https://www.alphaknockout.com

Mouse Hnrnph3 Knockout Project (CRISPR/Cas9)

Objective: To create a Hnrnph3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.

Strategy summary: The Hnrnph3 gene (NCBI Reference Sequence: NM_001079824 ; Ensembl: ENSMUSG00000020069 ) is located on Mouse chromosome 10. 10 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 10 (Transcript: ENSMUST00000020263). Exon 2~3 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 2 starts from the coding region. Exon 2~3 covers 24.18% of the coding region. The size of effective KO region: ~768 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 10

Legends Exon of mouse Hnrnph3 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. 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 534 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(24.4% 488) | C(17.5% 350) | T(35.05% 701) | 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(534bp) | A(29.4% 157) | C(10.67% 57) | T(41.01% 219) | G(18.91% 101)

Note: The 534 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% chr10 - 63019505 63021504 2000 browser details YourSeq 196 1170 1574 2000 87.4% chr12 + 3681162 3681492 331 browser details YourSeq 190 1165 1575 2000 92.8% chr11 + 107136927 107137497 571 browser details YourSeq 175 1214 1574 2000 91.5% chr1 - 181190738 181191248 511 browser details YourSeq 172 1259 1581 2000 93.9% chr1 - 93629714 93630103 390 browser details YourSeq 166 1229 1575 2000 87.0% chr9 + 64292402 64292611 210 browser details YourSeq 165 1178 1584 2000 82.0% chr4 - 96566092 96566311 220 browser details YourSeq 165 1251 1589 2000 84.2% chr2 + 28949584 28949828 245 browser details YourSeq 162 1305 1590 2000 92.6% chr12 - 55271927 55272365 439 browser details YourSeq 161 1172 1574 2000 94.5% chr10 + 82951205 83126196 174992 browser details YourSeq 158 1309 1566 2000 94.5% chr11 - 61844083 61844622 540 browser details YourSeq 156 1415 1594 2000 95.3% chr10 - 60738223 60738402 180 browser details YourSeq 156 1210 1522 2000 94.4% chr1 - 59666391 60028824 362434 browser details YourSeq 154 1259 1575 2000 92.4% chr12 + 78282678 78283162 485 browser details YourSeq 153 1395 1594 2000 91.1% chr7 - 126757128 126757326 199 browser details YourSeq 153 1362 1574 2000 92.8% chr4 - 101343316 101343532 217 browser details YourSeq 151 1308 1559 2000 90.3% chr12 - 77349275 77349520 246 browser details YourSeq 147 1419 1600 2000 92.9% chr13 - 40314978 40315160 183 browser details YourSeq 147 1422 1592 2000 94.6% chrX + 61097327 61097508 182 browser details YourSeq 147 1393 1573 2000 94.2% chr11 + 72440282 72440692 411

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 534 1 534 534 100.0% chr10 - 63018226 63018759 534 browser details YourSeq 41 243 523 534 95.5% chr10 + 59330269 59369756 39488 browser details YourSeq 32 191 258 534 97.2% chr1 + 67376229 67376298 70 browser details YourSeq 31 228 273 534 74.3% chr1 + 141105872 141105908 37 browser details YourSeq 31 227 275 534 70.6% chr1 + 34018313 34018347 35 browser details YourSeq 30 243 276 534 97.1% chr10 + 95499360 95499395 36 browser details YourSeq 29 245 273 534 100.0% chr10 - 128624933 128624961 29 browser details YourSeq 29 244 277 534 87.5% chr10 - 74014385 74014417 33 browser details YourSeq 29 245 273 534 100.0% chr1 - 3103418 3103446 29 browser details YourSeq 29 244 276 534 83.9% chr1 + 74515170 74515200 31 browser details YourSeq 27 247 277 534 82.8% chr1 + 42386193 42386221 29 browser details YourSeq 26 239 268 534 96.6% chr11 + 17348211 17348260 50 browser details YourSeq 25 250 277 534 84.7% chr9 - 114598291 114598316 26 browser details YourSeq 25 237 263 534 100.0% chr1 - 124545976 124546006 31 browser details YourSeq 23 383 406 534 100.0% chr10 - 117834433 117834457 25 browser details YourSeq 22 244 266 534 100.0% chr10 - 42649924 42649947 24 browser details YourSeq 21 356 376 534 100.0% chr5 - 90450866 90450886 21 browser details YourSeq 21 9 29 534 100.0% chr10 + 4495041 4495061 21 browser details YourSeq 20 187 206 534 100.0% chr11 - 38936965 38936984 20 browser details YourSeq 20 281 302 534 95.5% chr1 + 183251221 183251242 22

Note: The 534 bp section downstream of Exon 3 is BLAT searched against the genome. No significant similarity is found.

