https://www.alphaknockout.com

Mouse Parp3 Knockout Project (CRISPR/Cas9)

Objective: To create a Parp3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.

Strategy summary: The Parp3 gene (NCBI Reference Sequence: NM_145619 ; Ensembl: ENSMUSG00000023249 ) is located on Mouse chromosome 9. 11 exons are identified, with the ATG start codon in exon 2 and the TAA stop codon in exon 11 (Transcript: ENSMUST00000067218). Exon 3~11 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: Mice homozygous for a knock-out allele exhibit normal survival.

Exon 3 starts from about 11.24% of the coding region. Exon 3~11 covers 88.83% of the coding region. The size of effective KO region: ~3911 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 5 6 7 8 9 10 11

Legends Exon of mouse Parp3 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 stop codon 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.

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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(28.4% 568) | T(22.7% 454) | G(26.65% 533)

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(23.65% 473) | C(27.5% 550) | T(26.8% 536) | G(22.05% 441)

Note: The 2000 bp section downstream of stop codon 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% chr9 - 106475149 106477148 2000 browser details YourSeq 149 1381 1565 2000 91.3% chr19 + 32250040 32250222 183 browser details YourSeq 148 1381 1563 2000 93.0% chr12 - 25455118 25455335 218 browser details YourSeq 147 1380 1568 2000 93.1% chr3 - 152294996 152295185 190 browser details YourSeq 147 1382 1573 2000 90.3% chr14 + 99815177 99815366 190 browser details YourSeq 144 1380 1568 2000 87.5% chr9 - 57646314 57646482 169 browser details YourSeq 143 1379 1572 2000 91.5% chr15 - 79531065 79531573 509 browser details YourSeq 142 1406 1572 2000 94.4% chr4 - 137900806 137901177 372 browser details YourSeq 141 1381 1568 2000 92.4% chr2 - 105909700 105909887 188 browser details YourSeq 141 1396 1568 2000 90.0% chr3 + 152674149 152674312 164 browser details YourSeq 141 1411 1590 2000 87.6% chr11 + 88786371 88786533 163 browser details YourSeq 141 1382 1568 2000 87.2% chr10 + 45650893 45651062 170 browser details YourSeq 140 1382 1564 2000 87.4% chr3 - 24379316 24379489 174 browser details YourSeq 140 1381 1568 2000 86.3% chr19 - 10254230 10254409 180 browser details YourSeq 140 1383 1564 2000 91.3% chr2 + 93755917 93756108 192 browser details YourSeq 140 1383 1573 2000 85.8% chr19 + 23603569 23603741 173 browser details YourSeq 140 1382 1565 2000 87.0% chr14 + 86051679 86051854 176 browser details YourSeq 139 1381 1563 2000 91.7% chr16 + 37933670 37933856 187 browser details YourSeq 138 1395 1569 2000 92.1% chr2 + 156260630 156260946 317 browser details YourSeq 137 1381 1565 2000 87.4% chr5 - 130323940 130324103 164

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% chr9 - 106469236 106471235 2000 browser details YourSeq 63 1728 1820 2000 84.1% chr4 - 118084379 118084458 80 browser details YourSeq 63 1773 1856 2000 88.9% chr7 + 15893003 15893086 84 browser details YourSeq 61 1757 1849 2000 85.1% chr10 + 75875863 75875957 95 browser details YourSeq 58 134 334 2000 89.1% chr8 - 69837990 69838420 431 browser details YourSeq 58 1788 1859 2000 90.3% chr13 - 59691261 59691332 72 browser details YourSeq 57 1772 1851 2000 84.5% chr17 - 28570893 28570971 79 browser details YourSeq 57 1784 1857 2000 89.2% chr3 + 51676950 51677027 78 browser details YourSeq 56 1793 1854 2000 96.8% chr8 - 123063596 123063860 265 browser details YourSeq 56 1779 1859 2000 83.4% chr11 + 4245372 4245451 80 browser details YourSeq 55 1773 1859 2000 93.8% chr7 - 35755976 35756359 384 browser details YourSeq 53 1757 1854 2000 88.5% chr11 - 79221370 79221468 99 browser details YourSeq 52 1758 1853 2000 85.4% chr6 - 97209421 97209517 97 browser details YourSeq 52 1779 1859 2000 87.5% chr13 - 83743615 83743694 80 browser details YourSeq 52 1792 1859 2000 88.3% chr11 + 78340580 78340647 68 browser details YourSeq 52 280 374 2000 76.7% chr1 + 87656721 87656787 67 browser details YourSeq 51 1788 1861 2000 85.2% chr6 - 83532378 83532462 85 browser details YourSeq 51 1758 1824 2000 88.1% chr14 + 79948939 79949005 67 browser details YourSeq 49 1752 1854 2000 69.2% chr12 - 100893854 100893935 82 browser details YourSeq 48 1762 1820 2000 91.6% chrX - 37103717 37103777 61

