https://www.alphaknockout.com
Mouse Hmox2 Knockout Project (CRISPR/Cas9)
Objective: To create a Hmox2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Hmox2 gene (NCBI Reference Sequence: NM_001136066 ; Ensembl: ENSMUSG00000004070 ) is located on Mouse chromosome 16. 6 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 6 (Transcript: ENSMUST00000004172). Exon 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: Mice homozygous for disruptions in this gene are normal for the most part. However, they are sensitive to incrreases and decreases in oxygen levels and this results in some behavioral and nervous system response abnormalities.
Exon 3 starts from about 8.89% of the coding region. Exon 3 covers 12.49% of the coding region. The size of effective KO region: ~118 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 3 6
Legends Exon of mouse Hmox2 Knockout region
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Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 1051 bp section upstream of Exon 3 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 759 bp section downstream of Exon 3 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(1051bp) | A(29.21% 307) | C(20.84% 219) | T(26.74% 281) | G(23.22% 244)
Note: The 1051 bp section upstream 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.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(759bp) | A(26.35% 200) | C(18.58% 141) | T(31.36% 238) | G(23.72% 180)
Note: The 759 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 1051 1 1051 1051 100.0% chr16 + 4762679 4763729 1051 browser details YourSeq 83 439 560 1051 88.1% chr6 - 108717034 108717158 125 browser details YourSeq 76 463 554 1051 92.4% chr7 - 45999952 46000086 135 browser details YourSeq 76 436 567 1051 88.8% chr10 - 45353438 45353572 135 browser details YourSeq 75 440 565 1051 79.5% chrX + 13248814 13248923 110 browser details YourSeq 73 439 526 1051 92.0% chr2 + 144322881 144322970 90 browser details YourSeq 73 442 531 1051 89.7% chr16 + 44773234 44773322 89 browser details YourSeq 72 443 532 1051 91.2% chr5 - 108259153 108259262 110 browser details YourSeq 71 439 526 1051 89.5% chr4 - 126347452 126347538 87 browser details YourSeq 71 439 527 1051 91.0% chrX + 162755086 162755194 109 browser details YourSeq 71 436 520 1051 93.0% chr5 + 92879189 92879276 88 browser details YourSeq 69 439 520 1051 92.7% chr7 - 4720404 4720487 84 browser details YourSeq 69 446 532 1051 88.8% chr6 - 46725659 46725743 85 browser details YourSeq 69 443 532 1051 91.1% chr2 - 37509328 37509415 88 browser details YourSeq 69 439 530 1051 87.9% chr8 + 103872183 103872271 89 browser details YourSeq 69 439 531 1051 87.8% chr2 + 152715146 152715238 93 browser details YourSeq 69 443 520 1051 94.9% chr15 + 102527090 102527169 80 browser details YourSeq 68 439 520 1051 92.6% chr9 + 120067462 120067547 86 browser details YourSeq 68 442 549 1051 87.0% chr12 + 84691131 84691236 106 browser details YourSeq 67 438 516 1051 93.7% chr18 - 11949299 11949381 83
Note: The 1051 bp section upstream of Exon 3 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 759 1 759 759 100.0% chr16 + 4763848 4764606 759 browser details YourSeq 124 441 692 759 82.9% chr1 - 131695997 131696197 201 browser details YourSeq 122 449 638 759 89.7% chr10 - 126873588 126874205 618 browser details YourSeq 120 436 655 759 84.6% chr8 + 50153320 50153501 182 browser details YourSeq 119 214 569 759 91.7% chrX + 103651195 103651582 388 browser details YourSeq 118 449 689 759 83.3% chr17 - 78647734 78647905 172 browser details YourSeq 117 442 690 759 84.8% chr2 - 27012528 27012712 185 browser details YourSeq 116 450 689 759 83.4% chr1 - 135275536 135275719 184 browser details YourSeq 116 449 690 759 82.9% chr17 + 34108146 34108337 192 browser details YourSeq 114 449 640 759 89.2% chr2 - 25813088 25813682 595 browser details YourSeq 113 452 691 759 82.4% chr3 + 22225921 22226106 186 browser details YourSeq 112 449 690 759 81.8% chrX + 14337457 14337642 186 browser details YourSeq 111 339 574 759 79.2% chr1 - 54870051 54870222 172 browser details YourSeq 110 440 569 759 89.8% chr8 - 113060978 113061104 127 browser details YourSeq 109 441 573 759 89.6% chr10 - 21719750 21719878 129 browser details YourSeq 109 442 569 759 90.5% chr9 + 96332022 96332147 126 browser details YourSeq 109 438 569 759 92.3% chr4 + 117163157 117163297 141 browser details YourSeq 108 449 690 759 80.9% chr11 - 57736275 57736456 182 browser details YourSeq 107 449 569 759 94.3% chr9 - 21534488 21534608 121 browser details YourSeq 107 450 671 759 92.2% chr7 - 19134329 19134573 245
