https://www.alphaknockout.com
Mouse Pcdhgc3 Knockout Project (CRISPR/Cas9)
Objective: To create a Pcdhgc3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Pcdhgc3 gene (NCBI Reference Sequence: NM_033581 ; Ensembl: ENSMUSG00000102918 ) is located on Mouse chromosome 18. 4 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 4 (Transcript: ENSMUST00000076807). Exon 1 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 1 starts from the coding region. Exon 1 covers 86.72% of the coding region. The size of effective KO region: ~2430 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 4
Legends Exon of mouse Pcdhgc3 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 of Exon 1 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 of Exon 1 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(28.6% 572) | T(21.6% 432) | G(27.55% 551)
Note: The 2000 bp section of Exon 1 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(22.5% 450) | C(30.05% 601) | T(21.6% 432) | G(25.85% 517)
Note: The 2000 bp section of Exon 1 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% chr18 + 37806550 37808549 2000 browser details YourSeq 54 1031 1152 2000 72.2% chr18 + 37686414 37686535 122 browser details YourSeq 53 1236 1583 2000 57.8% chr18 + 37296201 37402626 106426 browser details YourSeq 34 1321 1583 2000 54.1% chr18 + 37321876 37322132 257 browser details YourSeq 31 372 406 2000 94.3% chr14 + 84446462 84446496 35 browser details YourSeq 30 1920 1957 2000 91.5% chr11 + 48882929 48883031 103 browser details YourSeq 24 1321 1583 2000 52.2% chr18 + 37413180 37413436 257 browser details YourSeq 22 108 129 2000 100.0% chr11 + 98316815 98316836 22 browser details YourSeq 22 1082 1106 2000 95.9% chr10 + 60369381 60369406 26 browser details YourSeq 20 237 256 2000 100.0% chr1 - 81752819 81752838 20
Note: The 2000 bp section of Exon 1 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% chr18 + 37806978 37808977 2000 browser details YourSeq 54 603 724 2000 72.2% chr18 + 37686414 37686535 122 browser details YourSeq 53 808 1155 2000 57.8% chr18 + 37296201 37402626 106426 browser details YourSeq 34 893 1155 2000 54.1% chr18 + 37321876 37322132 257 browser details YourSeq 30 1492 1529 2000 91.5% chr11 + 48882929 48883031 103 browser details YourSeq 24 893 1155 2000 52.2% chr18 + 37413180 37413436 257 browser details YourSeq 24 1642 1666 2000 100.0% chr10 + 17306641 17306675 35 browser details YourSeq 22 654 678 2000 95.9% chr10 + 60369381 60369406 26
Note: The 2000 bp section of Exon 1 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Pcdhgc3 protocadherin gamma subfamily C, 3 [ Mus musculus (house mouse) ] Gene ID: 93706, updated on 11-Sep-2019
Gene summary
Official Symbol Pcdhgc3 provided by MGI Official Full Name protocadherin gamma subfamily C, 3 provided by MGI Primary source MGI:MGI:1935201 See related Ensembl:ENSMUSG00000102918 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 PC43; Pcdh2 Expression Broad expression in adrenal adult (RPKM 57.2), frontal lobe adult (RPKM 54.5) and 24 other tissues See more Orthologs human all
Genomic context
Location: 18 B3; 18 19.67 cM See Pcdhgc3 in Genome Data Viewer Exon count: 4
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (37806410..37841873)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 18 NC_000084.5 (37966064..38001527)
Chromosome 18 - NC_000084.6
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Transcript information: This gene has 3 transcripts
Gene: Pcdhgc3 ENSMUSG00000102918
Description protocadherin gamma subfamily C, 3 [Source:MGI Symbol;Acc:MGI:1935201] Gene Synonyms PC43, Pcdh2 Location Chromosome 18: 37,806,364-37,841,873 forward strand. GRCm38:CM001011.2 About this gene This gene has 3 transcripts (splice variants), 43 orthologues, 69 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Pcdhgc3- ENSMUST00000076807.6 4687 934aa ENSMUSP00000076085.4 Protein coding CCDS29192 Q91XX1 TSL:1 201 GENCODE basic APPRIS P1
Pcdhgc3- ENSMUST00000192103.1 3588 78aa ENSMUSP00000141611.1 Nonsense mediated - A0A0A6YWM6 TSL:5 202 decay
Pcdhgc3- ENSMUST00000194447.1 3380 No - Retained intron - - TSL:NA 203 protein
55.51 kb Forward strand 37.80Mb 37.81Mb 37.82Mb 37.83Mb 37.84Mb 37.85Mb Genes Pcdhgb6-201 >protein coding (Comprehensive set...
