https://www.alphaknockout.com
Mouse Pnma2 Knockout Project (CRISPR/Cas9)
Objective: To create a Pnma2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Pnma2 gene (NCBI Reference Sequence: NM_175498 ; Ensembl: ENSMUSG00000046204 ) is located on Mouse chromosome 14. 3 exons are identified, with the ATG start codon in exon 3 and the TGA stop codon in exon 3 (Transcript: ENSMUST00000089236). Exon 3 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 0.09% of the coding region. Exon 3 covers 100.0% of the coding region. The size of effective KO region: ~1095 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
Legends Exon of mouse Pnma2 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. 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(25.05% 501) | C(23.1% 462) | T(27.55% 551) | G(24.3% 486)
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(22.55% 451) | T(29.3% 586) | G(20.05% 401)
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% chr14 + 66914130 66916129 2000 browser details YourSeq 125 180 493 2000 79.9% chr11 - 99358329 99358671 343 browser details YourSeq 111 146 425 2000 85.2% chr19 - 10131325 10131602 278 browser details YourSeq 106 149 469 2000 93.0% chr6 + 106847217 106847618 402 browser details YourSeq 106 147 447 2000 88.6% chr2 + 57989830 57990152 323 browser details YourSeq 105 149 448 2000 79.3% chr1 + 157885109 157885423 315 browser details YourSeq 102 147 447 2000 78.1% chr2 + 36153971 36154239 269 browser details YourSeq 99 156 421 2000 83.7% chr6 + 134393693 134393972 280 browser details YourSeq 97 146 447 2000 77.9% chr4 + 89176311 89176522 212 browser details YourSeq 93 146 433 2000 88.0% chr12 - 108130250 108130558 309 browser details YourSeq 93 147 430 2000 84.1% chr17 + 12099964 12100267 304 browser details YourSeq 91 146 447 2000 81.4% chr7 - 109882336 109882648 313 browser details YourSeq 91 149 442 2000 84.4% chr4 - 101626834 101627121 288 browser details YourSeq 91 151 430 2000 86.9% chr7 + 114838217 114838523 307 browser details YourSeq 90 183 430 2000 86.3% chr13 + 44367099 44367360 262 browser details YourSeq 89 179 414 2000 89.4% chrX - 151773810 151774176 367 browser details YourSeq 89 180 406 2000 80.7% chr3 + 89693724 89694071 348 browser details YourSeq 89 147 430 2000 86.8% chr1 + 33824144 33824465 322 browser details YourSeq 84 162 447 2000 89.7% chr8 - 125480819 125481114 296 browser details YourSeq 84 178 427 2000 82.9% chr1 - 178730875 178731152 278
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% chr14 + 66917225 66919224 2000 browser details YourSeq 85 448 641 2000 92.1% chr10 + 95006445 95006697 253 browser details YourSeq 67 1107 1203 2000 84.6% chr2 - 180527081 180527177 97 browser details YourSeq 62 529 659 2000 78.6% chr6 - 135001085 135001206 122 browser details YourSeq 59 545 638 2000 90.6% chr12 - 99073068 99073171 104 browser details YourSeq 57 454 724 2000 94.1% chr11 + 100602295 100602871 577 browser details YourSeq 55 458 641 2000 90.8% chr19 - 25213889 25214071 183 browser details YourSeq 54 1108 1198 2000 80.0% chrX - 101951731 101951822 92 browser details YourSeq 54 568 1459 2000 91.0% chr1 + 170039579 170342017 302439 browser details YourSeq 52 553 640 2000 87.2% chr11 + 40514768 40514863 96 browser details YourSeq 45 1099 1166 2000 84.7% chr12 - 95814235 95814306 72 browser details YourSeq 44 553 653 2000 90.8% chr19 - 38106500 38106612 113 browser details YourSeq 43 1146 1217 2000 80.3% chr7 - 144088269 144088341 73 browser details YourSeq 43 613 667 2000 94.0% chr5 - 115957275 115957336 62 browser details YourSeq 43 1138 1192 2000 89.1% chr1 + 88666276 88666330 55 browser details YourSeq 43 518 637 2000 93.8% chr1 + 62426170 62426304 135 browser details YourSeq 42 568 656 2000 93.8% chr13 - 99893202 99893297 96 browser details YourSeq 41 1130 1192 2000 82.6% chr5 + 126017375 126017437 63 browser details YourSeq 39 1428 1479 2000 93.4% chr18 + 74717685 74717766 82 browser details YourSeq 39 567 652 2000 97.6% chr13 + 95483507 95483592 86
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: Pnma2 paraneoplastic antigen MA2 [ Mus musculus (house mouse) ] Gene ID: 239157, updated on 12-Aug-2019
Gene summary
Official Symbol Pnma2 provided by MGI Official Full Name paraneoplastic antigen MA2 provided by MGI Primary source MGI:MGI:2444129 See related Ensembl:ENSMUSG00000046204 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 mKIAA0883; A830049P17Rik Expression Biased expression in CNS E18 (RPKM 4.3), cortex adult (RPKM 3.8) and 6 other tissues See more Orthologs human all
Genomic context
Location: 14; 14 D1 See Pnma2 in Genome Data Viewer Exon count: 5
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (66901589..66920063)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 14 NC_000080.5 (67530045..67538898)
Chromosome 14 - NC_000080.6
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Transcript information: This gene has 4 transcripts
Gene: Pnma2 ENSMUSG00000046204
Description paraneoplastic antigen MA2 [Source:MGI Symbol;Acc:MGI:2444129] Gene Synonyms A830049P17Rik Location Chromosome 14: 66,911,170-66,921,023 forward strand. GRCm38:CM001007.2 About this gene This gene has 4 transcripts (splice variants), 296 orthologues, 12 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Pnma2-201 ENSMUST00000089236.10 5518 365aa ENSMUSP00000086646.3 Protein coding CCDS27226 Q8BHK0 TSL:1 GENCODE basic APPRIS P1
Pnma2-202 ENSMUST00000122431.2 3143 365aa ENSMUSP00000112629.2 Protein coding CCDS27226 Q8BHK0 TSL:1 GENCODE basic APPRIS P1
Pnma2-203 ENSMUST00000165831.1 855 No protein - lncRNA - - TSL:3
Pnma2-204 ENSMUST00000168010.1 472 No protein - lncRNA - - TSL:3
29.85 kb Forward strand 66.91Mb 66.92Mb 66.93Mb Genes (Comprehensive set... Pnma2-201 >protein coding
Pnma2-202 >protein coding
Pnma2-204 >lncRNA
Pnma2-203 >lncRNA
Contigs AC165148.2 > Regulatory Build
66.91Mb 66.92Mb 66.93Mb Reverse strand 29.85 kb
Regulation Legend CTCF Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
RNA gene
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Transcript: ENSMUST00000089236
9.85 kb Forward strand
Pnma2-201 >protein coding
ENSMUSP00000086... MobiDB lite Low complexity (Seg) Pfam Paraneoplastic antigen Ma PANTHER Paraneoplastic antigen Ma2
Paraneoplastic antigen Ma
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend inframe deletion missense variant synonymous variant
Scale bar 0 40 80 120 160 200 240 280 320 365
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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