https://www.alphaknockout.com
Mouse Mbnl2 Knockout Project (CRISPR/Cas9)
Objective: To create a Mbnl2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Mbnl2 gene (NCBI Reference Sequence: NM_175341 ; Ensembl: ENSMUSG00000022139 ) is located on Mouse chromosome 14. 9 exons are identified, with the ATG start codon in exon 2 and the TAA stop codon in exon 9 (Transcript: ENSMUST00000088419). Exon 2 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: Mice homozygous for one gene trap exhibit myotonia, lordosis and altered skeletal muscle fiber morphology.
Exon 2 starts from the coding region. Exon 2 covers 15.55% of the coding region. The size of effective KO region: ~619 bp. The KO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele gRNA region 5' gRNA region 3'
1 2 9
Legends Exon of mouse Mbnl2 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 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(27.2% 544) | C(22.45% 449) | T(30.5% 610) | G(19.85% 397)
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(30.35% 607) | C(21.7% 434) | T(27.55% 551) | G(20.4% 408)
Note: The 2000 bp section downstream 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.
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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% chr14 + 120323240 120325239 2000 browser details YourSeq 80 419 548 2000 81.9% chr10 + 121507861 121507988 128 browser details YourSeq 70 227 557 2000 68.2% chr7 - 79760940 79761111 172 browser details YourSeq 68 446 543 2000 86.5% chr5 - 120734444 120734542 99 browser details YourSeq 61 442 615 2000 67.7% chr2 + 33916516 33916625 110 browser details YourSeq 59 429 530 2000 92.9% chrX - 5780774 5781022 249 browser details YourSeq 59 430 534 2000 82.4% chr9 - 120117179 120117274 96 browser details YourSeq 59 429 516 2000 78.8% chr11 - 62486654 62486734 81 browser details YourSeq 58 1160 1223 2000 96.8% chr17 + 58425175 58425243 69 browser details YourSeq 57 446 544 2000 86.2% chr12 + 90730660 90730757 98 browser details YourSeq 56 444 534 2000 91.2% chr5 - 136543355 136543445 91 browser details YourSeq 54 443 531 2000 83.8% chr11 - 105086496 105086585 90 browser details YourSeq 54 442 532 2000 83.8% chr11 + 72711432 72711523 92 browser details YourSeq 53 443 516 2000 87.4% chr9 - 56810179 56810253 75 browser details YourSeq 53 1160 1223 2000 87.1% chr12 - 54584202 54584263 62 browser details YourSeq 53 447 554 2000 93.6% chr12 + 85758704 85758813 110 browser details YourSeq 52 443 563 2000 85.8% chr2 - 172607289 172607402 114 browser details YourSeq 52 441 556 2000 86.2% chr19 - 9043706 9043822 117 browser details YourSeq 52 1153 1216 2000 89.7% chr6 + 111249875 111249937 63 browser details YourSeq 51 1158 1222 2000 94.8% chr5 + 115955788 115955865 78
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% chr14 + 120325414 120327413 2000 browser details YourSeq 156 1321 1601 2000 94.4% chr1 + 121111305 121111652 348 browser details YourSeq 140 1234 1648 2000 85.9% chr1 + 164707894 164708249 356 browser details YourSeq 138 1347 1648 2000 87.5% chr1 + 23721492 23721967 476 browser details YourSeq 124 1429 1597 2000 94.3% chr10 + 24151177 24151396 220 browser details YourSeq 122 1351 1648 2000 87.7% chr11 + 80920181 80920473 293 browser details YourSeq 119 1347 1586 2000 95.0% chr1 - 172392788 172393156 369 browser details YourSeq 118 1437 1648 2000 94.2% chr10 + 9049698 9049930 233 browser details YourSeq 110 1429 1618 2000 91.3% chr18 + 5432904 5433120 217 browser details YourSeq 110 1347 1594 2000 94.4% chr10 + 108317005 108317314 310 browser details YourSeq 107 1433 1640 2000 85.4% chr13 + 97739424 97739597 174 browser details YourSeq 105 1339 1619 2000 90.1% chr15 - 40344497 40344795 299 browser details YourSeq 100 1356 1571 2000 92.4% chr14 - 58296295 58296990 696 browser details YourSeq 98 1347 1600 2000 83.7% chr17 - 67097587 67097771 185 browser details YourSeq 97 1350 1624 2000 84.0% chr17 - 9277656 9277868 213 browser details YourSeq 97 1347 1646 2000 93.0% chr1 - 120080998 120081591 594 browser details YourSeq 97 1316 1642 2000 94.7% chr15 + 73495913 73496266 354 browser details YourSeq 96 1392 1640 2000 81.5% chr18 + 5171374 5171552 179 browser details YourSeq 95 1321 1640 2000 94.6% chr17 - 12598030 12598391 362 browser details YourSeq 92 1352 1549 2000 91.7% chr16 + 95670245 95873635 203391
