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Mouse Dhx29 Conditional Knockout Project (CRISPR/Cas9)
Objective: To create a Dhx29 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Dhx29 gene (NCBI Reference Sequence: NM_172594 ; Ensembl: ENSMUSG00000042426 ) is located on Mouse chromosome 13. 27 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 27 (Transcript: ENSMUST00000038574). Exon 7 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Dhx29 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-414J10 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice homozygous for a transgenic gene disruption exhibit embryonic lethality at E7.
Exon 7 starts from about 18.93% of the coding region. The knockout of Exon 7 will result in frameshift of the gene. The size of intron 6 for 5'-loxP site insertion: 4775 bp, and the size of intron 7 for 3'-loxP site insertion: 1173 bp. The size of effective cKO region: ~627 bp. The cKO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele gRNA region 5' gRNA region 3'
1 7 8 27 Targeting vector
Targeted allele
Constitutive KO allele (After Cre recombination)
Legends Exon of mouse Dhx29 Homology arm cKO region loxP site
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Overview of the Dot Plot Window size: 10 bp
Forward Reverse Complement
Sequence 12
Note: The sequence of homologous arms and cKO region 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 GC Content Distribution Window size: 300 bp
Sequence 12
Summary: Full Length(7127bp) | A(27.63% 1969) | C(21.1% 1504) | T(27.81% 1982) | G(23.46% 1672)
Note: The sequence of homologous arms and cKO region 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 3000 1 3000 3000 100.0% chr13 + 112937124 112940123 3000 browser details YourSeq 418 435 957 3000 91.9% chr8 + 87047694 87048228 535 browser details YourSeq 414 433 955 3000 91.5% chr7 - 88530392 88530926 535 browser details YourSeq 406 441 957 3000 91.2% chr8 - 119602117 119602645 529 browser details YourSeq 404 435 957 3000 90.8% chr11 - 61205667 61206201 535 browser details YourSeq 401 435 956 3000 90.6% chr7 - 133738427 133738960 534 browser details YourSeq 400 435 944 3000 91.8% chr7 - 116331510 116334133 2624 browser details YourSeq 387 434 957 3000 89.3% chr17 + 30603194 30603725 532 browser details YourSeq 361 435 948 3000 89.3% chr2 + 143855620 143856130 511 browser details YourSeq 350 439 958 3000 87.5% chr13 - 78286577 78287106 530 browser details YourSeq 315 435 952 3000 85.6% chr3 + 58404675 58405168 494 browser details YourSeq 291 522 955 3000 86.6% chr1 + 63038212 63038643 432 browser details YourSeq 283 520 949 3000 86.8% chr15 - 96648790 96649202 413 browser details YourSeq 274 528 953 3000 86.0% chr13 - 64361306 64361708 403 browser details YourSeq 226 573 945 3000 83.4% chr16 + 94016018 94016368 351 browser details YourSeq 207 435 957 3000 83.3% chr1 - 5617779 5618208 430 browser details YourSeq 151 445 885 3000 88.4% chr6 - 68000857 68001304 448 browser details YourSeq 122 2000 2180 3000 83.9% chr4 - 44021072 44021249 178 browser details YourSeq 117 2000 2170 3000 83.9% chr15 + 83004061 83004224 164 browser details YourSeq 117 2024 2183 3000 89.2% chr11 + 79171511 79171677 167
Note: The 3000 bp section upstream of Exon 7 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 3000 1 3000 3000 100.0% chr13 + 112940751 112943750 3000 browser details YourSeq 98 108 312 3000 82.2% chr19 + 5834096 5834290 195 browser details YourSeq 89 38 229 3000 88.8% chr1 - 82455348 82645456 190109 browser details YourSeq 73 149 270 3000 89.3% chr9 + 48783860 48783984 125 browser details YourSeq 72 147 265 3000 89.4% chr1 + 87883431 87883552 122 browser details YourSeq 66 145 270 3000 86.7% chr1 - 21269166 21269610 445 browser details YourSeq 66 105 273 3000 87.7% chr5 + 130761092 130761263 172 browser details YourSeq 65 143 270 3000 89.3% chr1 + 69828004 69828131 128 browser details YourSeq 64 1416 1693 3000 86.4% chr1 - 167118255 167361186 242932 browser details YourSeq 64 176 264 3000 86.4% chr19 + 17418589 17418678 90 browser details YourSeq 61 149 229 3000 93.0% chr16 + 13676387 13676470 84 browser details YourSeq 