https://www.alphaknockout.com
Mouse Baiap3 Knockout Project (CRISPR/Cas9)
Objective: To create a Baiap3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Baiap3 gene (NCBI Reference Sequence: NM_001163270 ; Ensembl: ENSMUSG00000047507 ) is located on Mouse chromosome 17. 34 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 34 (Transcript: ENSMUST00000182056). Exon 2~29 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 null allele are viable and fertile but exhibit increased PTZ-induced seizure propensity, as well as increased novelty-induced anxiety in both genders, with a more pronounced effect in females, and a faster developmentof tolerance to benzodiazepines in male mice.
Exon 2 starts from about 0.03% of the coding region. Exon 2~29 covers 80.35% of the coding region. The size of effective KO region: ~7336 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' 10 13 17 19 23 26 28 32
1 2 3 4 5 6 7 8 9 11 12 14 15 16 18 2021 22 24 25 27 29 3031 33 34
Legends Exon of mouse Baiap3 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 start 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.
Overview of the Dot Plot (down) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 2000 bp section downstream of Exon 29 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(22.65% 453) | C(24.5% 490) | T(23.3% 466) | G(29.55% 591)
Note: The 2000 bp section upstream of start 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.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(19.05% 381) | C(29.55% 591) | T(20.9% 418) | G(30.5% 610)
Note: The 2000 bp section downstream of Exon 29 is analyzed to determine the GC content. Significant high GC-content regions are found. The gRNA site is selected outside of these high GC-content regions.
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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% chr17 - 25252136 25254135 2000 browser details YourSeq 25 807 836 2000 93.4% chr4 - 117392965 117393006 42 browser details YourSeq 22 807 828 2000 100.0% chr1 + 82635665 82635686 22 browser details YourSeq 21 317 337 2000 100.0% chr2 - 77206981 77207001 21 browser details YourSeq 21 1765 1786 2000 100.0% chr10 - 26654549 26654571 23 browser details YourSeq 21 1596 1616 2000 100.0% chr7 + 83514271 83514291 21 browser details YourSeq 21 139 159 2000 100.0% chr13 + 45245031 45245051 21
Note: The 2000 bp section upstream of start codon 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% chr17 - 25242798 25244797 2000 browser details YourSeq 36 203 286 2000 95.0% chr1 + 152934078 152934483 406 browser details YourSeq 33 1507 1575 2000 81.6% chr3 - 146691805 146691869 65 browser details YourSeq 25 336 372 2000 69.3% chr10 - 80074690 80074715 26 browser details YourSeq 23 1431 1453 2000 100.0% chr1 - 152955459 152955481 23
Note: The 2000 bp section downstream of Exon 29 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Baiap3 BAI1-associated protein 3 [ Mus musculus (house mouse) ] Gene ID: 545192, updated on 10-Oct-2019
Gene summary
Official Symbol Baiap3 provided by MGI Official Full Name BAI1-associated protein 3 provided by MGI Primary source MGI:MGI:2685783 See related Ensembl:ENSMUSG00000047507 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 Bap3; Gm937 Expression Broad expression in thymus adult (RPKM 8.6), CNS E18 (RPKM 8.4) and 24 other tissues See more Orthologs human all
Genomic context
Location: 17; 17 A3.3 See Baiap3 in Genome Data Viewer Exon count: 36
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (25242659..25256364, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 17 NC_000083.5 (25379604..25393309, complement)
Chromosome 17 - NC_000083.6
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Transcript information: This gene has 9 transcripts
Gene: Baiap3 ENSMUSG00000047507
Description BAI1-associated protein 3 [Source:MGI Symbol;Acc:MGI:2685783] Gene Synonyms LOC381076 Location Chromosome 17: 25,242,659-25,256,364 reverse strand. GRCm38:CM001010.2 About this gene This gene has 9 transcripts (splice variants), 153 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 8 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Baiap3-202 ENSMUST00000182056.7 4645 1150aa ENSMUSP00000138188.1 Protein coding CCDS50033 S4R1E7 TSL:1 GENCODE basic APPRIS P2
Baiap3-206 ENSMUST00000182825.7 3862 1114aa ENSMUSP00000138254.1 Protein coding - S4R1K2 TSL:5 GENCODE basic
Baiap3-204 ENSMUST00000182435.7 3758 1122aa ENSMUSP00000138796.1 Protein coding - S4R2U8 TSL:5 GENCODE basic APPRIS ALT2
Baiap3-201 ENSMUST00000169109.2 3630 1127aa ENSMUSP00000129854.2 Protein coding - E9Q350 TSL:5 GENCODE basic APPRIS ALT2
Baiap3-205 ENSMUST00000182696.7 499 90aa ENSMUSP00000138454.1 Protein coding - S4R212 CDS 5' incomplete TSL:5
Baiap3-203 ENSMUST00000182126.1 1295 No protein - Retained intron - - TSL:1
Baiap3-207 ENSMUST00000182903.1 1020 No protein - Retained intron - - TSL:5
Baiap3-209 ENSMUST00000182978.1 608 No protein - Retained intron - - TSL:3
Baiap3-208 ENSMUST00000182922.1 505 No protein - Retained intron - - TSL:3
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33.71 kb Forward strand 25.24Mb 25.25Mb 25.26Mb Genes Unkl-202 >protein coding Tsr3-201 >protein coding (Comprehensive set...
Unkl-204 >protein coding
Unkl-201 >protein coding
Contigs AC130711.3 > AC122454.4 > Genes (Comprehensive set... < Gnptg-202protein coding < Baiap3-202protein coding < Ube2i-204retained intron
< Gnptg-201protein coding < Baiap3-203retained intron < Baiap3-209retained intron < Ube2i-201protein coding
< Baiap3-206protein coding < Ube2i-208protein coding
< Baiap3-205protein coding < Ube2i-211protein coding
< Baiap3-204protein coding < Ube2i-206protein coding
< Baiap3-201protein coding < Ube2i-214protein coding
< Baiap3-208retained intron < Ube2i-213protein coding
< Mir3547-201miRNA < Ube2i-212protein coding
< Baiap3-207retained intron < Ube2i-210protein coding
Regulatory Build
25.24Mb 25.25Mb 25.26Mb Reverse strand 33.71 kb
Regulation Legend CTCF Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript RNA gene
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Transcript: ENSMUST00000182056
< Baiap3-202protein coding
Reverse strand 13.71 kb
ENSMUSP00000138... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SSF49562 SMART C2 domain Pfam C2 domain PROSITE profiles Munc13 homology 1 Mammalian uncoordinated homology 13, domain 2
C2 domain PANTHER PTHR45999:SF1
PTHR45999 Gene3D 1.10.357.50 C2 domain superfamily
CDD cd08676 cd04009
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant splice region variant synonymous variant
Scale bar 0 100 200 300 400 500 600 700 800 900 1000 1150
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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