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

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Gene and protein information: Parp3 poly (ADP-ribose) polymerase family, member 3 [ Mus musculus (house mouse) ] Gene ID: 235587, updated on 10-Oct-2019

Gene summary

Official Symbol Parp3 provided by MGI Official Full Name poly (ADP-ribose) polymerase family, member 3 provided by MGI Primary source MGI:MGI:1891258 See related Ensembl:ENSMUSG00000023249 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 ARTD3; Adprt3; PARP-3; ADPRT-3; Adprtl3; AW990611; pADPRT-3; A930002C11Rik Expression Broad expression in subcutaneous fat pad adult (RPKM 25.0), bladder adult (RPKM 19.6) and 18 other tissues See more Orthologs human all

Genomic context

Location: 9; 9 F1 See Parp3 in Genome Data Viewer Exon count: 12

Annotation release Status Assembly Chr Location

108 current GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (106470322..106476949, complement)

Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (106372684..106378982, complement)

Chromosome 9 - NC_000075.6

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Transcript information: This gene has 9 transcripts

Gene: Parp3 ENSMUSG00000023249

Description poly (ADP-ribose) polymerase family, member 3 [Source:MGI Symbol;Acc:MGI:1891258] Gene Synonyms A930002C11Rik, Adprt3, Adprtl3, PARP-3 Location Chromosome 9: 106,470,322-106,476,949 reverse strand. GRCm38:CM001002.2 About this gene This gene has 9 transcripts (splice variants), 195 orthologues, 2 paralogues and is a member of 1 Ensembl protein family. Transcripts

Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags

Parp3-201 ENSMUST00000067218.13 2962 528aa ENSMUSP00000064513.7 Protein coding CCDS23480 Q3ULW8 TSL:1 GENCODE basic APPRIS P3

Parp3-203 ENSMUST00000123555.7 2495 528aa ENSMUSP00000123054.1 Protein coding CCDS23480 Q3ULW8 TSL:1 GENCODE basic APPRIS P3

Parp3-202 ENSMUST00000112479.8 2030 533aa ENSMUSP00000108098.2 Protein coding CCDS81066 Q3ULW8 TSL:1 GENCODE basic APPRIS ALT2

Parp3-209 ENSMUST00000214682.1 1180 351aa ENSMUSP00000149572.1 Protein coding - - CDS 3' incomplete TSL:5

Parp3-208 ENSMUST00000156426.7 636 202aa ENSMUSP00000117329.1 Protein coding - - CDS 3' incomplete TSL:3

Parp3-204 ENSMUST00000125850.1 591 171aa ENSMUSP00000119244.1 Protein coding - - CDS 3' incomplete TSL:3

Parp3-207 ENSMUST00000145396.7 2246 No protein - Retained intron - - TSL:2

Parp3-205 ENSMUST00000139362.1 667 No protein - Retained intron - - TSL:2

Parp3-206 ENSMUST00000140029.1 654 No protein - Retained intron - - TSL:2

26.63 kb Forward strand 106.465Mb 106.470Mb 106.475Mb 106.480Mb 106.485Mb Genes Pcbp4-206 >protein coding Rrp9-202 >lncRNA Rrp9-205 >retained intron (Comprehensive set...

