https://www.alphaknockout.com
Mouse Med12l Knockout Project (CRISPR/Cas9)
Objective: To create a Med12l knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Med12l gene (NCBI Reference Sequence: NM_177855 ; Ensembl: ENSMUSG00000056476 ) is located on Mouse chromosome 3. 44 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 44 (Transcript: ENSMUST00000199659). Exon 3~4 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 3 starts from about 3.13% of the coding region. Exon 3~4 covers 5.37% of the coding region. The size of effective KO region: ~4854 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 3 4 44
Legends Exon of mouse Med12l 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 3 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 4 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(27.35% 547) | C(20.35% 407) | T(31.25% 625) | G(21.05% 421)
Note: The 2000 bp section upstream of Exon 3 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(23.05% 461) | C(23.9% 478) | T(33.1% 662) | G(19.95% 399)
Note: The 2000 bp section downstream of Exon 4 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% chr3 + 59035561 59037560 2000 browser details YourSeq 135 498 737 2000 91.9% chr4 + 42128984 42143531 14548 browser details YourSeq 128 496 848 2000 81.4% chr6 + 127456028 127456329 302 browser details YourSeq 127 474 885 2000 79.0% chr1 + 163143055 163143364 310 browser details YourSeq 124 498 703 2000 91.9% chr4_JH584293_random - 32158 46698 14541 browser details YourSeq 123 471 885 2000 81.6% chr9 - 113016682 113017001 320 browser details YourSeq 120 486 844 2000 81.2% chr13 - 38019879 38020180 302 browser details YourSeq 117 499 849 2000 76.0% chr11 + 97494720 97494983 264 browser details YourSeq 116 466 870 2000 75.5% chr6 + 115147350 115147665 316 browser details YourSeq 114 483 906 2000 89.8% chr17 - 80631778 80632345 568 browser details YourSeq 111 503 864 2000 75.2% chr13 - 101905488 101905751 264 browser details YourSeq 111 494 868 2000 77.3% chr1 + 126330936 126331242 307 browser details YourSeq 110 498 826 2000 78.9% chr4_GL456350_random - 197980 198236 257 browser details YourSeq 109 517 902 2000 79.8% chr1 - 71759326 71759611 286 browser details YourSeq 108 472 667 2000 85.1% chr4 - 45680032 45680240 209 browser details YourSeq 106 498 885 2000 89.6% chr4 - 41796881 42076152 279272 browser details YourSeq 106 478 917 2000 77.1% chr15 + 91255959 91256294 336 browser details YourSeq 105 494 848 2000 81.3% chr11 - 50554635 50554947 313 browser details YourSeq 104 517 854 2000 82.4% chr1 - 178469132 178469431 300 browser details YourSeq 104 486 906 2000 81.7% chr5 + 33034720 33035121 402
Note: The 2000 bp section upstream of Exon 3 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% chr3 + 59042415 59044414 2000 browser details YourSeq 131 1665 1881 2000 85.9% chr6 + 126064427 126064644 218 browser details YourSeq 131 1661 1887 2000 82.6% chr12 + 85329331 85329554 224 browser details YourSeq 125 1665 1871 2000 84.1% chr19 - 25762474 25762679 206 browser details YourSeq 124 1664 1880 2000 89.9% chr6 + 91973628 92271919 298292 browser details YourSeq 122 1672 1873 2000 84.4% chr3 - 122193860 122194062 203 browser details YourSeq 115 1661 1845 2000 88.7% chr4 + 95573446 95573631 186 browser details YourSeq 114 1661 1900 2000 76.6% chr7 + 35195434 35195671 238 browser details YourSeq 113 1672 1872 2000 84.8% chr7 - 98251306 98251506 201 browser details YourSeq 113 1661 1874 2000 80.5% chr3 - 139597433 139597643 211 browser details YourSeq 113 1661 1868 2000 80.6% chr7 + 105091557 105091744 188 browser details YourSeq 113 1661 1905 2000 84.5% chr6 + 30209189 30209401 213 browser details YourSeq 113 1663 1886 2000 87.0% chr16 + 35493244 35493483 240 browser details YourSeq 112 1661 1879 2000 90.9% chr4 - 31857613 31857875 263 browser details YourSeq 112 1662 1879 2000 80.9% chr2 - 118319620 118319842 223 browser details YourSeq 111 1661 1840 2000 87.4% chr1 - 171114651 171114833 183 browser details YourSeq 110 1733 1890 2000 86.3% chr14 + 70561589 70561746 158 browser details YourSeq 106 1679 1871 2000 82.0% chr11 + 35497740 35497922 183 browser details YourSeq 105 1661 1854 2000 90.7% chr2 - 122755666 122755859 194 browser details YourSeq 105 1664 1885 2000 85.1% chr15 - 84789542 84789759 218
