https://www.alphaknockout.com
Mouse Srxn1 Knockout Project (CRISPR/Cas9)
Objective: To create a Srxn1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Srxn1 gene (NCBI Reference Sequence: NM_029688 ; Ensembl: ENSMUSG00000032802 ) is located on Mouse chromosome 2. 2 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 2 (Transcript: ENSMUST00000041500). Exon 1~2 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 a knock-out allele exhibit increased sensitivity to LPS-induced shock.
Exon 1 starts from about 0.22% of the coding region. Exon 1~2 covers 100.0% of the coding region. The size of effective KO region: ~3506 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
Legends Exon of mouse Srxn1 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(23.95% 479) | C(23.8% 476) | T(24.8% 496) | G(27.45% 549)
Note: The 2000 bp section upstream of start codon is analyzed to determine the GC content. Significant high GC-content regions are found. The gRNA site is selected outside of these high GC-content regions.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(24.35% 487) | C(24.85% 497) | T(25.7% 514) | G(25.1% 502)
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% chr2 + 152103685 152105684 2000 browser details YourSeq 336 359 985 2000 88.3% chr6 + 37778589 37779322 734 browser details YourSeq 331 428 976 2000 88.9% chr18 + 74413778 74414530 753 browser details YourSeq 326 374 1034 2000 83.5% chr14 - 54105524 54106041 518 browser details YourSeq 314 374 942 2000 85.7% chr4 - 143331416 143332207 792 browser details YourSeq 309 359 1034 2000 88.9% chr10 - 53681943 53719288 37346 browser details YourSeq 289 495 983 2000 87.0% chrX - 105045391 105046104 714 browser details YourSeq 288 380 1034 2000 86.6% chr17 + 41531738 41760710 228973 browser details YourSeq 286 380 948 2000 86.3% chr17 - 7859336 7860135 800 browser details YourSeq 286 335 1033 2000 82.1% chr8 + 45415823 45416347 525 browser details YourSeq 283 374 1034 2000 81.8% chr13 + 49404001 49404535 535 browser details YourSeq 281 312 756 2000 85.0% chr8 - 95049691 95050299 609 browser details YourSeq 281 358 1034 2000 81.3% chr13 - 64564857 64565388 532 browser details YourSeq 280 358 781 2000 85.9% chr7 + 99860137 99860593 457 browser details YourSeq 278 401 1034 2000 83.3% chr8 - 85474822 85475286 465 browser details YourSeq 276 343 1034 2000 80.6% chrX + 121039515 121040045 531 browser details YourSeq 275 382 770 2000 87.4% chr11 + 17917444 17917827 384 browser details YourSeq 274 359 795 2000 88.8% chr7 + 127157465 127157927 463 browser details YourSeq 269 374 1034 2000 84.6% chr9 + 22268868 22269329 462 browser details YourSeq 268 374 1035 2000 85.9% chr6 - 35578712 35579182 471
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% chr2 + 152109191 152111190 2000 browser details YourSeq 1131 30 1941 2000 88.5% chr18 + 14308808 14310560 1753 browser details YourSeq 94 1251 1395 2000 85.8% chr10 - 110722278 110722415 138 browser details YourSeq 90 1255 1392 2000 84.0% chr2 - 157441092 157441221 130 browser details YourSeq 89 1254 1390 2000 86.7% chr11 - 62435912 62436044 133 browser details YourSeq 88 1254 1390 2000 85.2% chr11 + 5594323 5594455 133 browser details YourSeq 88 1249 1390 2000 84.7% chr10 + 63525364 63525496 133 browser details YourSeq 85 1261 1390 2000 86.3% chr11 - 49688019 49688143 125 browser details YourSeq 84 1260 1382 2000 88.3% chr1 + 8005107 8005225 119 browser details YourSeq 82 1249 1390 2000 84.3% chr12 - 54604807 54604935 129 browser details YourSeq 81 1254 1390 2000 82.7% chr9 + 111877270 111877397 128 browser details YourSeq 80 1260 1381 2000 91.5% chr18 + 38234256 38234378 123 browser details YourSeq 80 1260 1381 2000 87.8% chr11 + 72743545 72743662 118 browser details YourSeq 79 1265 1381 2000 87.7% chr2 + 120363065 120363177 113 browser details YourSeq 75 1249 1390 2000 91.2% chr11 - 87971427 87971577 151 browser details YourSeq 75 1245 1354 2000 90.5% chr10 - 50863460 50863569 110 browser details YourSeq 73 1260 1381 2000 84.7% chr1 - 191942946 191943064 119 browser details YourSeq 73 1254 1380 2000 82.4% chr11 + 97710475 97710588 114 browser details YourSeq 71 1249 1339 2000 87.9% chr18 - 77753721 77753808 88 browser details YourSeq 71 1280 1381 2000 88.1% chr2 + 34801887 34801986 100
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: Srxn1 sulfiredoxin 1 homolog (S. cerevisiae) [ Mus musculus (house mouse) ] Gene ID: 76650, updated on 12-Aug-2019
Gene summary
Official Symbol Srxn1 provided by MGI Official Full Name sulfiredoxin 1 homolog (S. cerevisiae) provided by MGI Primary source MGI:MGI:104971 See related Ensembl:ENSMUSG00000032802 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 Srx; Npn3; Srx1; TX01; AI854065; AW488194; 1700127B04Rik Expression Broad expression in duodenum adult (RPKM 100.0), adrenal adult (RPKM 95.3) and 21 other tissues See more Orthologs human all
Genomic context
Location: 2; 2 G3 See Srxn1 in Genome Data Viewer Exon count: 2
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (152105524..152111376)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (151931466..151937089)
Chromosome 2 - NC_000068.7
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Transcript information: This gene has 3 transcripts
Gene: Srxn1 ENSMUSG00000032802
Description sulfiredoxin 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:104971] Gene Synonyms 1700127B04Rik, Npn3, Srx, Srx1 Location Chromosome 2: 152,105,516-152,111,376 forward strand. GRCm38:CM000995.2 About this gene This gene has 3 transcripts (splice variants), 174 orthologues, is a member of 1 Ensembl protein family and is associated with 4 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Srxn1-201 ENSMUST00000041500.7 2812 155aa ENSMUSP00000046196.7 Protein coding CCDS16877 A2AQU8 TSL:1 GENCODE basic APPRIS P1
Srxn1-203 ENSMUST00000137751.1 446 No protein - lncRNA - - TSL:2
Srxn1-202 ENSMUST00000128882.1 375 No protein - lncRNA - - TSL:3
25.86 kb Forward strand 152.10Mb 152.11Mb 152.12Mb Genes (Comprehensive set... Scrt2-201 >protein coding Srxn1-202 >lncRNA
Srxn1-203 >lncRNA
Srxn1-201 >protein coding
Contigs AL845161.5 > Regulatory Build
152.10Mb 152.11Mb 152.12Mb Reverse strand 25.86 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana
Non-Protein Coding
RNA gene
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Transcript: ENSMUST00000041500
5.85 kb Forward strand
Srxn1-201 >protein coding
ENSMUSP00000046... Low complexity (Seg) Superfamily ParB/Sulfiredoxin superfamily
SMART ParB/Sulfiredoxin Pfam ParB/Sulfiredoxin
PIRSF Sulfiredoxin
PANTHER Sulfiredoxin
PTHR21348:SF2 Gene3D 3.90.1530.10
CDD cd16395
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
synonymous variant
Scale bar 0 20 40 60 80 100 120 155
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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