https://www.alphaknockout.com
Mouse Fam193a Conditional Knockout Project (CRISPR/Cas9)
Objective: To create a Fam193a conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Fam193a gene (NCBI Reference Sequence: NM_001243123 ; Ensembl: ENSMUSG00000037210 ) is located on Mouse chromosome 5. 21 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 21 (Transcript: ENSMUST00000180376). Exon 3~4 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Fam193a gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-429E19 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 3 starts from about 10.24% of the coding region. The knockout of Exon 3~4 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 9174 bp, and the size of intron 4 for 3'-loxP site insertion: 5315 bp. The size of effective cKO region: ~1451 bp. The cKO 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 3 4 21 Targeting vector
Targeted allele
Constitutive KO allele (After Cre recombination)
Legends Exon of mouse Fam193a 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. Tandem repeats are found in the dot plot matrix. It may be difficult to construct this targeting vector.
Overview of the GC Content Distribution Window size: 300 bp
Sequence 12
Summary: Full Length(7951bp) | A(27.42% 2180) | C(19.41% 1543) | T(31.34% 2492) | G(21.83% 1736)
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% chr5 + 34416752 34419751 3000 browser details YourSeq 38 186 233 3000 95.2% chr11 + 54060809 54060865 57 browser details YourSeq 36 363 467 3000 97.5% chr12 - 15647260 15647366 107 browser details YourSeq 33 436 468 3000 100.0% chr7 + 118276401 118276433 33 browser details YourSeq 32 436 467 3000 100.0% chr6 - 106036675 106036706 32 browser details YourSeq 30 204 233 3000 100.0% chr10 - 117439484 117439513 30 browser details YourSeq 29 205 233 3000 100.0% chr1 - 172699531 172699559 29 browser details YourSeq 29 205 233 3000 100.0% chr1 - 119641759 119641787 29 browser details YourSeq 29 10 96 3000 90.4% chr9 + 122028731 122028816 86 browser details YourSeq 28 206 233 3000 100.0% chr7 - 83319288 83319315 28 browser details YourSeq 28 793 834 3000 83.4% chr3 - 19951635 19951676 42 browser details YourSeq 28 810 837 3000 100.0% chr11 - 23511536 23511563 28 browser details YourSeq 28 206 233 3000 100.0% chr10 - 71617900 71617927 28 browser details YourSeq 28 204 231 3000 100.0% chr1 - 55069966 55069993 28 browser details YourSeq 27 205 231 3000 100.0% chr10 + 90669635 90669661 27 browser details YourSeq 27 69 95 3000 100.0% chr1 + 156091795 156091821 27 browser details YourSeq 24 276 313 3000 81.6% chr3 - 32106065 32106102 38
Note: The 3000 bp section upstream of Exon 3 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% chr5 + 34421203 34424202 3000 browser details YourSeq 207 1355 1830 3000 86.6% chr2 - 4010051 4010550 500 browser details YourSeq 206 1628 2049 3000 84.7% chr16 + 4797609 4797989 381 browser details YourSeq 194 1348 1775 3000 81.9% chr1 - 9928249 9928652 404 browser details YourSeq 168 1715 2004 3000 89.3% chr10 - 4529244 4529542 299 browser details YourSeq 163 1670 2359 3000 81.2% chr11 + 87957775 87958197 423 browser details YourSeq 148 1738 2387 3000 78.0% chr5 - 150424261 150424656 396 browser details YourSeq 147 1912 2391 3000 92.0% chr4 - 86910285 86910828 544 browser details YourSeq 145 1630 2259 3000 76.1% chr11 + 21343664 21344061 398 browser details YourSeq 133 1450 2027 3000 81.6% chr16 - 90156047 90156303 257 browser details YourSeq 133 1853 2023 3000 95.9% chr2 + 14061153 14061353 201 browser details YourSeq 132 1738 2390 3000 71.5% chr7 + 30680499 30680897 399 browser details YourSeq 131 1629 2120 3000 79.1% chr11 - 51103858 51104178 321 browser details YourSeq 129 1630 2108 3000 78.7% chr18 + 49657558 49657880 323 browser details YourSeq 128 1912 2056 3000 95.7% chr5 + 20815671 20815816 146 browser details YourSeq 123 1914 2053 3000 94.3% chr17 - 78566388 78566528 141 browser details YourSeq 122 1858 2052 3000 92.4% chr12 - 23738558 23738756 199 browser details YourSeq 120 1630 2112 3000 77.4% chr1 + 10191771 10192070 300 browser details YourSeq 118 1638 2251 3000 75.8% chr11 + 38313147 38313488 342 browser details YourSeq 117 1638 1837 3000 77.6% chr17 - 7317550 7317738 189
Note: The 3000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Fam193a family with sequence homology 193, member A [ Mus musculus (house mouse) ] Gene ID: 231128, updated on 12-Aug-2019
Gene summary
Official Symbol Fam193a provided by MGI Official Full Name family with sequence homology 193, member A provided by MGI Primary source MGI:MGI:2447768 See related Ensembl:ENSMUSG00000037210 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 Expression Ubiquitous expression in testis adult (RPKM 28.6), CNS E14 (RPKM 15.6) and 28 other tissues See more Orthologs human all
Genomic context
Location: 5; 5 B2 See Fam193a in Genome Data Viewer Exon count: 21
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (34369933..34486458)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (34763500..34829105)
Chromosome 5 - NC_000071.6
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Transcript information: This gene has 5 transcripts
Gene: Fam193a ENSMUSG00000037210
Description family with sequence homology 193, member A [Source:MGI Symbol;Acc:MGI:2447768] Location Chromosome 5: 34,369,933-34,486,456 forward strand. GRCm38:CM000998.2 About this gene This gene has 5 transcripts (splice variants), 202 orthologues, 1 paralogue and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Fam193a-202 ENSMUST00000180376.7 5536 1517aa ENSMUSP00000138082.1 Protein coding - M0QWZ1 TSL:5 GENCODE basic APPRIS P5
Fam193a-201 ENSMUST00000094867.7 3696 1231aa ENSMUSP00000092463.4 Protein coding - Q8CGI1 TSL:5 GENCODE basic APPRIS ALT2
Fam193a-203 ENSMUST00000181379.1 2283 134aa ENSMUSP00000137979.1 Protein coding - M0QWS6 CDS 5' incomplete TSL:1
Fam193a-205 ENSMUST00000202503.1 581 193aa ENSMUSP00000143922.1 Protein coding - A0A0J9YTZ5 CDS 5' and 3' incomplete TSL:3
Fam193a-204 ENSMUST00000201005.1 385 129aa ENSMUSP00000143885.1 Protein coding - A0A0J9YTW8 CDS 5' and 3' incomplete TSL:5
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136.52 kb Forward strand 34.36Mb 34.38Mb 34.40Mb 34.42Mb 34.44Mb 34.46Mb 34.48Mb Genes (Comprehensive set... Fam193a-202 >protein coding
Fam193a-201 >protein coding
Fam193a-205 >protein coding Fam193a-203 >protein coding
Fam193a-204 >protein coding Gm42559-201 >TEC
Gm43457-201 >TEC
Contigs < AC102620.11 Genes < Gm26931-201processed pseudogene (Comprehensive set...
< Tnip2-202protein coding
< Tnip2-201protein coding
< Tnip2-203protein coding
Regulatory Build
34.36Mb 34.38Mb 34.40Mb 34.42Mb 34.44Mb 34.46Mb 34.48Mb Reverse strand 136.52 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
pseudogene processed transcript
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Transcript: ENSMUST00000180376
116.52 kb Forward strand
Fam193a-202 >protein coding
ENSMUSP00000138... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Pfam FAM193, C-terminal
PANTHER FAM193 family
Protein FAM193A
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant splice region variant synonymous variant
Scale bar 0 200 400 600 800 1000 1200 1517
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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