Note: The 759 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: Hmox2 heme oxygenase 2 [ Mus musculus (house mouse) ] Gene ID: 15369, updated on 10-Oct-2019
Gene summary
Official Symbol Hmox2 provided by MGI Official Full Name heme oxygenase 2 provided by MGI Primary source MGI:MGI:109373 See related Ensembl:ENSMUSG00000004070 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 HO2; HO-2 Expression Broad expression in testis adult (RPKM 136.2), cerebellum adult (RPKM 25.6) and 26 other tissues See more Orthologs human all
Genomic context
Location: 16 A1; 16 2.46 cM See Hmox2 in Genome Data Viewer Exon count: 8
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (4726361..4766741)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 16 NC_000082.5 (4726361..4766249)
Chromosome 16 - NC_000082.6
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Transcript information: This gene has 6 transcripts
Gene: Hmox2 ENSMUSG00000004070
Description heme oxygenase 2 [Source:MGI Symbol;Acc:MGI:109373] Gene Synonyms HO-2, HO2 Location Chromosome 16: 4,726,361-4,766,742 forward strand. GRCm38:CM001009.2 About this gene This gene has 6 transcripts (splice variants), 243 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 24 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Hmox2-201 ENSMUST00000004172.14 1730 315aa ENSMUSP00000004172.8 Protein coding CCDS27924 O70252 Q544R7 TSL:1 GENCODE basic APPRIS P1
Hmox2-202 ENSMUST00000118885.7 1392 315aa ENSMUSP00000113110.1 Protein coding CCDS27924 O70252 Q544R7 TSL:1 GENCODE basic APPRIS P1
Hmox2-203 ENSMUST00000120232.7 1287 315aa ENSMUSP00000112397.1 Protein coding CCDS27924 O70252 Q544R7 TSL:1 GENCODE basic APPRIS P1
Hmox2-204 ENSMUST00000121529.1 856 228aa ENSMUSP00000112378.1 Protein coding - D3YX62 CDS 3' incomplete TSL:2
Hmox2-205 ENSMUST00000140367.7 584 93aa ENSMUSP00000115932.1 Protein coding - D3YXN4 CDS 3' incomplete TSL:2
Hmox2-206 ENSMUST00000154117.1 354 65aa ENSMUSP00000122699.1 Protein coding - D3Z4A2 CDS 3' incomplete TSL:2
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60.38 kb Forward strand 4.72Mb 4.73Mb 4.74Mb 4.75Mb 4.76Mb 4.77Mb Genes Hmox2-206 >protein coding (Comprehensive set...
Hmox2-201 >protein coding
Gm15859-201 >lncRNA Hmox2-203 >protein coding
Hmox2-205 >protein coding
Hmox2-202 >protein coding
Hmox2-204 >protein coding
Contigs < AC166903.2 Genes < Nmral1-204protein coding < Cdip1-205protein coding (Comprehensive set...
< Nmral1-202protein coding < Cdip1-201protein coding
< Nmral1-203protein coding < Cdip1-203protein coding
< Nmral1-201protein coding < Cdip1-204retained intron
< Nmral1-205retained intron < Cdip1-202protein coding
< Nmral1-206retained intron < Cdip1-206retained intron
Regulatory Build
4.72Mb 4.73Mb 4.74Mb 4.75Mb 4.76Mb 4.77Mb Reverse strand 60.38 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
RNA gene processed transcript
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Transcript: ENSMUST00000004172
40.38 kb Forward strand
Hmox2-201 >protein coding
ENSMUSP00000004... Transmembrane heli... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily Haem oxygenase-like, multi-helical
Prints Haem oxygenase Pfam Haem oxygenase-like
PROSITE patterns Haem oxygenase conserved site
PIRSF Haem oxygenase
PANTHER PTHR10720:SF2
Haem oxygenase Gene3D Haem oxygenase-like, multi-helical CDD cd19165
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant synonymous variant
Scale bar 0 40 80 120 160 200 240 315
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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