https://www.alphaknockout.com
Mouse Tubd1 Knockout Project (CRISPR/Cas9)
Objective: To create a Tubd1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Tubd1 gene (NCBI Reference Sequence: NM_001199045 ; Ensembl: ENSMUSG00000020513 ) is located on Mouse chromosome 11. 10 exons are identified, with the ATG start codon in exon 2 and the TAA stop codon in exon 10 (Transcript: ENSMUST00000020821). Exon 2~7 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:
Exon 2 starts from the coding region. Exon 2~7 covers 70.44% of the coding region. The size of effective KO region: ~9107 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 7 10
Legends Exon of mouse Tubd1 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 2000 bp section downstream of Exon 7 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(29.85% 597) | C(21.55% 431) | T(28.5% 570) | G(20.1% 402)
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(2000bp) | A(25.15% 503) | C(23.0% 460) | T(29.4% 588) | G(22.45% 449)
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 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% chr11 + 86546832 86548831 2000 browser details YourSeq 222 578 1221 2000 89.5% chr7 + 127653695 127654216 522 browser details YourSeq 220 882 1221 2000 87.8% chr5 - 142786557 142887981 101425 browser details YourSeq 215 676 1221 2000 87.5% chr2 - 30271081 30271459 379 browser details YourSeq 211 676 1221 2000 91.7% chr11 + 95917784 96082599 164816 browser details YourSeq 206 676 1232 2000 86.5% chr12 - 78898544 78898938 395 browser details YourSeq 199 678 1219 2000 86.9% chr2 - 132674929 132675299 371 browser details YourSeq 197 882 1236 2000 94.6% chr11 - 80440752 80441323 572 browser details YourSeq 197 882 1238 2000 91.0% chr1 - 58455908 58456255 348 browser details YourSeq 194 676 1221 2000 87.2% chr9 + 53457999 53458365 367 browser details YourSeq 191 676 1221 2000 86.3% chr13 + 106862710 106863078 369 browser details YourSeq 189 1036 1567 2000 94.9% chr4 + 116630276 117012734 382459 browser details YourSeq 185 882 1221 2000 93.9% chr9 + 57662024 57662702 679 browser details YourSeq 184 1038 1221 2000 100.0% chr18 + 34392597 34392780 184 browser details YourSeq 183 988 1221 2000 96.5% chr10 - 39800612 39801213 602 browser details YourSeq 181 669 1223 2000 89.2% chr13 - 67577187 67577686 500 browser details YourSeq 179 676 1221 2000 89.3% chr4 + 123540717 123541191 475 browser details YourSeq 178 1038 1556 2000 87.4% chr1 - 83180715 83181186 472 browser details YourSeq 178 1038 1657 2000 86.9% chr1 + 192219521 192219849 329 browser details YourSeq 175 581 1221 2000 84.6% chr2 - 180757628 180757852 225
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 2000 1 2000 2000 100.0% chr11 + 86557891 86559890 2000 browser details YourSeq 247 645 942 2000 95.0% chr6 + 149102727 149300937 198211 browser details YourSeq 222 643 942 2000 93.1% chr8 + 18838009 18838480 472 browser details YourSeq 219 635 940 2000 92.0% chr1 + 118337084 118337424 341 browser details YourSeq 215 651 1233 2000 87.5% chr6 + 38348264 38348788 525 browser details YourSeq 209 688 1231 2000 85.0% chr4 - 126941372 126941824 453 browser details YourSeq 206 645 942 2000 92.5% chr6 + 28493305 28631606 138302 browser details YourSeq 202 649 942 2000 94.8% chr7 - 12957153 12957499 347 browser details YourSeq 199 645 957 2000 93.1% chr16 - 87162203 87162589 387 browser details YourSeq 198 669 942 2000 93.2% chr15 - 100538361 100538851 491 browser details YourSeq 196 645 942 2000 92.7% chrX + 162219158 162219791 634 browser details YourSeq 196 690 956 2000 90.2% chr14 + 47302375 47302643 269 browser details YourSeq 194 693 942 2000 93.0% chr9 - 110112103 110112746 644 browser details YourSeq 193 645 942 2000 88.4% chr4 + 55321603 55321891 289 browser details YourSeq 190 634 905 2000 90.3% chr9 + 50816059 50816339 281 browser details YourSeq 184 708 939 2000 91.9% chr16 - 3775250 3775495 246 browser details YourSeq 177 786 1233 2000 89.1% chr8 - 109589079 109589432 354 browser details YourSeq 177 781 1231 2000 86.8% chr5 - 119923635 119923997 363 browser details YourSeq 173 648 897 2000 87.8% chr17 - 23589999 23590592 594 browser details YourSeq 172 790 1185 2000 94.8% chr3 - 94548445 94548962 518
Note: The 2000 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: Tubd1 tubulin, delta 1 [ Mus musculus (house mouse) ] Gene ID: 56427, updated on 10-Oct-2019
Gene summary
Official Symbol Tubd1 provided by MGI Official Full Name tubulin, delta 1 provided by MGI Primary source MGI:MGI:1891826 See related Ensembl:ENSMUSG00000020513 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 Tubd; 4930550G19Rik Expression Ubiquitous expression in testis adult (RPKM 6.5), liver E14 (RPKM 3.3) and 28 other tissues See more Orthologs human all
Genomic context
Location: 11; 11 C See Tubd1 in Genome Data Viewer Exon count: 10
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (86544991..86571608)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (86358510..86380862)
Chromosome 11 - NC_000077.6
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Transcript information: This gene has 5 transcripts
Gene: Tubd1 ENSMUSG00000020513
Description tubulin, delta 1 [Source:MGI Symbol;Acc:MGI:1891826] Gene Synonyms 4930550G19Rik Location Chromosome 11: 86,544,991-86,567,360 forward strand. GRCm38:CM001004.2 About this gene This gene has 5 transcripts (splice variants), 202 orthologues, 20 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Tubd1- ENSMUST00000020821.9 2070 486aa ENSMUSP00000020821.3 Protein coding CCDS56794 Q8CDD3 TSL:1 201 GENCODE basic
Tubd1- ENSMUST00000167178.8 1976 455aa ENSMUSP00000130909.2 Protein coding CCDS25202 Q5SWF8 Q9R1K7 TSL:1 205 GENCODE basic APPRIS P1
Tubd1- ENSMUST00000108030.8 1964 486aa ENSMUSP00000103665.2 Protein coding CCDS56794 Q8CDD3 TSL:1 203 GENCODE basic
Tubd1- ENSMUST00000069503.12 1871 455aa ENSMUSP00000064383.6 Protein coding CCDS25202 Q5SWF8 Q9R1K7 TSL:1 202 GENCODE basic APPRIS P1
Tubd1- ENSMUST00000164931.1 783 189aa ENSMUSP00000130621.1 Protein coding - F6Q5J9 CDS 5' incomplete 204 TSL:3
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42.37 kb Forward strand 86.54Mb 86.55Mb 86.56Mb 86.57Mb Genes (Comprehensive set... Tubd1-205 >protein coding
Tubd1-202 >protein coding
Tubd1-201 >protein coding
Tubd1-203 >protein coding
Tubd1-204 >protein coding
Contigs AL604063.4 >
Genes < Rps6kb1-207protein coding (Comprehensive set...
< Rps6kb1-201retained intron
< Rps6kb1-202protein coding
< Rps6kb1-204protein coding
Regulatory Build
86.54Mb 86.55Mb 86.56Mb 86.57Mb Reverse strand 42.37 kb
Regulation Legend
CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
processed transcript
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Transcript: ENSMUST00000020821
22.37 kb Forward strand
Tubd1-201 >protein coding
ENSMUSP00000020... Superfamily Tubulin/FtsZ, GTPase domain superfamily Tubulin/FtsZ, C-terminal
SMART Tubulin/FtsZ, GTPase domain Prints Tubulin
Delta tubulin Pfam Tubulin/FtsZ, GTPase domain PROSITE patterns Tubulin, conserved site PANTHER Delta tubulin
Tubulin Gene3D Tubulin, C-terminal CDD cd02189
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend frameshift variant missense variant splice region variant synonymous variant
Scale bar 0 60 120 180 240 300 360 420 486
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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