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Gene and protein information: Hnrnph3 heterogeneous nuclear ribonucleoprotein H3 [ Mus musculus (house mouse) ] Gene ID: 432467, updated on 24-Oct-2019

Gene summary

Official Symbol Hnrnph3 provided by MGI Official Full Name heterogeneous nuclear ribonucleoprotein H3 provided by MGI Primary source MGI:MGI:1926462 See related Ensembl:ENSMUSG00000020069 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 Hnrph3; AA693301; AI666703 Expression Broad expression in CNS E11.5 (RPKM 51.4), CNS E14 (RPKM 36.9) and 21 other tissues See more Orthologs human all

Genomic context

Location: 10; 10 B4 See Hnrnph3 in Genome Data Viewer Exon count: 12

Annotation release Status Assembly Chr Location

108 current GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (63014664..63023980, complement)

Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (62477412..62486597, complement)

Chromosome 10 - NC_000076.6

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Transcript information: This gene has 6 transcripts

Gene: Hnrnph3 ENSMUSG00000020069

Description heterogeneous nuclear ribonucleoprotein H3 [Source:MGI Symbol;Acc:MGI:1926462] Gene Synonyms Hnrph3, hnRNP 2H9 Location Chromosome 10: 63,014,664-63,024,217 reverse strand. GRCm38:CM001003.2 About this gene This gene has 6 transcripts (splice variants), 210 orthologues, 10 paralogues and is a member of 1 Ensembl protein family. Transcripts

Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags

Hnrnph3- ENSMUST00000020263.13 2213 346aa ENSMUSP00000020263.7 Protein coding CCDS48583 D3Z3N4 TSL:5 201 GENCODE basic APPRIS P3

Hnrnph3- ENSMUST00000118898.7 2168 331aa ENSMUSP00000112424.1 Protein coding CCDS83704 D3YWT1 TSL:5 202 GENCODE basic APPRIS ALT1

Hnrnph3- ENSMUST00000119814.2 682 71aa ENSMUSP00000113134.2 Protein coding - D3Z6Y3 TSL:1 203 GENCODE basic

Hnrnph3- ENSMUST00000140743.7 1633 71aa ENSMUSP00000118444.1 Nonsense mediated - D3Z6Y3 TSL:5 204 decay

Hnrnph3- ENSMUST00000143689.2 802 No - Retained intron - - TSL:3 206 protein

Hnrnph3- ENSMUST00000141616.1 651 No - Retained intron - - TSL:2 205 protein

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29.55 kb Forward strand 63.01Mb 63.02Mb 63.03Mb Genes Rufy2-202 >protein coding Pbld2-202 >protein coding (Comprehensive set...

Rufy2-205 >nonsense mediated decay Pbld2-201 >protein coding

Rufy2-206 >retained intron

Contigs AC113107.15 > AC113107.15 > Genes (Comprehensive set... < Hnrnph3-202protein coding

< Hnrnph3-201protein coding

< Hnrnph3-204nonsense mediated decay

< Hnrnph3-205retained intron

< Hnrnph3-206retained intron

< Hnrnph3-203protein coding

Regulatory Build

63.01Mb 63.02Mb 63.03Mb Reverse strand 29.55 kb

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

Gene Legend Protein Coding

Ensembl protein coding merged Ensembl/Havana

Non-Protein Coding

processed transcript

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Transcript: ENSMUST00000020263

< Hnrnph3-201protein coding

Reverse strand 9.23 kb

ENSMUSP00000020... Low complexity (Seg) Superfamily RNA-binding domain superfamily SMART RNA recognition motif domain Pfam RNA recognition motif domain PROSITE profiles RNA recognition motif domain PANTHER PTHR13976

PTHR13976:SF36 Gene3D Nucleotide-binding alpha-beta plait domain superfamily CDD hnRNPH3, RNA recognition motif 2 hnRNPH3, RNA recognition motif 3

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

Variant Legend synonymous variant

Scale bar 0 40 80 120 160 200 240 280 346

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

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