Note: The 2000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Mbnl2 muscleblind like splicing factor 2 [ Mus musculus (house mouse) ] Gene ID: 105559, updated on 24-Oct-2019
Gene summary
Official Symbol Mbnl2 provided by MGI Official Full Name muscleblind like splicing factor 2 provided by MGI Primary source MGI:MGI:2145597 See related Ensembl:ENSMUSG00000022139 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 MBLL; R75232; AI047808; AI837313; AI849185; AL118326; mKIAA4072; 1110002M11Rik Expression Ubiquitous expression in bladder adult (RPKM 30.1), cerebellum adult (RPKM 20.2) and 28 other tissues See more Orthologs human all
Genomic context
Location: 14; 14 E4 See Mbnl2 in Genome Data Viewer Exon count: 11
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (120275652..120431698)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 14 NC_000080.5 (120674891..120830920)
Chromosome 14 - NC_000080.6
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Transcript information: This gene has 10 transcripts
Gene: Mbnl2 ENSMUSG00000022139
Description muscleblind like splicing factor 2 [Source:MGI Symbol;Acc:MGI:2145597] Gene Synonyms 1110002M11Rik Location Chromosome 14: 120,275,669-120,431,697 forward strand. GRCm38:CM001007.2 About this gene This gene has 10 transcripts (splice variants), 255 orthologues, 3 paralogues, is a member of 1 Ensembl protein family and is associated with 18 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Mbnl2- ENSMUST00000088419.12 4552 373aa ENSMUSP00000085763.6 Protein coding CCDS49567 Q8C181 TSL:1 201 GENCODE basic APPRIS P4
Mbnl2- ENSMUST00000226800.1 3328 355aa ENSMUSP00000154734.1 Protein coding CCDS49568 Q8C181 GENCODE basic 203 APPRIS ALT1
Mbnl2- ENSMUST00000227012.1 2390 355aa ENSMUSP00000153973.1 Protein coding CCDS49568 Q8C181 GENCODE basic 204 APPRIS ALT1
Mbnl2- ENSMUST00000227594.1 2334 373aa ENSMUSP00000154559.1 Protein coding CCDS49567 Q8C181 GENCODE basic 208 APPRIS P4
Mbnl2- ENSMUST00000167459.2 4534 385aa ENSMUSP00000126186.2 Protein coding - A0A2K6EDM5 TSL:1 202 GENCODE basic APPRIS ALT1
Mbnl2- ENSMUST00000228115.1 758 253aa ENSMUSP00000154652.1 Protein coding - A0A2I3BRX8 CDS 5' and 3' 210 incomplete
Mbnl2- ENSMUST00000227484.1 5561 No - Retained - - - 206 protein intron
Mbnl2- ENSMUST00000227508.1 3789 No - Retained - - - 207 protein intron
Mbnl2- ENSMUST00000227153.1 2881 No - lncRNA - - - 205 protein
Mbnl2- ENSMUST00000227644.1 339 No - lncRNA - - - 209 protein
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176.03 kb Forward strand 120.30Mb 120.35Mb 120.40Mb Genes (Comprehensive set... Mbnl2-201 >protein coding
Mbnl2-204 >protein coding
Mbnl2-206 >retained intron Mbnl2-205 >lncRNA
Mbnl2-202 >protein coding
Mbnl2-207 >retained intron Mbnl2-210 >protein coding
Mbnl2-203 >protein coding
Mbnl2-208 >protein coding
Mbnl2-209 >lncRNA
Contigs AC154811.2 > CT009559.20 >
Genes < Gm26679-201lncRNA (Comprehensive set...
Regulatory Build
120.30Mb 120.35Mb 120.40Mb Reverse strand 176.03 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
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Transcript: ENSMUST00000088419
156.03 kb Forward strand
Mbnl2-201 >protein coding
ENSMUSP00000085... Low complexity (Seg) SMART Zinc finger, CCCH-type Pfam Zinc finger, CCCH-type PROSITE profiles Zinc finger, CCCH-type PANTHER PTHR12675
PTHR12675:SF4 Gene3D 1.10.150.840
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 40 80 120 160 200 240 280 320 373
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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