https://www.alphaknockout.com
Mouse Rfc3 Knockout Project (CRISPR/Cas9)
Objective: To create a Rfc3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Rfc3 gene (NCBI Reference Sequence: NM_027009 ; Ensembl: ENSMUSG00000033970 ) is located on Mouse chromosome 5. 9 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 9 (Transcript: ENSMUST00000038131). Exon 1~9 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 1 starts from about 0.09% of the coding region. Exon 1~9 covers 100.0% of the coding region. The size of effective KO region: ~8236 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 7 8 9
Legends Exon of mouse Rfc3 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. 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 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(27.25% 545) | C(20.95% 419) | T(29.15% 583) | G(22.65% 453)
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(23.65% 473) | C(27.4% 548) | T(28.1% 562) | G(20.85% 417)
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% chr5 - 151651153 151653152 2000 browser details YourSeq 215 200 518 2000 85.3% chr7 + 46073016 46073333 318 browser details YourSeq 206 227 526 2000 84.6% chr15 - 79558653 79558945 293 browser details YourSeq 198 221 520 2000 87.0% chr12 + 7857862 7858163 302 browser details YourSeq 193 221 526 2000 82.5% chr13 - 9007803 9008107 305 browser details YourSeq 192 208 526 2000 85.8% chr4 - 125956367 125956690 324 browser details YourSeq 189 212 526 2000 90.0% chr14 - 62675946 62676279 334 browser details YourSeq 188 211 478 2000 85.9% chr13 - 107059006 107059274 269 browser details YourSeq 186 274 526 2000 87.5% chr10 - 59922421 60324695 402275 browser details YourSeq 185 244 519 2000 83.9% chr15 - 74475831 74476105 275 browser details YourSeq 185 227 526 2000 83.6% chr2 + 28235829 28236126 298 browser details YourSeq 184 212 526 2000 86.1% chr15 + 8504456 8504786 331 browser details YourSeq 182 227 526 2000 86.2% chr15 + 76316711 76317028 318 browser details YourSeq 181 228 521 2000 88.8% chr14 + 73725109 73725418 310 browser details YourSeq 178 244 520 2000 83.1% chr1 - 156817254 156817528 275 browser details YourSeq 178 245 526 2000 83.4% chr8 + 31086437 31086715 279 browser details YourSeq 178 230 501 2000 84.5% chr3 + 62439093 62439365 273 browser details YourSeq 178 207 526 2000 87.8% chr17 + 88210035 88210353 319 browser details YourSeq 178 207 520 2000 83.6% chr11 + 32387116 32387425 310 browser details YourSeq 177 237 526 2000 83.0% chr18 + 83819819 83820112 294
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% chr5 - 151640915 151642914 2000 browser details YourSeq 466 235 1219 2000 87.4% chr1 - 75910349 75911343 995 browser details YourSeq 442 244 1185 2000 91.3% chr4 - 127455878 127456870 993 browser details YourSeq 440 232 1177 2000 87.9% chr10 - 57204128 57205825 1698 browser details YourSeq 438 244 887 2000 88.3% chr5 + 133930891 133931589 699 browser details YourSeq 407 234 897 2000 89.3% chrX + 160911369 160912076 708 browser details YourSeq 406 232 895 2000 91.5% chr1 + 40570585 40571480 896 browser details YourSeq 403 234 1116 2000 89.3% chr8 + 67379532 67380537 1006 browser details YourSeq 400 239 804 2000 88.2% chr9 + 51479426 51480128 703 browser details YourSeq 395 234 823 2000 90.5% chr5 - 27250239 27268345 18107 browser details YourSeq 389 234 910 2000 88.7% chr16 + 20088653 20089364 712 browser details YourSeq 387 234 1170 2000 88.0% chr4 - 115580126 115581060 935 browser details YourSeq 385 233 931 2000 86.4% chr3 - 20607996 20608761 766 browser details YourSeq 380 234 796 2000 88.8% chr1 + 10933242 10933907 666 browser details YourSeq 379 234 765 2000 88.2% chr13 + 14658143 14658736 594 browser details YourSeq 376 232 820 2000 87.7% chr4 - 32547578 32548191 614 browser details YourSeq 373 228 918 2000 85.8% chr10 + 104327896 104328636 741 browser details YourSeq 372 234 1186 2000 88.6% chr13 + 112013868 112014801 934 browser details YourSeq 370 287 846 2000 86.1% chr11 - 47610304 47610955 652 browser details YourSeq 368 238 948 2000 87.8% chr7 - 29671012 29671705 694