Pcdhga9-201 >protein coding
Pcdhgb8-201 >polymorphic pseudogene
Pcdhgb8-202 >protein coding
Pcdhga7-201 >protein coding
Pcdhga2-201 >protein coding
Pcdhga12-201 >protein coding
Pcdhgb2-202 >protein coding
Pcdhgb5-201 >protein coding
Pcdhga10-201 >protein coding
Pcdhga4-201 >protein coding
Pcdhga6-201 >protein coding
Gm42416-201 >protein coding
Pcdhgb4-202 >protein coding
Pcdhgb1-201 >protein coding
Pcdhga5-201 >protein coding
Gm37388-201 >protein coding
Pcdhgb7-201 >protein coding
Pcdhga3-201 >protein coding Page 7 of 10
Pcdhga11-201 >protein coding
Pcdhga8-201 >protein coding
Pcdhga1-201 >protein coding
Gm37013-201 >protein coding
Pcdhgc3-203 >retained intronPcdhgc4-201 >protein coding
Pcdhgc3-201 >protein coding
Pcdhgc3-202 >nonsense mediated decay
Pcdhgc4-203 >protein coding
Pcdhgc4-202 >retained introGnm38182-203 >lncRNA
Pcdhgc5-201 >protein coding
Pcdhgc5-203 >protein coding
Pcdhgc5-204 >protein coding
Pcdhgc5-202 >retained intron
Gm38182-201 >lncRNA
Gm38182-202 >lncRNA
Gm38182-204 >lncRNA
Gm38182-205 >lncRNA
Contigs AC020971.3 > AC129315.3 > Genes < BC037039-201lncRNA < Gm29994-201lncRNA < Diaph1-205protein coding (Comprehensive set...
< Diaph1-204protein coding
< Diaph1-201protein coding
< Diaph1-203protein coding
< Diaph1-202protein coding
< Diaph1-207lncRNA
Regulatory Build
37.80Mb 37.81Mb 37.82Mb 37.83Mb 37.84Mb 37.85Mb Reverse strand 55.51 kb
Regulation Legend CTCF Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript pseudogene RNA gene 55.51 kb Forward strand 37.80Mb 37.81Mb 37.82Mb 37.83Mb 37.84Mb 37.85Mb Genes Pcdhgb6-201 >protein coding (Comprehensive set...
Pcdhga9-201 >protein coding
Pcdhgb8-201 >polymorphic pseudogene
Pcdhgb8-202 >protein coding
Pcdhga7-201 >protein coding
Pcdhga2-201 >protein coding
Pcdhga12-201 >protein coding
Pcdhgb2-202 >protein coding
Pcdhgb5-201 >protein coding
Pcdhga10-201 >protein coding
Pcdhga4-201 >protein coding
Pcdhga6-201 >protein coding
Gm42416-201 >protein coding
Pcdhgb4-202 >protein coding
Pcdhgb1-201 >protein coding
Pcdhga5-201 >protein coding
Gm37388-201 >protein coding
Pcdhgb7-201 >protein coding https://www.alphaknockout.com
Pcdhga3-201 >protein coding
Pcdhga11-201 >protein coding
Pcdhga8-201 >protein coding
Pcdhga1-201 >protein coding
Gm37013-201 >protein coding
Pcdhgc3-203 >retained intronPcdhgc4-201 >protein coding
Pcdhgc3-201 >protein coding
Pcdhgc3-202 >nonsense mediated decay
Pcdhgc4-203 >protein coding
Pcdhgc4-202 >retained introGnm38182-203 >lncRNA
Pcdhgc5-201 >protein coding
Pcdhgc5-203 >protein coding
Pcdhgc5-204 >protein coding
Pcdhgc5-202 >retained intron
Gm38182-201 >lncRNA
Gm38182-202 >lncRNA
Gm38182-204 >lncRNA
Gm38182-205 >lncRNA
Contigs AC020971.3 > AC129315.3 > Genes < BC037039-201lncRNA < Gm29994-201lncRNA < Diaph1-205protein coding (Comprehensive set...