Pcbp4-201 >protein coding Rrp9-201 >protein coding

Pcbp4-221 >protein coding Rrp9-203 >retained intron

Pcbp4-222 >protein coding Rrp9-204 >retained intron Rrp9-207 >nonsense mediated decay

Pcbp4-220 >protein coding Rrp9-208 >retained intron

Pcbp4-208 >retained intron Rrp9-206 >retained intron

Pcbp4-203 >protein coding

Pcbp4-215 >protein coding

Pcbp4-216 >retained intron

Pcbp4-212 >protein coding

Pcbp4-223 >retained intron

Pcbp4-202 >nonsense mediated decay

Pcbp4-217 >protein coding Page 7 of 9

Pcbp4-218 >nonsense mediated decay

Pcbp4-213 >retained intron

Pcbp4-214 >protein coding

Pcbp4-219 >nonsense mediated decay

Pcbp4-207 >lncRNA

Pcbp4-210 >protein coding

Pcbp4-211 >retained intron

Contigs AC151729.6 >

Genes < Gpr62-201protein coding < Parp3-201protein coding (Comprehensive set...

< Parp3-203protein coding

< Parp3-202protein coding

< Parp3-207retained intron

< Parp3-205retained intron

< Parp3-209protein coding

< Parp3-208protein coding

< Parp3-206retained intron

< Parp3-204protein coding

Regulatory Build

106.465Mb 106.470Mb 106.475Mb 106.480Mb 106.485Mb Reverse strand 26.63 kb

Regulation Legend

CTCF Enhancer Open Chromatin Promoter Promoter Flank

Gene Legend Protein Coding

merged Ensembl/Havana Ensembl protein coding

Non-Protein Coding

RNA gene processed transcript 26.63 kb Forward strand 106.465Mb 106.470Mb 106.475Mb 106.480Mb 106.485Mb Genes Pcbp4-206 >protein coding Rrp9-202 >lncRNA Rrp9-205 >retained intron (Comprehensive set...

Pcbp4-201 >protein coding Rrp9-201 >protein coding

Pcbp4-221 >protein coding Rrp9-203 >retained intron

Pcbp4-222 >protein coding Rrp9-204 >retained intron Rrp9-207 >nonsense mediated decay

Pcbp4-220 >protein coding Rrp9-208 >retained intron

Pcbp4-208 >retained intron Rrp9-206 >retained intron

Pcbp4-203 >protein coding

Pcbp4-215 >protein coding

Pcbp4-216 >retained intron

Pcbp4-212 >protein coding

Pcbp4-223 >retained intron

Pcbp4-202 >nonsense mediated decay https://www.alphaknockout.com

Pcbp4-217 >protein coding

Pcbp4-218 >nonsense mediated decay

Pcbp4-213 >retained intron

Pcbp4-214 >protein coding

Pcbp4-219 >nonsense mediated decay

Pcbp4-207 >lncRNA

Pcbp4-210 >protein coding

Pcbp4-211 >retained intron

Contigs AC151729.6 >

Genes (Comprehensive set... < Gpr62-201protein coding < Parp3-201protein coding

< Parp3-203protein coding

< Parp3-202protein coding

< Parp3-207retained intron

< Parp3-205retained intron

< Parp3-209protein coding

< Parp3-208protein coding

< Parp3-206retained intron

< Parp3-204protein coding

Regulatory Build

106.465Mb 106.470Mb 106.475Mb 106.480Mb 106.485Mb Reverse strand 26.63 kb

Regulation Legend

CTCF Enhancer Open Chromatin Promoter Promoter Flank

Gene Legend Protein Coding

merged Ensembl/Havana Ensembl protein coding

Non-Protein Coding

RNA gene processed transcript

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Transcript: ENSMUST00000067218

< Parp3-201protein coding

Reverse strand 6.63 kb

ENSMUSP00000064... MobiDB lite Low complexity (Seg) Superfamily WGR domain superfamily SSF56399

Poly(ADP-ribose) polymerase, regulatory domain superfamily SMART WGR domain Pfam WGR domain Poly(ADP-ribose) polymerase, catalytic domain

Poly(ADP-ribose) polymerase, regulatory domain PROSITE profiles Poly(ADP-ribose) polymerase, regulatory domain

Poly(ADP-ribose) polymerase, catalytic domain PANTHER Protein mono-ADP-ribosyltransferase PARP3

PTHR10459 Gene3D WGR domain superfamily 3.90.228.10

Poly(ADP-ribose) polymerase, regulatory domain superfamily CDD cd01437

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

Variant Legend missense variant synonymous variant

Scale bar 0 60 120 180 240 300 360 420 528

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

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