https://www.alphaknockout.com
Mouse Bnip3 Knockout Project (CRISPR/Cas9)
Objective: To create a Bnip3 knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Bnip3 gene (NCBI Reference Sequence: NM_009760 ; Ensembl: ENSMUSG00000078566 ) is located on Mouse chromosome 7. 6 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 6 (Transcript: ENSMUST00000106112). Exon 2~5 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 exhibit decreased post-ischemic ventricular remodeling.
Exon 2 starts from about 5.7% of the coding region. Exon 2~5 covers 86.81% of the coding region. The size of effective KO region: ~4449 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
Legends Exon of mouse Bnip3 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 2000 bp section downstream of Exon 5 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(26.45% 529) | C(22.0% 440) | T(30.35% 607) | G(21.2% 424)
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(19.75% 395) | C(26.2% 524) | T(32.1% 642) | G(21.95% 439)
Note: The 2000 bp section downstream of Exon 5 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% chr7 - 138898829 138900828 2000 browser details YourSeq 587 158 1526 2000 90.2% chr4 - 20052672 20066111 13440 browser details YourSeq 173 416 1064 2000 86.2% chrX + 13196006 13196489 484 browser details YourSeq 169 414 614 2000 94.3% chr6 + 124447112 124447324 213 browser details YourSeq 164 400 598 2000 92.4% chrX + 144247323 144247527 205 browser details YourSeq 163 415 609 2000 93.2% chr2 - 119296437 119296662 226 browser details YourSeq 163 390 598 2000 88.2% chr1 + 59601053 59601238 186 browser details YourSeq 162 416 598 2000 94.6% chr17 - 83564957 83565378 422 browser details YourSeq 162 415 996 2000 83.8% chr11 - 83267363 83267839 477 browser details YourSeq 161 411 601 2000 93.1% chr1 - 163951622 163951821 200 browser details YourSeq 161 415 619 2000 88.1% chr2 + 35405277 35405473 197 browser details YourSeq 157 415 600 2000 92.4% chrX - 62211349 62211534 186 browser details YourSeq 157 410 598 2000 92.0% chr17 - 35006179 35006370 192 browser details YourSeq 156 400 596 2000 89.8% chrX - 41943670 41943869 200 browser details YourSeq 156 411 597 2000 92.4% chr2 - 148063023 148063214 192 browser details YourSeq 156 415 598 2000 92.9% chr3 + 95878298 95878488 191 browser details YourSeq 156 413 598 2000 92.4% chr2 + 30389861 30390049 189 browser details YourSeq 155 416 598 2000 92.8% chr4 - 134323961 134324143 183 browser details YourSeq 155 425 598 2000 94.8% chr10 - 80925273 80925450 178 browser details YourSeq 155 414 598 2000 93.3% chr1 - 59839731 59839921 191
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% chr7 - 138892380 138894379 2000 browser details YourSeq 172 1036 1273 2000 93.5% chr16 - 11160654 11160893 240 browser details YourSeq 163 1032 1280 2000 94.5% chr3 + 89533245 89533492 248 browser details YourSeq 152 964 1280 2000 87.2% chr12 + 29946970 29947141 172 browser details YourSeq 147 1098 1274 2000 90.3% chr15 - 41473703 41473868 166 browser details YourSeq 145 922 1281 2000 87.1% chr13 + 113799825 113800030 206 browser details YourSeq 140 1150 1407 2000 94.4% chr5 + 92382613 92382997 385 browser details YourSeq 140 1066 1280 2000 93.8% chr4 + 42970461 42970675 215 browser details YourSeq 135 964 1280 2000 84.3% chr19 + 57819466 57819621 156 browser details YourSeq 134 1128 1280 2000 95.9% chr17 + 46149456 46149624 169 browser details YourSeq 131 1150 1284 2000 98.6% chr12 - 18961901 18962035 135 browser details YourSeq 131 981 1278 2000 84.9% chr15 + 