https://www.alphaknockout.com
Mouse Vps29 Knockout Project (CRISPR/Cas9)
Objective: To create a Vps29 knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Vps29 gene (NCBI Reference Sequence: NM_019780 ; Ensembl: ENSMUSG00000029462 ) is located on Mouse chromosome 5. 4 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 4 (Transcript: ENSMUST00000155671). 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 0.73% of the coding region. Exon 2~4 covers 99.45% of the coding region. The size of effective KO region: ~2907 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
Legends Exon of mouse Vps29 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 stop codon 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(25.0% 500) | C(21.0% 420) | T(34.9% 698) | G(19.1% 382)
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(29.45% 589) | C(20.9% 418) | T(29.35% 587) | G(20.3% 406)
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% chr5 + 122358014 122360013 2000 browser details YourSeq 103 1163 1389 2000 85.6% chr11 - 68727071 68939092 212022 browser details YourSeq 86 1190 1365 2000 89.8% chr14 - 56805348 56805635 288 browser details YourSeq 81 1161 1358 2000 87.2% chr19 - 45547737 45547967 231 browser details YourSeq 79 1238 1364 2000 90.8% chr4 + 148133832 148390541 256710 browser details YourSeq 73 1095 1291 2000 77.1% chr12 + 85855545 85855708 164 browser details YourSeq 60 1162 1272 2000 95.5% chr18 - 6151373 6151485 113 browser details YourSeq 60 355 434 2000 90.8% chr17 - 28980546 28980645 100 browser details YourSeq 59 1161 1283 2000 94.1% chr3 - 34633261 34633383 123 browser details YourSeq 58 1137 1283 2000 90.5% chr5 + 54384915 54385076 162 browser details YourSeq 57 1161 1280 2000 90.8% chr12 - 75706254 75706372 119 browser details YourSeq 56 1306 1389 2000 83.4% chr9 - 121747676 121747759 84 browser details YourSeq 56 1162 1283 2000 93.8% chr14 - 63189917 63190038 122 browser details YourSeq 56 1310 1389 2000 85.0% chrX + 10685308 10685387 80 browser details YourSeq 55 1151 1295 2000 88.6% chr1 - 105776170 105776315 146 browser details YourSeq 55 1161 1283 2000 93.7% chr5 + 25260850 25260981 132 browser details YourSeq 55 1161 1276 2000 72.1% chr10 + 82773448 82773561 114 browser details YourSeq 54 338 436 2000 76.1% chr12 + 36641356 36641441 86 browser details YourSeq 53 1152 1270 2000 82.8% chr11 - 65449872 65449981 110 browser details YourSeq 53 347 439 2000 78.5% chr1 + 171130955 171131047 93
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% chr5 + 122362921 122364920 2000 browser details YourSeq 274 1660 2000 2000 91.2% chrX - 38506024 38506371 348 browser details YourSeq 199 875 1240 2000 93.2% chr17 + 45496555 45497137 583 browser details YourSeq 196 792 1182 2000 93.4% chr4 - 149326748 149729196 402449 browser details YourSeq 188 695 1179 2000 88.3% chr11 + 78043600 78044359 760 browser details YourSeq 184 870 1647 2000 80.0% chr11 + 68575033 68575564 532 browser details YourSeq 183 810 1067 2000 87.0% chr10 - 80041931 80042176 246 browser details YourSeq 175 720 1063 2000 82.6% chr16 + 33220387 33220651 265 browser details YourSeq 174 413 1054 2000 89.2% chr13 - 95485143 95485787 645 browser details YourSeq 170 810 1065 2000 91.8% chr4 - 126983856 126984416 561 browser details YourSeq 167 872 1068 2000 90.2% chr14 + 11773884 11774076 193 browser details YourSeq 167 868 1186 2000 92.9% chr10 + 42292065 42292687 623 browser details YourSeq 165 811 1077 2000 87.0% chr11 + 99204907 99205154 248 browser details YourSeq 161 705 1038 2000 91.3% chr17 - 7525057 7525604 548 browser details YourSeq 160 871 1262 2000 85.1% chr5 + 31459943 31460128 186 browser details YourSeq 158 873 1060 2000 93.9% chr10 + 69518112 69518308 197 browser details YourSeq 157 872 1060 2000 91.6% chr5 - 129861770 129861958 189 browser details YourSeq 157 894 1224 2000 90.3% chr11 - 75129626 75130209 584 browser details YourSeq 157 810 1061 2000 92.1% chr10 - 77028088 77028368 281 browser details YourSeq 156 882 1061 2000 93.4% chr2 - 31868120 31868299 180