Note: The 2000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Med12l mediator complex subunit 12-like [ Mus musculus (house mouse) ] Gene ID: 329650, updated on 12-Aug-2019
Gene summary
Official Symbol Med12l provided by MGI Official Full Name mediator complex subunit 12-like provided by MGI Primary source MGI:MGI:2139916 See related Ensembl:ENSMUSG00000056476 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 AU044581; TRALPUSH; A130035F20; A630079M02 Expression Broad expression in cerebellum adult (RPKM 4.7), CNS E18 (RPKM 3.5) and 23 other tissues See more Orthologs human all
Genomic context
Location: 3; 3 D See Med12l in Genome Data Viewer Exon count: 48
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (59005419..59318446)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (58810900..59122338)
Chromosome 3 - NC_000069.6
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Transcript information: This gene has 6 transcripts
Gene: Med12l ENSMUSG00000056476
Description mediator complex subunit 12-like [Source:MGI Symbol;Acc:MGI:2139916] Location Chromosome 3: 59,005,825-59,318,682 forward strand. GRCm38:CM000996.2 About this gene This gene has 6 transcripts (splice variants), 129 orthologues, 1 paralogue and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Med12l- ENSMUST00000199659.4 11006 2185aa ENSMUSP00000142903.1 Protein coding CCDS79912 A0A0G2JET8 TSL:5 206 GENCODE basic APPRIS P2
Med12l- ENSMUST00000164225.5 10264 2192aa ENSMUSP00000127038.1 Protein coding - Q8BQM9 TSL:5 204 GENCODE basic APPRIS ALT2
Med12l- ENSMUST00000040325.13 10159 2157aa ENSMUSP00000042269.7 Protein coding - Q8BQM9 TSL:5 202 GENCODE basic APPRIS ALT2
Med12l- ENSMUST00000040846.14 3747 756aa ENSMUSP00000041859.9 Protein coding - Q8BQM9 TSL:1 203 GENCODE basic
Med12l- ENSMUST00000029393.14 2295 756aa ENSMUSP00000029393.8 Protein coding - Q8BQM9 TSL:5 201 GENCODE basic
Med12l- ENSMUST00000197374.1 3900 301aa ENSMUSP00000143419.1 Nonsense mediated - A0A0G2JG45 CDS 5' 205 decay incomplete TSL:1
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332.86 kb Forward strand 59.0Mb 59.1Mb 59.2Mb 59.3Mb Genes (Comprehensive set... Gm27793-201 >misc RNA Med12l-205 >nonsense mediated decay
Med12l-203 >protein coding Gm43589-201 >TEC
Med12l-206 >protein coding
Med12l-204 >protein coding
Med12l-202 >protein coding
Med12l-201 >protein coding
Contigs < AC115919.14 < AC122038.3 Genes < Gm43570-201lncRNA < Gpr171-201protein coding< P2ry14-204retained intron < P2ry13-201protein coding < Igsf10-201protein coding (Comprehensive set...
< P2ry14-206protein coding < Gpr87-203protein coding < Igsf10-203protein coding
< P2ry14-203protein coding < Gpr87-202retained intron < Igsf10-202protein coding
< P2ry14-201protein coding < Gpr87-201protein coding
< P2ry14-202protein coding < P2ry12-203protein coding
< P2ry14-205protein coding < P2ry12-201protein coding
< P2ry14-208protein coding < P2ry12-202protein coding
< P2ry14-207protein coding < P2ry12-204protein coding
< P2ry14-209protein coding < P2ry12-205protein coding
Regulatory Build
59.0Mb 59.1Mb 59.2Mb 59.3Mb Reverse strand 332.86 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript RNA gene
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Transcript: ENSMUST00000199659
312.20 kb Forward strand
Med12l-206 >protein coding
ENSMUSP00000142... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) SMART Mediator complex, subunit Med12
Pfam Mediator complex, subunit Med12, LCEWAV-domain Mediator complex, subunit Med12, catenin-binding
Mediator complex, subunit Med12 PANTHER PTHR46007
PTHR46007:SF3
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
inframe deletion missense variant splice region variant synonymous variant
Scale bar 0 200 400 600 800 1000 1200 1400 1600 1800 2185
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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