https://www.alphaknockout.com

Mouse Jazf1 Knockout Project (CRISPR/Cas9)

Objective: To create a Jazf1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.

Strategy summary: The Jazf1 (NCBI Reference Sequence: NM_173406 ; Ensembl: ENSMUSG00000063568 ) is located on Mouse 6. 5 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 5 (Transcript: ENSMUST00000074541). Exon 3 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 3 starts from about 25.93% of the coding region. Exon 3 covers 27.02% of the coding region. The size of effective KO region: ~197 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 3 5

Legends Exon of mouse Jazf1 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 3 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 3 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(28.65% 573) | C(21.75% 435) | T(27.7% 554) | G(21.9% 438)

Note: The 2000 bp section upstream of Exon 3 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(25.7% 514) | C(22.55% 451) | T(27.3% 546) | G(24.45% 489)

Note: The 2000 bp section downstream of Exon 3 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% chr6 - 52812300 52814299 2000 browser details YourSeq 23 1717 1739 2000 100.0% chr12 - 98663296 98663318 23 browser details YourSeq 22 655 676 2000 100.0% chr12 - 70908491 70908512 22 browser details YourSeq 21 119 139 2000 100.0% chr13 + 54561386 54561406 21 browser details YourSeq 20 1314 1335 2000 95.5% chr1 - 112974325 112974346 22 browser details YourSeq 20 1947 1966 2000 100.0% chr1 + 80440002 80440021 20

Note: The 2000 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 2000 1 2000 2000 100.0% chr6 - 52810103 52812102 2000 browser details YourSeq 35 527 635 2000 95.0% chr18 - 33180076 33180240 165 browser details YourSeq 24 1832 1855 2000 100.0% chr1 + 141124526 141124549 24 browser details YourSeq 23 259 284 2000 96.2% chr1 - 48262325 48262354 30 browser details YourSeq 23 1248 1271 2000 100.0% chr1 - 36568073 36568097 25 browser details YourSeq 22 282 303 2000 100.0% chr13 - 101032480 101032501 22 browser details YourSeq 22 1284 1309 2000 84.0% chr1 + 95346766 95346790 25 browser details YourSeq 21 1804 1824 2000 100.0% chr12 - 21416401 21416421 21 browser details YourSeq 21 1848 1868 2000 100.0% chr10 + 121095236 121095256 21

Note: The 2000 bp section downstream of Exon 3 is BLAT searched against the genome. No significant similarity is found.

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Gene and information: Jazf1 JAZF zinc finger 1 [ Mus musculus (house mouse) ] Gene ID: 231986, updated on 10-Oct-2019

Gene summary

Official Symbol Jazf1 provided by MGI Official Full Name JAZF zinc finger 1 provided by MGI Primary source MGI:MGI:2141450 See related Ensembl:ENSMUSG00000063568 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 Jaz1; Tip27; AI591476; C820002C15 Expression Biased expression in testis adult (RPKM 14.8), CNS E18 (RPKM 12.6) and 13 other tissues See more Orthologs human all

Genomic context

Location: 6 B3; 6 25.74 cM See Jazf1 in Genome Data Viewer Exon count: 8

Annotation release Status Assembly Chr Location

108 current GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (52768065..53068624, complement)

Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (52718062..53018618, complement)

Chromosome 6 - NC_000072.6

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Transcript information: This gene has 3 transcripts

Gene: Jazf1 ENSMUSG00000063568

Description JAZF zinc finger 1 [Source:MGI Symbol;Acc:MGI:2141450] Gene Synonyms Jaz1, Tip27 Location Chromosome 6: 52,768,797-53,068,631 reverse strand. GRCm38:CM000999.2 About this gene This gene has 3 transcripts (splice variants), 247 orthologues and is a member of 1 Ensembl protein family. Transcripts

Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags

Jazf1-201 ENSMUST00000074541.5 2203 243aa ENSMUSP00000074129.5 Protein coding CCDS20152 Q80ZQ5 TSL:1 GENCODE basic APPRIS P1

Jazf1-203 ENSMUST00000136250.5 2197 No protein - lncRNA - - TSL:1

Jazf1-202 ENSMUST00000128282.3 1914 No protein - lncRNA - - TSL:3

319.83 kb Forward strand

52.8Mb 52.9Mb 53.0Mb Tax1bp1-201 >protein coding Gm15573-201 >processed pseudogene (Comprehensive set...

Tax1bp1-206 >retained intron

Contigs < AC117212.5 AC107317.3 >

Genes (Comprehensive set... < Jazf1-201protein coding

< Jazf1-203lncRNA < Gm26215-201scaRNA

< Jazf1-202lncRNA < Gm15572-201processed pseudogene

Regulatory Build

52.8Mb 52.9Mb 53.0Mb Reverse strand 319.83 kb

Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site

Gene Legend Protein Coding

merged Ensembl/Havana

Non-Protein Coding

RNA gene pseudogene processed transcript

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Transcript: ENSMUST00000074541

< Jazf1-201protein coding

Reverse strand 299.83 kb

ENSMUSP00000074... MobiDB lite Low complexity (Seg) Superfamily Zinc finger C2H2 superfamily

SMART Zinc finger C2H2-type PROSITE patterns Zinc finger C2H2-type PANTHER PTHR23057

PTHR23057:SF1 Gene3D 3.30.160.60

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

Variant Legend

missense variant synonymous variant

Scale bar 0 40 80 120 160 200 243

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

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