https://www.alphaknockout.com

Mouse Parp12 Knockout Project (CRISPR/Cas9)

Objective: To create a Parp12 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.

Strategy summary: The Parp12 (NCBI Reference Sequence: NM_172893 ; Ensembl: ENSMUSG00000038507 ) is located on Mouse 6. 12 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 12 (Transcript: ENSMUST00000038398). Exon 2~4 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 2 starts from about 16.6% of the coding region. Exon 2~4 covers 25.27% of the coding region. The size of effective KO region: ~8412 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 2 3 4 12

Legends Exon of mouse Parp12 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 2 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 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.

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Overview of the GC Content Distribution (up) Window size: 300 bp

Sequence 12

Summary: Full Length(2000bp) | A(22.25% 445) | C(21.25% 425) | T(33.45% 669) | G(23.05% 461)

Note: The 2000 bp section upstream of Exon 2 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(23.3% 466) | C(20.95% 419) | T(33.2% 664) | G(22.55% 451)

Note: The 2000 bp section downstream 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.

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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 - 39114302 39116301 2000 browser details YourSeq 215 728 1264 2000 86.3% chr11 - 4894620 4894919 300 browser details YourSeq 211 729 1267 2000 83.2% chr11 + 4914956 4915286 331 browser details YourSeq 194 728 1248 2000 88.3% chr18 - 66423996 66424678 683 browser details YourSeq 193 728 1225 2000 83.8% chr1 - 152951213 152951470 258 browser details YourSeq 189 728 1267 2000 93.2% chr14 + 25953875 26233200 279326 browser details YourSeq 186 728 1260 2000 91.2% chr14 - 27358811 27359452 642 browser details YourSeq 184 728 1267 2000 82.8% chr9 + 57618203 57618614 412 browser details YourSeq 180 727 1081 2000 85.7% chr12 - 110671623 110671951 329 browser details YourSeq 180 728 1267 2000 86.4% chr5 + 150643503 150644019 517 browser details YourSeq 177 730 1265 2000 91.6% chr12 - 65192261 65192805 545 browser details YourSeq 175 728 1148 2000 90.4% chr13 - 55145093 55364641 219549 browser details YourSeq 174 728 1200 2000 91.5% chr9 - 108659443 108660071 629 browser details YourSeq 173 728 924 2000 94.9% chr4 - 32505607 32771780 266174 browser details YourSeq 166 728 1250 2000 87.4% chr6 + 39593856 39594312 457 browser details YourSeq 166 730 943 2000 89.2% chr11 + 71120569 71120767 199 browser details YourSeq 164 728 1224 2000 91.5% chr8 + 70705713 70706371 659 browser details YourSeq 162 713 911 2000 90.8% chr9 - 72211040 72211228 189 browser details YourSeq 162 730 1267 2000 91.4% chr11 + 96068861 96069430 570 browser details YourSeq 161 729 913 2000 94.0% chr4 - 150622476 150622663 188

Note: The 2000 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 2000 1 2000 2000 100.0% chr6 - 39103890 39105889 2000 browser details YourSeq 59 735 859 2000 73.9% chrX + 153540120 153540241 122 browser details YourSeq 55 734 843 2000 78.7% chr13 - 54890154 54890262 109 browser details YourSeq 52 697 780 2000 86.4% chr11 - 11569979 11570061 83 browser details YourSeq 52 747 844 2000 74.2% chr3 + 144156893 144156985 93 browser details YourSeq 46 774 851 2000 79.5% chr11 - 113605551 113605628 78 browser details YourSeq 44 724 801 2000 90.6% chr13 - 36790961 36791041 81 browser details YourSeq 42 770 843 2000 81.2% chr16 + 90855344 90855419 76 browser details YourSeq 39 770 918 2000 84.3% chr12 + 52408505 52409007 503 browser details YourSeq 38 724 782 2000 95.3% chr10 - 117128353 117128639 287 browser details YourSeq 38 726 782 2000 91.4% chr19 + 45641685 45641744 60 browser details YourSeq 38 747 844 2000 83.0% chr15 + 38133325 38133420 96 browser details YourSeq 37 674 801 2000 64.3% chr2 - 35373186 35373242 57 browser details YourSeq 37 770 844 2000 74.7% chr16 - 37967556 37967630 75 browser details YourSeq 37 734 783 2000 95.2% chr18 + 67174029 67174079 51 browser details YourSeq 37 734 801 2000 77.7% chr1 + 187955978 187956046 69 browser details YourSeq 35 725 801 2000 80.4% chr11 + 66164432 66164507 76 browser details YourSeq 34 724 784 2000 84.3% chr8 - 31938877 31938934 58 browser details YourSeq 34 775 844 2000 74.3% chr2 - 52012057 52012126 70 browser details YourSeq 34 770 853 2000 88.7% chr1 - 37946304 37946388 85

