https://www.alphaknockout.com
Mouse Taar3 Knockout Project (CRISPR/Cas9)
Objective: To create a Taar3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Taar3 gene (NCBI Reference Sequence: NM_001008429 ; Ensembl: ENSMUSG00000069708 ) is located on Mouse chromosome 10. 1 exon is identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 1 (Transcript: ENSMUST00000045152). Exon 1 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 1 starts from about 0.1% of the coding region. Exon 1 covers 100.0% of the coding region. The size of effective KO region: ~1029 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
Legends Exon of mouse Taar3 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 start codon 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 stop codon 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(31.05% 621) | C(17.8% 356) | T(31.4% 628) | G(19.75% 395)
Note: The 2000 bp section upstream of start codon 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(28.1% 562) | C(22.3% 446) | T(30.1% 602) | G(19.5% 390)
Note: The 2000 bp section downstream of stop codon 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% chr10 + 23947559 23949558 2000 browser details YourSeq 86 1720 1841 2000 85.3% chr10 - 24742642 24742763 122 browser details YourSeq 86 1715 1842 2000 85.3% chr10 + 111182402 111182531 130 browser details YourSeq 85 1717 1841 2000 84.0% chr13 - 77720904 77721028 125 browser details YourSeq 85 1717 1841 2000 84.0% chr15 + 31464925 31465049 125 browser details YourSeq 84 1659 1826 2000 83.5% chr10 + 71431029 71431511 483 browser details YourSeq 83 1716 1826 2000 87.4% chr10 + 77312060 77312170 111 browser details YourSeq 82 1680 1826 2000 76.6% chr2 - 82402905 82403041 137 browser details YourSeq 82 1706 1826 2000 84.3% chr11 - 75113873 75186764 72892 browser details YourSeq 82 1717 1842 2000 82.6% chr14 + 26152094 26152219 126 browser details YourSeq 82 1716 1829 2000 86.0% chr11 + 115580278 115580391 114 browser details YourSeq 81 1717 1841 2000 82.4% chr10 + 80612919 80613043 125 browser details YourSeq 79 1717 1829 2000 85.0% chr8 - 93927870 93927982 113 browser details YourSeq 79 1718 1843 2000 87.0% chr16 - 64522141 64522266 126 browser details YourSeq 79 1692 1818 2000 79.3% chr12 - 82453065 82453182 118 browser details YourSeq 78 1717 1826 2000 85.5% chr4 - 149956564 149956673 110 browser details YourSeq 78 1717 1826 2000 85.5% chr15 - 98552203 98552312 110 browser details YourSeq 78 1717 1826 2000 85.5% chr12 - 93131784 93131893 110 browser details YourSeq 78 1717 1824 2000 86.2% chr15 + 93484914 93485021 108 browser details YourSeq 77 1718 1826 2000 83.4% chrX - 160925408 160925515 108
Note: The 2000 bp section upstream of start codon 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% chr10 + 23950588 23952587 2000 browser details YourSeq 122 261 1093 2000 85.9% chr14 + 54095151 54182289 87139 browser details YourSeq 109 930 1122 2000 89.8% chr3 + 58225051 58225265 215 browser details YourSeq 104 236 532 2000 87.2% chr11 + 60724043 60724338 296 browser details YourSeq 101 929 1131 2000 85.3% chr13 + 44233201 44233401 201 browser details YourSeq 95 930 1119 2000 86.9% chr5 - 30726881 30727076 196 browser details YourSeq 90 260 541 2000 91.1% chr9 - 40551366 40551647 282 browser details YourSeq 89 930 1126 2000 90.1% chr1 - 9204008 9204211 204 browser details YourSeq 87 930 1102 2000 83.4% chr14 - 64862625 64862807 183 browser details YourSeq 87 932 1125 2000 85.9% chr11 - 89535971 89536162 192 browser details YourSeq 87 939 1124 2000 90.0% chr13 + 12591230 12591438 209 browser details YourSeq 87 990 1126 2000 85.9% chr10 + 117862907 117863050 144 browser details YourSeq 85 990 1125 2000 88.4% chr16 - 37437921 37438062 142 browser details YourSeq 84 932 1120 2000 81.9% chr13 - 103651195 103651409 215 browser details YourSeq 84 930 1126 2000 91.3% chr1 - 43068191 43068409 219 browser details YourSeq 83 930 1125 2000 89.5% chr1 - 42630395 42630602 208 browser details YourSeq 82 930 1125 2000 79.4% chr14 - 30466520 30466708 189 browser details YourSeq 82 932 1126 2000 87.3% chr1 + 40854421 40854649 229 browser details YourSeq 81 931 1124 2000 89.5% chr14 - 52325501 52325717 217 browser details YourSeq 81 300 504 2000 89.3% chr14 + 80116769 80116974 206
Note: The 2000 bp section downstream of stop codon is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Taar3 trace amine-associated receptor 3 [ Mus musculus (house mouse) ] Gene ID: 493809, updated on 12-Aug-2019
Gene summary
Official Symbol Taar3 provided by MGI Official Full Name trace amine-associated receptor 3 provided by MGI Primary source MGI:MGI:3527427 See related Ensembl:ENSMUSG00000069708 Gene type protein coding RefSeq status PROVISIONAL Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Genomic context
Location: 10; 10 A4 See Taar3 in Genome Data Viewer
Exon count: 1
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (23949558..23950589)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (23669364..23670395)
Chromosome 10 - NC_000076.6
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Transcript information: This gene has 1 transcript
Gene: Taar3 ENSMUSG00000069708
Description trace amine-associated receptor 3 [Source:MGI Symbol;Acc:MGI:3527427] Location Chromosome 10: 23,949,558-23,950,589 forward strand. GRCm38:CM001003.2 About this gene This gene has 1 transcript (splice variant), 60 orthologues, 32 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Taar3-201 ENSMUST00000045152.5 1032 343aa ENSMUSP00000036817.4 Protein coding CCDS23736 D8KZH8 Q5QD16 TSL:NA GENCODE basic APPRIS P1
21.03 kb Forward strand
23.94Mb 23.95Mb 23.96Mb Genes (Comprehensive set... Taar2-201 >protein coding Taar3-201 >protein coding Taar4-201 >protein coding
Contigs < AC117837.4 Regulatory Build
23.94Mb 23.95Mb 23.96Mb Reverse strand 21.03 kb
Regulation Legend
CTCF Enhancer Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana
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Transcript: ENSMUST00000045152
1.03 kb Forward strand
Taar3-201 >protein coding
ENSMUSP00000036... Transmembrane heli... Superfamily SSF81321
SMART G protein-coupled receptor, rhodopsin-like
Prints Trace amine associated receptor family
G protein-coupled receptor, rhodopsin-like Pfam G protein-coupled receptor, rhodopsin-like
PROSITE profiles GPCR, rhodopsin-like, 7TM
PROSITE patterns G protein-coupled receptor, rhodopsin-like
PANTHER PTHR24249:SF82
PTHR24249 Gene3D 1.20.1070.10
CDD cd15312
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend synonymous variant
Scale bar 0 40 80 120 160 200 240 280 343
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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