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: Vps29 VPS29 retromer complex component [ Mus musculus (house mouse) ] Gene ID: 56433, updated on 14-Aug-2019
Gene summary
Official Symbol Vps29 provided by MGI Official Full Name VPS29 retromer complex component provided by MGI Primary source MGI:MGI:1928344 See related Ensembl:ENSMUSG00000029462 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 PEP11; AW049835; 2010015D08Rik Expression Ubiquitous expression in CNS E18 (RPKM 27.9), placenta adult (RPKM 22.1) and 28 other tissues See more Orthologs human all
Genomic context
Location: 5; 5 F See Vps29 in Genome Data Viewer Exon count: 6
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (122354328..122364984)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (122804422..122813296)
Chromosome 5 - NC_000071.6
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Transcript information: This gene has 9 transcripts
Gene: Vps29 ENSMUSG00000029462
Description VPS29 retromer complex component [Source:MGI Symbol;Acc:MGI:1928344] Gene Synonyms 2010015D08Rik, PEP11 Location Chromosome 5: 122,354,369-122,364,984 forward strand. GRCm38:CM000998.2 About this gene This gene has 9 transcripts (splice variants), 234 orthologues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Vps29- ENSMUST00000155671.7 2716 182aa ENSMUSP00000121020.1 Protein coding CCDS39256 Q9QZ88 TSL:1 208 GENCODE basic APPRIS P3
Vps29- ENSMUST00000118830.7 1014 186aa ENSMUSP00000113525.1 Protein coding CCDS84954 Q9QZ88 TSL:1 204 GENCODE basic APPRIS ALT1
Vps29- ENSMUST00000117868.7 720 144aa ENSMUSP00000113345.1 Protein coding - D3Z645 TSL:2 202 GENCODE basic
Vps29- ENSMUST00000118765.7 713 91aa ENSMUSP00000112579.1 Protein coding - D3YW98 TSL:3 203 GENCODE basic
Vps29- ENSMUST00000145821.1 407 124aa ENSMUSP00000123593.1 Protein coding - D3YYD5 CDS 3' 206 incomplete TSL:3
Vps29- ENSMUST00000111729.9 874 53aa ENSMUSP00000107358.3 Nonsense mediated - H7BXA2 TSL:2 201 decay
Vps29- ENSMUST00000154686.1 488 37aa ENSMUSP00000118991.1 Nonsense mediated - D6RH43 TSL:5 207 decay
Vps29- ENSMUST00000199086.1 3364 No - Retained intron - - TSL:NA 209 protein
Vps29- ENSMUST00000132785.1 529 No - lncRNA - - TSL:5 205 protein
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30.62 kb Forward strand 122.35Mb 122.36Mb 122.37Mb Genes (Comprehensive set... Vps29-208 >protein coding Gpn3-203 >nonsense mediated decay
Vps29-204 >protein coding Gpn3-202 >nonsense mediated decay
Vps29-202 >protein coding Gpn3-206 >retained intron
Vps29-205 >lncRNA Gpn3-201 >protein coding
Vps29-203 >protein coding
Vps29-201 >nonsense mediated decay
Vps29-206 >protein coding
Vps29-207 >nonsense mediated decay
Vps29-209 >retained intron
Contigs < AC093473.6 < AC113285.9 Genes < Rad9b-202protein coding < Fam216a-201protein coding (Comprehensive set...
< Rad9b-204protein coding < Rad9b-205retained intron
< Rad9b-201protein coding
< Rad9b-203protein coding
Regulatory Build
122.35Mb 122.36Mb 122.37Mb Reverse strand 30.62 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
RNA gene processed transcript
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Transcript: ENSMUST00000155671
10.62 kb Forward strand
Vps29-208 >protein coding
ENSMUSP00000121... PDB-ENSP mappings TIGRFAM Phosphodiesterase MJ0936/Vps29
Superfamily SSF56300
Pfam Calcineurin-like phosphoesterase domain, lpxH-type PANTHER Phosphodiesterase MJ0936/Vps29
Vacuolar protein sorting-associated protein 29 Gene3D Metallo-dependent phosphatase-like CDD Vacuolar protein sorting-associated protein 29
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend synonymous variant
Scale bar 0 20 40 60 80 100 120 140 160 182
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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