https://www.alphaknockout.com
Mouse Cutc Knockout Project (CRISPR/Cas9)
Objective: To create a Cutc knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Cutc gene (NCBI Reference Sequence: NM_001113562 ; Ensembl: ENSMUSG00000025193 ) is located on Mouse chromosome 19. 9 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 9 (Transcript: ENSMUST00000112047). Exon 2~6 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:
Exon 2 starts from about 7.23% of the coding region. Exon 2~6 covers 62.75% of the coding region. The size of effective KO region: ~7387 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 9
Legends Exon of mouse Cutc 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. 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 1953 bp section downstream of Exon 6 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(29.9% 598) | C(16.6% 332) | T(32.35% 647) | G(21.15% 423)
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(1953bp) | A(29.8% 582) | C(16.54% 323) | T(33.9% 662) | G(19.76% 386)
Note: The 1953 bp section downstream of Exon 6 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% chr19 + 43753621 43755620 2000 browser details YourSeq 155 845 1356 2000 82.3% chr10 - 117658228 117658419 192 browser details YourSeq 155 844 1033 2000 89.4% chr9 + 63192293 63192480 188 browser details YourSeq 154 846 1033 2000 89.2% chr4 - 59849047 59849231 185 browser details YourSeq 154 845 1033 2000 91.4% chr5 + 129921003 129921202 200 browser details YourSeq 153 843 1033 2000 89.1% chr2 - 76611444 76611630 187 browser details YourSeq 153 844 1033 2000 89.2% chr10 + 27573064 27573250 187 browser details YourSeq 152 845 1034 2000 90.6% chr7 - 143550663 143839316 288654 browser details YourSeq 152 844 1033 2000 87.6% chr6 - 31533860 31534044 185 browser details YourSeq 152 847 1034 2000 90.5% chr2 - 125915992 125916179 188 browser details YourSeq 149 837 1041 2000 85.2% chr4 - 141829755 141829954 200 browser details YourSeq 149 845 1033 2000 87.8% chr17 - 22187264 22187444 181 browser details YourSeq 149 844 1033 2000 90.5% chr15 + 73181051 73181239 189 browser details YourSeq 149 845 1033 2000 91.6% chr10 + 119425082 119585711 160630 browser details YourSeq 148 845 1032 2000 91.1% chrX - 160219175 160219364 190 browser details YourSeq 148 852 1045 2000 91.6% chr7 - 46960006 46960265 260 browser details YourSeq 148 852 1041 2000 87.5% chr5 - 29698148 29698334 187 browser details YourSeq 147 845 1033 2000 88.3% chr6 - 136884861 136885048 188 browser details YourSeq 147 845 1033 2000 87.1% chr4 - 130363165 130363350 186 browser details YourSeq 147 844 1028 2000 88.6% chr18 - 73892666 73892849 184
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 1953 1 1953 1953 100.0% chr19 + 43763008 43764960 1953 browser details YourSeq 268 43 1724 1953 93.0% chr7 + 142149893 142537050 387158 browser details YourSeq 222 43 1715 1953 93.4% chr4 + 117789701 117920710 131010 browser details YourSeq 205 42 1682 1953 94.8% chr17 - 56235966 56640651 404686 browser details YourSeq 167 43 1719 1953 91.6% chr1 - 9710109 10172361 462253 browser details YourSeq 162 43 656 1953 89.1% chr5 + 20977211 20977738 528 browser details YourSeq 146 39 189 1953 98.7% chr10 + 86836263 86836414 152 browser details YourSeq 143 43 193 1953 98.7% chr4 - 59070996 59071161 166 browser details YourSeq 143 43 193 1953 98.7% chr11 - 119468562 119468712 151 browser details YourSeq 143 41 190 1953 98.7% chr9 + 119827904 119828063 160 browser details YourSeq 142 42 203 1953 95.0% chr7 - 19896530 19896783 254 browser details YourSeq 142 39 193 1953 96.8% chr17 - 35674115 35674271 157 browser details YourSeq 141 42 193 1953 96.8% chr12 - 3530790 3530943 154 browser details YourSeq 140 43 195 1953 94.7% chr2 - 129341786 129341936 151 browser details YourSeq 140 43 193 1953 96.7% chr12 - 100189214 100189376 163 browser details YourSeq 140 44 191 1953 96.6% chr11 - 117055556 117055702 147 browser details YourSeq 140 43 193 1953 97.4% chr11 - 84184031 84184182 152 browser details YourSeq 140 42 193 1953 97.4% chr10 - 120611265 120611872 608 browser details YourSeq 140 44 193 1953 96.7% chr7 + 4745201 4745350 150 browser details YourSeq 140 43 195 1953 96.7% chr17 + 46542346 46542499 154
Note: The 1953 bp section downstream of Exon 6 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Cutc cutC copper transporter [ Mus musculus (house mouse) ] Gene ID: 66388, updated on 12-Aug-2019
Gene summary
Official Symbol Cutc provided by MGI Official Full Name cutC copper transporter provided by MGI Primary source MGI:MGI:1913638 See related Ensembl:ENSMUSG00000025193 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 CGI-32; AI326282; 2310039I18Rik Expression Ubiquitous expression in testis adult (RPKM 6.5), bladder adult (RPKM 4.1) and 28 other tissues See more Orthologs human all
Genomic context
Location: 19; 19 C3 See Cutc in Genome Data Viewer Exon count: 9
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (43753023..43768638)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 19 NC_000085.5 (43827513..43843128)
Chromosome 19 - NC_000085.6
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Transcript information: This gene has 4 transcripts
Gene: Cutc ENSMUSG00000025193
Description cutC copper transporter [Source:MGI Symbol;Acc:MGI:1913638] Gene Synonyms 2310039I18Rik, CGI-32 Location Chromosome 19: 43,752,996-43,768,638 forward strand. GRCm38:CM001012.2 About this gene This gene has 4 transcripts (splice variants), 192 orthologues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Cutc-201 ENSMUST00000026199.13 1298 262aa ENSMUSP00000026199.7 Protein coding CCDS29837 F8WHX2 TSL:1 GENCODE basic
Cutc-202 ENSMUST00000112047.9 1233 272aa ENSMUSP00000107678.3 Protein coding CCDS50443 Q9D8X1 TSL:1 GENCODE basic APPRIS P1
Cutc-204 ENSMUST00000153295.1 788 254aa ENSMUSP00000118906.1 Protein coding - D3YY50 CDS 3' incomplete TSL:3
Cutc-203 ENSMUST00000123564.1 685 No protein - Retained intron - - TSL:3
35.64 kb Forward strand 43.75Mb 43.76Mb 43.77Mb Genes Cutc-201 >protein coding (Comprehensive set...
Cutc-202 >protein coding
Cutc-204 >protein coding
Cutc-203 >retained intron
Contigs < AC141888.4 Genes < Cox15-201protein coding (Comprehensive set...
Regulatory Build
43.75Mb 43.76Mb 43.77Mb Reverse strand 35.64 kb
Regulation Legend CTCF Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript
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Transcript: ENSMUST00000112047
15.54 kb Forward strand
Cutc-202 >protein coding
ENSMUSP00000107... Superfamily Copper homeostasis (CutC) domain superfamily Pfam Copper homeostasis CutC domain PANTHER Copper homeostasis protein CutC HAMAP Copper homeostasis protein CutC Gene3D Copper homeostasis (CutC) domain superfamily
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 40 80 120 160 200 272
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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