60 149 270 3000 89.9% chr4 + 50952023 50952142 120 browser details YourSeq 60 153 270 3000 87.5% chr1 + 21220641 21220837 197 browser details YourSeq 59 136 292 3000 94.1% chr6 - 135049429 135049590 162 browser details YourSeq 59 172 269 3000 94.3% chr11 - 23266298 23266397 100 browser details YourSeq 59 1300 1473 3000 96.9% chr9 + 43042767 43042966 200 browser details YourSeq 59 172 270 3000 84.8% chr18 + 75347586 75347689 104 browser details YourSeq 57 153 227 3000 89.2% chr5 + 67285846 67285925 80 browser details YourSeq 57 153 270 3000 91.4% chr2 + 165184935 165185055 121 browser details YourSeq 56 172 273 3000 91.2% chr1 - 26949960 26950064 105
Note: The 3000 bp section downstream of Exon 7 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Dhx29 DEAH (Asp-Glu-Ala-His) box polypeptide 29 [ Mus musculus (house mouse) ] Gene ID: 218629, updated on 10-Oct-2019
Gene summary
Official Symbol Dhx29 provided by MGI Official Full Name DEAH (Asp-Glu-Ala-His) box polypeptide 29 provided by MGI Primary source MGI:MGI:2145374 See related Ensembl:ENSMUSG00000042426 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 Ddxx; AU043276; 3732415M03; E130202M19Rik Expression Ubiquitous expression in CNS E11.5 (RPKM 7.2), CNS E18 (RPKM 5.8) and 26 other tissues See more Orthologs human all
Genomic context
Location: 13; 13 D2.2 See Dhx29 in Genome Data Viewer
Exon count: 27
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (112927680..112969432)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 13 NC_000079.5 (113718001..113759395)
Chromosome 13 - NC_000079.6
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Transcript information: This gene has 4 transcripts
Gene: Dhx29 ENSMUSG00000042426
Description DEAH (Asp-Glu-Ala-His) box polypeptide 29 [Source:MGI Symbol;Acc:MGI:2145374] Gene Synonyms E130202M19Rik Location Chromosome 13: 112,927,454-112,969,432 forward strand. GRCm38:CM001006.2 About this gene This gene has 4 transcripts (splice variants), 201 orthologues, 18 paralogues, is a member of 1 Ensembl protein family and is associated with 19 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Dhx29- ENSMUST00000038574.6 4682 1365aa ENSMUSP00000035244.5 Protein coding CCDS26779 Q6PGC1 TSL:1 201 GENCODE basic APPRIS P1
Dhx29- ENSMUST00000224176.1 1272 272aa ENSMUSP00000153182.1 Nonsense mediated - Q8BN72 - 203 decay
Dhx29- ENSMUST00000223866.1 1736 No - Retained intron - - - 202 protein
Dhx29- ENSMUST00000226022.1 497 No - Retained intron - - - 204 protein
61.98 kb Forward strand 112.92Mb 112.93Mb 112.94Mb 112.95Mb 112.96Mb 112.97Mb Genes (Comprehensive set... Dhx29-201 >protein coding
Dhx29-203 >nonsense mediated decay
Dhx29-202 >retained intron Gm8795-201 >processed pseudogene
Dhx29-204 >retained intron
Contigs AC165265.2 > Genes < Mtrex-201protein coding (Comprehensive set...
< Mtrex-206retained intron
< Mtrex-205retained intron
Regulatory Build
112.92Mb 112.93Mb 112.94Mb 112.95Mb 112.96Mb 112.97Mb Reverse strand 61.98 kb
Regulation Legend CTCF Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana
Non-Protein Coding
pseudogene processed transcript
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Transcript: ENSMUST00000038574
41.98 kb Forward strand
Dhx29-201 >protein coding
ENSMUSP00000035... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily P-loop containing nucleoside triphosphate hydrolase
SMART Helicase superfamily 1/2, ATP-binding domain Helicase-associated domain
Helicase, C-terminal Pfam DEAD/DEAH box helicase domain Domain of unknown function DUF1605
Helicase, C-terminal
Helicase-associated domain PROSITE profiles Helicase superfamily 1/2, ATP-binding domain
Helicase, C-terminal PROSITE patterns DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site
PANTHER PTHR18934
PTHR18934:SF202 HAMAP ATP-dependent RNA helicase DHX29
Gene3D 3.40.50.300 1.20.120.1080
CDD cd17975 cd18791
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
stop gained inframe insertion missense variant splice region variant synonymous variant
Scale bar 0 200 400 600 800 1000 1365
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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