< Diaph1-204protein coding
< Diaph1-201protein coding
< Diaph1-203protein coding
< Diaph1-202protein coding
< Diaph1-207lncRNA
Regulatory Build
37.80Mb 37.81Mb 37.82Mb 37.83Mb 37.84Mb 37.85Mb Reverse strand 55.51 kb
Regulation Legend CTCF Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript pseudogene RNA gene Page 8 of 10 55.51 kb Forward strand 37.80Mb 37.81Mb 37.82Mb 37.83Mb 37.84Mb 37.85Mb Genes Pcdhgb6-201 >protein coding (Comprehensive set...
Pcdhga9-201 >protein coding
Pcdhgb8-201 >polymorphic pseudogene
Pcdhgb8-202 >protein coding
Pcdhga7-201 >protein coding
Pcdhga2-201 >protein coding
Pcdhga12-201 >protein coding
Pcdhgb2-202 >protein coding
Pcdhgb5-201 >protein coding
Pcdhga10-201 >protein coding
Pcdhga4-201 >protein coding
Pcdhga6-201 >protein coding
Gm42416-201 >protein coding
Pcdhgb4-202 >protein coding
Pcdhgb1-201 >protein coding
Pcdhga5-201 >protein coding
Gm37388-201 >protein coding
Pcdhgb7-201 >protein coding
Pcdhga3-201 >protein coding
Pcdhga11-201 >protein coding
Pcdhga8-201 >protein coding
Pcdhga1-201 >protein coding
Gm37013-201 >protein coding
Pcdhgc3-203 >retained intronPcdhgc4-201 >protein coding
Pcdhgc3-201 >protein coding
Pcdhgc3-202 >nonsense mediated decay
Pcdhgc4-203 >protein coding
Pcdhgc4-202 >retained introGnm38182-203 >lncRNA
Pcdhgc5-201 >protein coding
Pcdhgc5-203 >protein coding
Pcdhgc5-204 >protein coding
Pcdhgc5-202 >retained intron
Gm38182-201 >lncRNA
Gm38182-202 >lncRNA
Gm38182-204 >lncRNA
Gm38182-205 >lncRNA
Contigs AC020971.3 > AC129315.3 > Genes < BC037039-201lncRNA < Gm29994-201lncRNA < Diaph1-205protein coding (Comprehensive set...
< Diaph1-204protein coding
< Diaph1-201protein coding
< Diaph1-203protein coding
< Diaph1-202protein coding
< Diaph1-207lncRNA
Regulatory Build
37.80Mb 37.81Mb 37.82Mb 37.83Mb 37.84Mb 37.85Mb Reverse strand 55.51 kb
Regulation Legend CTCF Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript https://www.alphaknockout.com pseudogene RNA gene
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Transcript: ENSMUST00000076807
35.46 kb Forward strand
Pcdhgc3-201 >protein coding
ENSMUSP00000076... Transmembrane heli... PDB-ENSP mappings MobiDB lite Low complexity (Seg) Cleavage site (Sign... Superfamily Cadherin-like superfamily SMART Cadherin-like Prints Cadherin-like Pfam Cadherin-like Cadherin, C-terminal catenin-binding domain
Cadherin, N-terminal Cadherin, cytoplasmic C-terminal domain PROSITE profiles PS50268 PROSITE patterns Cadherin conserved site PANTHER Protocadherin gamma-C3
PTHR24028 Gene3D 2.60.40.60 CDD cd11304
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 800 934
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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