https://www.alphaknockout.com

Mouse Fam13c Knockout Project (CRISPR/Cas9)

Objective: To create a Fam13c knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.

Strategy summary: The Fam13c (NCBI Reference Sequence: NM_001143777 ; Ensembl: ENSMUSG00000043259 ) is located on Mouse 10. 15 exons are identified, with the ATG start codon in exon 4 and the TGA stop codon in exon 15 (Transcript: ENSMUST00000105436). Exon 5 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 5 starts from about 4.88% of the coding region. Exon 5 covers 7.64% of the coding region. The size of effective KO region: ~119 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 5 15

Legends Exon of mouse Fam13c 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 5 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.

Overview of the Dot Plot (down) Window size: 15 bp

Forward Reverse Complement

Sequence 12

Note: The 2000 bp section downstream of Exon 5 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(27.9% 558) | C(20.25% 405) | T(31.25% 625) | G(20.6% 412)

Note: The 2000 bp section upstream of Exon 5 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(24.1% 482) | C(21.7% 434) | T(27.6% 552) | G(26.6% 532)

Note: The 2000 bp section downstream of Exon 5 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% chr10 + 70475155 70477154 2000 browser details YourSeq 195 229 588 2000 98.6% chr7 - 131023216 131023829 614 browser details YourSeq 185 228 461 2000 89.7% chr18 - 67653287 67653521 235 browser details YourSeq 184 232 455 2000 91.1% chr10 - 120758224 120758447 224 browser details YourSeq 174 228 433 2000 91.1% chr6 - 48684009 48684211 203 browser details YourSeq 173 212 435 2000 89.9% chr19 - 45985833 45986041 209 browser details YourSeq 171 228 434 2000 92.0% chr2 - 123910925 123911116 192 browser details YourSeq 171 229 429 2000 94.3% chr16 - 95564456 95564656 201 browser details YourSeq 170 215 433 2000 93.3% chr4 - 151331754 151331958 205 browser details YourSeq 169 227 438 2000 93.9% chr15 + 38073055 38073255 201 browser details YourSeq 168 228 430 2000 91.8% chr2 - 153453866 153454052 187 browser details YourSeq 168 228 461 2000 96.2% chr4 + 129179186 129179521 336 browser details YourSeq 168 229 448 2000 97.2% chr2 + 59516959 59517194 236 browser details YourSeq 166 228 430 2000 91.3% chr4 + 150299906 150300092 187 browser details YourSeq 166 229 433 2000 95.7% chr2 + 156864836 156865059 224 browser details YourSeq 165 228 434 2000 93.2% chr2 + 79676961 79677153 193 browser details YourSeq 164 208 382 2000 97.2% chr3 - 90116346 90116520 175 browser details YourSeq 164 229 440 2000 97.7% chr19 + 36385958 36386171 214 browser details YourSeq 164 227 433 2000 92.6% chr18 + 77166301 77166491 191 browser details YourSeq 164 226 430 2000 93.1% chr17 + 32261384 32261575 192

Note: The 2000 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 2000 1 2000 2000 100.0% chr10 + 70477274 70479273 2000 browser details YourSeq 96 1501 2000 2000 86.5% chr6 - 37568250 37568772 523 browser details YourSeq 89 1892 2000 2000 92.4% chr10 + 115344383 115344759 377 browser details YourSeq 87 1872 1995 2000 90.7% chr14 - 52153888 52154012 125 browser details YourSeq 86 1892 1995 2000 91.4% chr3 - 127714381 127714484 104 browser details YourSeq 85 1892 2000 2000 90.5% chr9 - 66096735 66097148 414 browser details YourSeq 85 1892 1995 2000 87.0% chr2 + 156220291 156220390 100 browser details YourSeq 84 1892 2000 2000 84.8% chr5 - 114487492 114487596 105 browser details YourSeq 84 1892 2000 2000 84.8% chr3 + 32328586 32328690 105 browser details YourSeq 84 1892 1996 2000 86.2% chr16 + 93689952 93690052 101 browser details YourSeq 84 1892 2000 2000 84.8% chr1 + 121363551 121363655 105 browser details YourSeq 83 1892 2000 2000 86.9% chr5 - 135614416 135614520 105 browser details YourSeq 82 1892 2000 2000 91.1% chr9 + 57649387 57649776 390 browser details YourSeq 82 1876 1995 2000 83.4% chr6 + 108742875 108742982 108 browser details YourSeq 82 1892 1995 2000 88.5% chr13 + 64317133 64317233 101 browser details YourSeq 81 1892 2000 2000 85.9% chr2 - 132693787 132693891 105 browser details YourSeq 81 1874 1992 2000 91.8% chr10 - 91230335 91230454 120 browser details YourSeq 81 1892 1987 2000 88.1% chr4 + 135384718 135384809 92 browser details YourSeq 81 1892 2000 2000 85.9% chr19 + 18719408 18719512 105 browser details YourSeq 81 1892 1991 2000 86.5% chr12 + 21349496 21349591 96

Note: The 2000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found.