Note: The 2000 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: Parp12 poly (ADP-ribose) polymerase family, member 12 [ Mus musculus (house mouse) ] Gene ID: 243771, updated on 12-Aug-2019

Gene summary

Official Symbol Parp12 provided by MGI Official Full Name poly (ADP-ribose) polymerase family, member 12 provided by MGI Primary source MGI:MGI:2143990 See related Ensembl:ENSMUSG00000038507 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 ARTD12; PARP-12; Zc3hdc1; AA409132; AA536654; 9930021O16 Expression Ubiquitous expression in small intestine adult (RPKM 28.4), colon adult (RPKM 27.7) and 26 other tissues See more Orthologs all

Genomic context

Location: 6; 6 B1 See Parp12 in Genome Data Viewer Exon count: 12

Annotation release Status Assembly Chr Location

108 current GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (39086412..39118349, complement)

Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (39036411..39068348, complement)

Chromosome 6 - NC_000072.6

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Transcript information: This gene has 2 transcripts

Gene: Parp12 ENSMUSG00000038507

Description poly (ADP-ribose) polymerase family, member 12 [Source:MGI Symbol;Acc:MGI:2143990] Gene Synonyms Zc3hdc1 Location Chromosome 6: 39,086,410-39,118,349 reverse strand. GRCm38:CM000999.2 About this gene This gene has 2 transcripts (splice variants), 229 orthologues, 7 paralogues, is a member of 1 Ensembl protein family and is associated with 4 phenotypes. Transcripts

Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags

Parp12-201 ENSMUST00000038398.6 3231 711aa ENSMUSP00000039704.6 Protein coding CCDS20019 Q8BZ20 TSL:1 GENCODE basic APPRIS P1

Parp12-202 ENSMUST00000129916.1 1009 No protein - Retained intron - - TSL:2

51.94 kb Forward strand 39.08Mb 39.09Mb 39.10Mb 39.11Mb 39.12Mb Tbxas1-201 >protein coding 4930599N23Rik-201 >lncRNA (Comprehensive set...

Tbxas1-205 >retained intron

Contigs AC125327.4 > < AC153818.5 Genes (Comprehensive set... < Parp12-201protein coding < Gm42963-201TEC

< Parp12-202retained intron

Regulatory Build

39.08Mb 39.09Mb 39.10Mb 39.11Mb 39.12Mb Reverse strand 51.94 kb

Regulation Legend

CTCF Enhancer Promoter Promoter Flank Transcription Factor Binding Site

Gene Legend Protein Coding

merged Ensembl/Havana

Non-Protein Coding

processed transcript RNA gene

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Transcript: ENSMUST00000038398

< Parp12-201protein coding

Reverse strand 31.94 kb

ENSMUSP00000039... MobiDB lite Low complexity (Seg) Superfamily SSF56399

WWE domain superfamily SMART Zinc finger, CCCH-type Pfam Zinc finger, CCCH-type WWE domain Poly(ADP-ribose) polymerase, catalytic domain

PROSITE profiles Zinc finger, CCCH-type Poly(ADP-ribose) polymerase, catalytic domain

WWE domain PANTHER PTHR45740

PTHR45740:SF9 Gene3D WWE domain superfamily

3.90.228.10 CDD cd01439

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

Variant Legend

missense variant synonymous variant

Scale bar 0 60 120 180 240 300 360 420 480 540 600 711

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

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