(28.14% 2003) | G(22.83% 1625)
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.
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BLAT Search Results (up)
QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ------browser details YourSeq 3000 1 3000 3000 100.0% chr1 - 67034492 67037491 3000 browser details YourSeq 105 2422 2918 3000 85.8% chr2 - 154897632 155090525 192894 browser details YourSeq 90 2766 2919 3000 76.3% chr16 - 11235994 11236137 144 browser details YourSeq 80 2788 2919 3000 81.2% chr14 - 124107031 124107161 131 browser details YourSeq 79 2422 2915 3000 70.5% chr14 + 114719974 114720246 273 browser details YourSeq 74 2793 2919 3000 88.2% chr14 - 21699273 21699398 126 browser details YourSeq 73 2442 2567 3000 79.4% chr2 + 118400300 118400427 128 browser details YourSeq 72 2788 2915 3000 87.1% chr13 - 43031055 43031181 127 browser details YourSeq 72 2424 2869 3000 72.8% chr12 - 108354880 108355089 210 browser details YourSeq 72 2790 2919 3000 89.2% chr17 + 15669584 15669711 128 browser details YourSeq 72 2789 2919 3000 77.1% chr14 + 64675594 64675722 129 browser details YourSeq 71 2422 2569 3000 90.0% chr2 - 179451959 179452112 154 browser details YourSeq 71 2790 2919 3000 88.1% chr1 + 72800965 72801092 128 browser details YourSeq 70 2788 2915 3000 85.8% chr4 - 11669276 11669402 127 browser details YourSeq 70 2422 2569 3000 79.9% chr2 + 164033346 164033490 145 browser details YourSeq 69 2788 2915 3000 88.4% chr2 + 32805260 32805386 127 browser details YourSeq 68 2788 2915 3000 92.5% chr1 + 4778355 4778493 139 browser details YourSeq 67 2791 2915 3000 89.9% chr19 - 20371192 20371315 124 browser details YourSeq 67 2788 2919 3000 87.1% chr10 - 87417026 87417156 131 browser details YourSeq 67 2431 2835 3000 86.9% chr1 - 12939616 12951053 11438
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% chr1 - 67030874 67033873 3000 browser details YourSeq 62 575 673 3000 85.4% chr12 - 24268178 24268285 108 browser details YourSeq 58 575 667 3000 89.4% chr17 - 57352929 57353028 100 browser details YourSeq 56 575 664 3000 84.2% chr10 - 61631634 61631730 97 browser details YourSeq 48 584 658 3000 82.5% chr5 + 34379466 34379547 82 browser details YourSeq 48 548 624 3000 85.5% chr14 + 45731776 45731851 76 browser details YourSeq 47 580 669 3000 86.0% chr13 - 37720440 37720530 91 browser details YourSeq 47 578 669 3000 84.4% chr11 - 85109731 85109821 91 browser details YourSeq 47 553 639 3000 77.1% chr17 + 27908696 27908782 87 browser details YourSeq 47 575 639 3000 86.2% chr16 + 74445530 74445594 65 browser details YourSeq 45 576 648 3000 80.9% chr5 + 73326110 73326182 73 browser details YourSeq 44 579 667 3000 94.2% chr3 - 121431799 121431893 95 browser details YourSeq 43 581 645 3000 83.1% chr17 - 65989183 65989247 65 browser details YourSeq 42 455 669 3000 60.5% chr9 - 66518676 66518738 63 browser details YourSeq 42 575 644 3000 80.0% chr1 + 155674648 155674717 70 browser details YourSeq 40 577 644 3000 79.5% chr14 - 46382936 46383003 68 browser details YourSeq 40 564 623 3000 83.4% chr11 - 117569150 117569209 60 browser details YourSeq 38 594 639 3000 93.5% chr11 + 48831377 48831706 330 browser details YourSeq 37 578 636 3000 81.4% chr1 - 37561643 37561701 59 browser details YourSeq 36 575 652 3000 77.1% chr17 - 48327101 48327173 73
Note: The 3000 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: Lancl1 LanC (bacterial lantibiotic synthetase component C)-like 1 [ Mus musculus (house mouse) ] Gene ID: 14768, updated on 12-Aug-2019
Gene summary
Official Symbol Lancl1 provided by MGI Official Full Name LanC (bacterial lantibiotic synthetase component C)-like 1 provided by MGI Primary source MGI:MGI:1336997 See related Ensembl:ENSMUSG00000026000 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 p40; Gpr69; Gpr69a; AW124738 Expression Broad expression in testis adult (RPKM 84.4), cortex adult (RPKM 23.2) and 20 other tissues See more Orthologs human all
Genomic context
Location: 1; 1 C3 See Lancl1 in Genome Data Viewer
Exon count: 11
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (67000517..67038891, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (67047091..67085439, complement)
Chromosome 1 - NC_000067.6
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Transcript information: This gene has 6 transcripts
Gene: Lancl1 ENSMUSG00000026000
Description LanC (bacterial lantibiotic synthetase component C)-like 1 [Source:MGI Symbol;Acc:MGI:1336997] Gene Synonyms Gpr69a, LanC-like protein 1, p40 Location Chromosome 1: 67,000,517-67,038,872 reverse strand. GRCm38:CM000994.2 About this gene This gene has 6 transcripts (splice variants), 200 orthologues, 2 paralogues, is a member of 1 Ensembl protein family and is associated with 7 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Lancl1-202 ENSMUST00000113979.9 4461 399aa ENSMUSP00000109612.3 Protein coding CCDS15025 O89112 TSL:1 GENCODE basic APPRIS P1
Lancl1-201 ENSMUST00000027149.11 4270 399aa ENSMUSP00000027149.5 Protein coding CCDS15025 O89112 TSL:1 GENCODE basic APPRIS P1
Lancl1-203 ENSMUST00000119559.7 1385 399aa ENSMUSP00000113080.1 Protein coding CCDS15025 O89112 TSL:1 GENCODE basic APPRIS P1
Lancl1-205 ENSMUST00000149996.1 570 173aa ENSMUSP00000122752.1 Protein coding - B2KGR2 CDS 3' incomplete TSL:3
Lancl1-206 ENSMUST00000189210.1 2610 No protein - Retained intron - - TSL:NA
Lancl1-204 ENSMUST00000133508.1 388 No protein - lncRNA - - TSL:3
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58.36 kb Forward strand 67.00Mb 67.01Mb 67.02Mb 67.03Mb 67.04Mb Contigs < AC133187.3 Genes (Comprehensive set... < Lancl1-201protein coding
< Lancl1-202protein coding
< Lancl1-203protein coding
< Lancl1-204lncRNA
< Lancl1-205protein coding
< Lancl1-206retained intron
Regulatory Build
67.00Mb 67.01Mb 67.02Mb 67.03Mb 67.04Mb Reverse strand 58.36 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript RNA gene
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Transcript: ENSMUST00000113979
< Lancl1-202protein coding
Reverse strand 38.36 kb
ENSMUSP00000109... Superfamily SSF158745
SMART Lanthionine synthetase C-like
Prints Lanthionine synthetase C-like
LanC-like protein, eukaryotic Pfam Lanthionine synthetase C-like PANTHER PTHR12736:SF5
PTHR12736 Gene3D Six-hairpin glycosidase-like superfamily CDD LanC-like protein, eukaryotic
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 40 80 120 160 200 240 280 320 399
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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