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Gene and protein information: Fam13c family with sequence similarity 13, member C [ Mus musculus (house mouse) ] Gene ID: 71721, updated on 12-Aug-2019

Gene summary

Official Symbol Fam13c provided by MGI Official Full Name family with sequence similarity 13, member C provided by MGI Primary source MGI:MGI:1918971 See related Ensembl:ENSMUSG00000043259 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 mKIAA1796; 1200015N20Rik; C030038O19Rik Expression Broad expression in frontal lobe adult (RPKM 7.6), cortex adult (RPKM 5.7) and 16 other tissues See more Orthologs human all

Genomic context

Location: 10; 10 B5.3 See Fam13c in Genome Data Viewer Exon count: 16

Annotation release Status Assembly Chr Location

108 current GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (70439972..70558736)

Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (69903416..70021480)

Chromosome 10 - NC_000076.6

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Transcript information: This gene has 7 transcripts

Gene: Fam13c ENSMUSG00000043259

Description family with sequence similarity 13, member C [Source:MGI Symbol;Acc:MGI:1918971] Gene Synonyms 1200015N20Rik, C030038O19Rik Location : 70,440,481-70,558,736 forward strand. GRCm38:CM001003.2 About this gene This gene has 7 transcripts (splice variants), 242 orthologues, 2 paralogues and is a member of 1 Ensembl protein family. Transcripts

Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags

Fam13c-202 ENSMUST00000105436.8 3380 519aa ENSMUSP00000101076.2 Protein coding CCDS48592 G3X9S1 TSL:5 GENCODE basic APPRIS ALT2

Fam13c-203 ENSMUST00000173042.8 3310 600aa ENSMUSP00000134648.1 Protein coding CCDS56709 Q8BLV7 TSL:1 GENCODE basic APPRIS ALT2

Fam13c-201 ENSMUST00000062883.6 3262 601aa ENSMUSP00000051375.6 Protein coding CCDS35932 Q9DBR2 TSL:1 GENCODE basic APPRIS P3

Fam13c-205 ENSMUST00000219514.1 4820 No protein - Retained intron - - TSL:2

Fam13c-206 ENSMUST00000220159.1 3464 No protein - Retained intron - - TSL:1

Fam13c-207 ENSMUST00000220442.1 2720 No protein - Retained intron - - TSL:1

Fam13c-204 ENSMUST00000218542.1 2585 No protein - Retained intron - - TSL:1

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138.26 kb Forward strand 70.44Mb 70.46Mb 70.48Mb 70.50Mb 70.52Mb 70.54Mb 70.56Mb (Comprehensive set... Fam13c-204 >retained intron

Fam13c-202 >protein coding

Fam13c-207 >retained intron

Fam13c-205 >retained intron

Fam13c-203 >protein coding

Fam13c-206 >retained intron

Fam13c-201 >protein coding

Contigs < AC079681.38 AC122896.4 > Genes < Gm22320-201misc RNA < Phyhipl-207retained intron (Comprehensive set...

< Gm29783-201processed pseudogene < Phyhipl-210retained intron

< Phyhipl-201protein coding

< Phyhipl-206protein coding

< Phyhipl-205protein coding

Regulatory Build

70.44Mb 70.46Mb 70.48Mb 70.50Mb 70.52Mb 70.54Mb 70.56Mb Reverse strand 138.26 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

pseudogene RNA gene processed transcript

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Transcript: ENSMUST00000105436

118.06 kb Forward strand

Fam13c-202 >protein coding

ENSMUSP00000101... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) PANTHER Protein FAM13

PTHR15904:SF19

All sequence SNPs/i... Sequence variants (dbSNP and all other sources)

Variant Legend

missense variant synonymous variant

Scale bar 0 60 120 180 240 300 360 420 519

We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.

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