82266689 82266845 157 browser details YourSeq 129 1144 1280 2000 97.1% chr13 + 61920225 61920361 137 browser details YourSeq 125 1150 1280 2000 97.8% chr18 - 60773375 60773505 131 browser details YourSeq 125 966 1146 2000 91.3% chrX + 129955189 129955407 219 browser details YourSeq 125 1144 1280 2000 95.7% chrX + 94136191 94136327 137 browser details YourSeq 125 1128 1274 2000 94.4% chr6 + 121531665 121531815 151 browser details YourSeq 125 1144 1280 2000 95.7% chr4 + 98943006 98943142 137 browser details YourSeq 125 1100 1280 2000 94.3% chr12 + 67655605 67655785 181 browser details YourSeq 124 1148 1283 2000 95.6% chr16 - 93943042 93943177 136
Note: The 2000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Bnip3 BCL2/adenovirus E1B interacting protein 3 [ Mus musculus (house mouse) ] Gene ID: 12176, updated on 24-Sep-2019
Gene summary
Official Symbol Bnip3 provided by MGI Official Full Name BCL2/adenovirus E1B interacting protein 3 provided by MGI Primary source MGI:MGI:109326 See related Ensembl:ENSMUSG00000078566 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 Nip3 Expression Broad expression in liver E18 (RPKM 92.5), placenta adult (RPKM 48.1) and 20 other tissues See more Orthologs human all
Genomic context
Location: 7; 7 F4 See Bnip3 in Genome Data Viewer Exon count: 6
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (138890836..138909506, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 7 NC_000073.5 (146082519..146101189, complement)
Chromosome 7 - NC_000073.6
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Transcript information: This gene has 5 transcripts
Gene: Bnip3 ENSMUSG00000078566
Description BCL2/adenovirus E1B interacting protein 3 [Source:MGI Symbol;Acc:MGI:109326] Gene Synonyms Nip3 Location Chromosome 7: 138,890,836-138,909,519 reverse strand. GRCm38:CM001000.2 About this gene This gene has 5 transcripts (splice variants), 204 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 2 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Bnip3-201 ENSMUST00000106112.1 1756 187aa ENSMUSP00000101718.1 Protein coding CCDS40168 O55003 TSL:1 GENCODE basic APPRIS P1
Bnip3-203 ENSMUST00000130500.7 719 173aa ENSMUSP00000148170.1 Protein coding - A0A1B0GT26 TSL:2 GENCODE basic
Bnip3-205 ENSMUST00000148970.1 446 No protein - Retained intron - - TSL:2
Bnip3-204 ENSMUST00000141223.1 388 No protein - Retained intron - - TSL:1
Bnip3-202 ENSMUST00000125359.1 293 No protein - lncRNA - - TSL:3
38.68 kb Forward strand 138.89Mb 138.90Mb 138.91Mb Genes Ppp2r2d-201 >protein coding Gm45507-201 >lncRNA Gm18258-201 >processed pseudogene Gm9358-201 >processed pseudogene (Comprehensive set...
Ppp2r2d-207 >protein coding
Contigs AC149221.2 > AC140248.3 > Genes (Comprehensive set... < Bnip3-201protein coding
< Bnip3-203protein coding
< Bnip3-204retained intron
< Bnip3-205retained intron
< Bnip3-202lncRNA
Regulatory Build
138.89Mb 138.90Mb 138.91Mb Reverse strand 38.68 kb
Regulation Legend
CTCF Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
pseudogene RNA gene processed transcript
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Transcript: ENSMUST00000106112
< Bnip3-201protein coding
Reverse strand 18.67 kb
ENSMUSP00000101... Transmembrane heli... MobiDB lite Low complexity (Seg) Pfam BNIP3 PANTHER PTHR15186:SF4
BNIP3
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend splice region variant synonymous variant
Scale bar 0 20 40 60 80 100 120 140 160 187
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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