Mouse Cd44 Knockout Project (CRISPR/Cas9) Objective: To create a Cd44 knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Cd44 gene (NCBI Reference Sequence: NM_009851 ; Ensembl: ENSMUSG00000005087 ) is located on Mouse chromosome 2. 19 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 19 (Transcript: ENSMUST00000005218). Exon 4~7 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: Homozygotes for targeted null mutations exhibit impaired T lymphocyte trafficking resulting in muted inflammatory responses, altered myeloid progenitor distribution, reduced growth of tumors, and impaired uterine involution and maintenance of lactation. Exon 4 starts from about 16.37% of the coding region. Exon 4~7 covers 22.82% of the coding region. The size of effective KO region: ~9565 bp. The KO region does not have any other known gene. http://www.alphaknockout.com/ Page 1 of 9
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Mouse Cd44 Knockout Project (CRISPR/Cas9)
Objective:To create a Cd44 knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering.
Strategy summary:The Cd44 gene (NCBI Reference Sequence: NM_009851 ; Ensembl: ENSMUSG00000005087 ) is located onMouse chromosome 2.19 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 19 (Transcript:ENSMUST00000005218).Exon 4~7 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: Homozygotes for targeted null mutations exhibit impaired T lymphocyte trafficking resulting in muted inflammatoryresponses, altered myeloid progenitor distribution, reduced growth of tumors, and impaired uterine involution andmaintenance of lactation.
Exon 4 starts from about 16.37% of the coding region. Exon 4~7 covers 22.82% of the coding region.
Note: The 2000 bp section upstream of Exon 4 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is foundin the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis.
Sequence 1Sequence 2
Reverse ComplementForward
Window size: 15 bp
Note: The 2000 bp section downstream of Exon 7 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat isfound in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis.
Note: The 2000 bp section upstream of Exon 4 is analyzed to determine the GC content. No significant high GC-content region is found. So thisregion is suitable for PCR screening or sequencing analysis.
Note: The 2000 bp section downstream of Exon 7 is analyzed to determine the GC content. No significant high GC-content region is found. So thisregion is suitable for PCR screening or sequencing analysis.
Also known as Ly-24; Pgp-1; HERMES; AU023126; AW121933; AW146109Expression Broad expression in lung adult (RPKM 13.1), spleen adult (RPKM 8.5) and 23 other tissues See more
Orthologs human all
See Cd44 in Genome Data ViewerLocation: 2 E2; 2 54.13 cM
Gene and protein information:Cd44 CD44 antigen [ Mus musculus (house mouse) ]Gene ID: 12505, updated on 10-Oct-2019
Gene summary
Genomic context
Exon count: 20
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (102811141..102901669, complement)
About this gene This gene has 9 transcripts (splice variants), 184 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and isassociated with 84 phenotypes.
Transcripts
Transcript information: This gene has 9 transcripts
Gene: Cd44 ENSMUSG00000005087
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags