https://www.alphaknockout.com
Mouse Mtmr12 Knockout Project (CRISPR/Cas9)
Objective: To create a Mtmr12 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Mtmr12 gene (NCBI Reference Sequence: NM_172958 ; Ensembl: ENSMUSG00000039458 ) is located on Mouse chromosome 15. 16 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 16 (Transcript: ENSMUST00000038172). 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 3.66% of the coding region. Exon 2~6 covers 22.4% of the coding region. The size of effective KO region: ~7746 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 16
Legends Exon of mouse Mtmr12 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. 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 Exon 6 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(22.65% 453) | C(22.75% 455) | T(33.4% 668) | G(21.2% 424)
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(26.25% 525) | C(22.35% 447) | T(28.2% 564) | G(23.2% 464)
Note: The 2000 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% chr15 + 12228275 12230274 2000 browser details YourSeq 278 1000 1346 2000 90.6% chr17 - 29085756 29086096 341 browser details YourSeq 272 1000 1349 2000 91.3% chr3 + 65886739 65887217 479 browser details YourSeq 268 1003 1339 2000 90.7% chr9 - 47524649 47524991 343 browser details YourSeq 263 1000 1347 2000 91.0% chr13 - 58162097 58162440 344 browser details YourSeq 255 1027 1347 2000 92.7% chr19 + 8649925 8650292 368 browser details YourSeq 235 1024 1346 2000 88.6% chr11 - 3207823 3208137 315 browser details YourSeq 235 1033 1347 2000 91.5% chr17 + 71524527 71525123 597 browser details YourSeq 231 1029 1344 2000 88.3% chr17 - 56254415 56254791 377 browser details YourSeq 217 1019 1345 2000 87.0% chr5 + 121514487 121514804 318 browser details YourSeq 209 1039 1349 2000 91.7% chr17 - 34924990 35181233 256244 browser details YourSeq 202 1103 1351 2000 93.6% chr19 - 29746614 29747157 544 browser details YourSeq 196 1038 1347 2000 88.0% chr4 - 145534033 145534711 679 browser details YourSeq 174 1172 1602 2000 86.9% chr8 - 33990901 33991198 298 browser details YourSeq 174 1171 1348 2000 98.9% chr6 - 125456576 125456753 178 browser details YourSeq 170 1112 1350 2000 89.5% chr8 + 120599963 120600486 524 browser details YourSeq 168 1171 1348 2000 97.2% chr5 + 92641333 92641510 178 browser details YourSeq 166 1171 1348 2000 96.7% chr2 - 127031412 127031589 178 browser details YourSeq 165 1175 1595 2000 93.7% chr11 - 105324178 105324680 503 browser details YourSeq 165 1173 1348 2000 95.5% chr8 + 94198680 94198853 174
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% chr15 + 12238021 12240020 2000 browser details YourSeq 211 469 844 2000 83.9% chr13 - 58336066 58336446 381 browser details YourSeq 206 503 856 2000 89.7% chr4 - 132619826 132620236 411 browser details YourSeq 201 476 860 2000 80.8% chr2 + 125609596 125610047 452 browser details YourSeq 201 469 776 2000 84.3% chr13 + 96260655 96678436 417782 browser details YourSeq 200 469 804 2000 87.7% chr7 + 35860537 35915167 54631 browser details YourSeq 199 468 845 2000 83.3% chr6 - 82865614 82865982 369 browser details YourSeq 199 491 774 2000 90.3% chr5 - 112614023 112614346 324 browser details YourSeq 198 502 799 2000 87.8% chr4 - 107900750 107901068 319 browser details YourSeq 198 508 858 2000 83.3% chr19 + 9101968 9102337 370 browser details YourSeq 196 469 810 2000 84.6% chr17 - 30862899 30863243 345 browser details YourSeq 194 537 859 2000 88.7% chr12 + 8898180 8898501 322 browser details YourSeq 192 524 853 2000 85.7% chr11 + 80306744 80307072 329 browser details YourSeq 190 467 758 2000 91.4% chr1 + 135775571 135775883 313 browser details YourSeq 189 585 1142 2000 76.3% chr16 + 97192026 97192457 432 browser details YourSeq 188 570 859 2000 87.7% chr4 + 41617183 41617489 307 browser details YourSeq 186 530 845 2000 83.6% chr1 - 178293308 178293628 321 browser details YourSeq 186 569 869 2000 83.1% chr6 + 82054328 82054643 316 browser details YourSeq 185 469 780 2000 85.8% chr9 - 70092233 70312671 220439 browser details YourSeq 185 233 758 2000 87.3% chr7 - 142449091 142449619 529
Note: The 2000 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: Mtmr12 myotubularin related protein 12 [ Mus musculus (house mouse) ] Gene ID: 268783, updated on 12-Aug-2019
Gene summary
Official Symbol Mtmr12 provided by MGI Official Full Name myotubularin related protein 12 provided by MGI Primary source MGI:MGI:2443034 See related Ensembl:ENSMUSG00000039458 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 3Pap; Pip3ap; mKIAA1682; 4932703C11; C730015A02Rik Expression Ubiquitous expression in thymus adult (RPKM 13.2), testis adult (RPKM 11.0) and 28 other tissues See more Orthologs human all
Genomic context
Location: 15; 15 A1 See Mtmr12 in Genome Data Viewer Exon count: 16
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (12204970..12272240)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 15 NC_000081.5 (12134849..12201995)
Chromosome 15 - NC_000081.6
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Transcript information: This gene has 5 transcripts
Gene: Mtmr12 ENSMUSG00000039458
Description myotubularin related protein 12 [Source:MGI Symbol;Acc:MGI:2443034] Gene Synonyms C730015A02Rik, Pip3ap Location Chromosome 15: 12,205,028-12,274,496 forward strand. GRCm38:CM001008.2 About this gene This gene has 5 transcripts (splice variants), 169 orthologues, 12 paralogues, is a member of 1 Ensembl protein family and is associated with 8 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Mtmr12- ENSMUST00000038172.15 6840 747aa ENSMUSP00000041227.8 Protein coding CCDS27388 Q80TA6 TSL:1 201 GENCODE basic APPRIS P1
Mtmr12- ENSMUST00000071993.12 3351 437aa ENSMUSP00000071883.6 Protein coding - Q80TA6 TSL:1 202 GENCODE basic
Mtmr12- ENSMUST00000174160.2 4489 526aa ENSMUSP00000134293.1 Nonsense mediated - G3UZ04 TSL:1 204 decay
Mtmr12- ENSMUST00000174418.7 4359 159aa ENSMUSP00000133285.1 Nonsense mediated - G3XA69 TSL:1 205 decay
Mtmr12- ENSMUST00000173071.1 772 No - lncRNA - - TSL:5 203 protein
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89.47 kb Forward strand
12.20Mb 12.22Mb 12.24Mb 12.26Mb 12.28Mb Genes (Comprehensive set... Mtmr12-201 >protein coding
Mtmr12-202 >protein coding
Mtmr12-205 >nonsense mediated decay
Mtmr12-204 >nonsense mediated decay
Mtmr12-203 >lncRNA
Contigs < AC150560.5
Genes < Gm49240-201lncRNA (Comprehensive set...
< Gm2581-201processed pseudogene
Regulatory Build
12.20Mb 12.22Mb 12.24Mb 12.26Mb 12.28Mb Reverse strand 89.47 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
RNA gene processed transcript pseudogene
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Transcript: ENSMUST00000038172
69.47 kb Forward strand
Mtmr12-201 >protein coding
ENSMUSP00000041... MobiDB lite Low complexity (Seg) Superfamily SSF50729 Protein-tyrosine phosphatase-like
Pfam Myotubularin-like phosphatase domain Myotubularin-related 12-like C-terminal domain
PROSITE profiles Myotubularin-like phosphatase domain
PANTHER Myotubularin-related protein 12
Myotubularin family CDD cd14594
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 747
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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