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: Rfc3 replication factor C (activator 1) 3 [ Mus musculus (house mouse) ] Gene ID: 69263, updated on 12-Aug-2019
Gene summary
Official Symbol Rfc3 provided by MGI Official Full Name replication factor C (activator 1) 3 provided by MGI Primary source MGI:MGI:1916513 See related Ensembl:ENSMUSG00000033970 Gene type protein coding RefSeq status PROVISIONAL Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as 38kDa; Recc3; AU022547; 2810416I22Rik Expression Broad expression in CNS E11.5 (RPKM 28.7), liver E14 (RPKM 20.7) and 26 other tissues See more Orthologs human all
Genomic context
Location: 5; 5 G3 See Rfc3 in Genome Data Viewer Exon count: 10
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (151642817..151651208, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (152445399..152453783, complement)
Chromosome 5 - NC_000071.6
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Transcript information: This gene has 7 transcripts
Gene: Rfc3 ENSMUSG00000033970
Description replication factor C (activator 1) 3 [Source:MGI Symbol;Acc:MGI:1916513] Gene Synonyms 2810416I22Rik, 38kDa, Recc3 Location Chromosome 5: 151,642,756-151,651,242 reverse strand. GRCm38:CM000998.2 About this gene This gene has 7 transcripts (splice variants), 199 orthologues, 3 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Rfc3-201 ENSMUST00000038131.9 1317 356aa ENSMUSP00000039621.9 Protein coding CCDS39413 Q3TKD1 Q8R323 TSL:1 GENCODE basic APPRIS P1
Rfc3-206 ENSMUST00000145106.7 2726 No protein - Retained intron - - TSL:1
Rfc3-205 ENSMUST00000140067.7 1062 No protein - Retained intron - - TSL:1
Rfc3-203 ENSMUST00000132709.1 906 No protein - Retained intron - - TSL:1
Rfc3-202 ENSMUST00000127366.1 706 No protein - Retained intron - - TSL:2
Rfc3-204 ENSMUST00000136752.1 605 No protein - Retained intron - - TSL:2
Rfc3-207 ENSMUST00000156667.1 503 No protein - Retained intron - - TSL:2
28.49 kb Forward strand 151.64Mb 151.65Mb 151.66Mb Genes AC120011.1-201 >unprocessed pseudogene (Comprehensive set...
Contigs < AC120011.16 Genes (Comprehensive set... < Rfc3-201protein coding
< Rfc3-202retained intron < Rfc3-203retained intron
< Rfc3-207retained intron < Rfc3-204retained intron
< Rfc3-206retained intron
< Rfc3-205retained intron
Regulatory Build
151.64Mb 151.65Mb 151.66Mb Reverse strand 28.49 kb
Regulation Legend CTCF Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana
Non-Protein Coding
pseudogene processed transcript
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Transcript: ENSMUST00000038131
< Rfc3-201protein coding
Reverse strand 8.49 kb
ENSMUSP00000039... Superfamily P-loop containing nucleoside triphosphate hydrolase DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal
SMART AAA+ ATPase domain Pfam PF13177 PANTHER PTHR11669
PTHR11669:SF1 Gene3D 3.40.50.300 1.10.8.60 1.20.272.10
CDD cd00009 cd18140
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 40 80 120 160 200 240 280 356
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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