https://www.alphaknockout.com
Mouse Rab11fip2 Knockout Project (CRISPR/Cas9)
Objective: To create a Rab11fip2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Rab11fip2 gene (NCBI Reference Sequence: NM_001164367 ; Ensembl: ENSMUSG00000040022 ) is located on Mouse chromosome 19. 5 exons are identified, with the ATG start codon in exon 2 and the TAG stop codon in exon 5 (Transcript: ENSMUST00000171986). 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:
Exon 2 starts from the coding region. Exon 2 covers 33.33% of the coding region. The size of effective KO region: ~443 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 5
Legends Exon of mouse Rab11fip2 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 913 bp section downstream 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(28.25% 565) | C(17.65% 353) | T(36.35% 727) | G(17.75% 355)
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(913bp) | A(29.24% 267) | C(18.18% 166) | T(31.65% 289) | G(20.92% 191)
Note: The 913 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% chr19 - 59937358 59939357 2000 browser details YourSeq 27 338 373 2000 93.6% chr2 + 24845660 24845712 53
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 913 1 913 913 100.0% chr19 - 59936075 59936987 913 browser details YourSeq 55 361 498 913 85.6% chr4 + 150207744 150207881 138 browser details YourSeq 52 277 503 913 80.7% chr16 - 14274491 14274706 216 browser details YourSeq 48 277 505 913 69.3% chr15 - 99290813 99290981 169 browser details YourSeq 47 359 462 913 94.5% chr17 + 80167067 80167172 106 browser details YourSeq 44 277 506 913 92.4% chr2 + 4825988 4826218 231 browser details YourSeq 43 393 503 913 83.1% chr19 + 54991959 54992069 111 browser details YourSeq 42 395 506 913 68.8% chr14 - 63406348 63406459 112 browser details YourSeq 42 360 502 913 70.7% chr3 + 27383040 27383163 124 browser details YourSeq 37 358 524 913 95.2% chr12 - 109939633 109939829 197 browser details YourSeq 34 464 505 913 89.5% chr12 + 78161401 78161441 41 browser details YourSeq 33 443 504 913 97.3% chr1 - 120010400 120010464 65 browser details YourSeq 32 321 370 913 92.2% chr7 - 100436598 100436655 58 browser details YourSeq 32 360 503 913 69.6% chr4 - 8895221 8895355 135 browser details YourSeq 32 443 501 913 91.5% chr2 - 168976617 168976674 58 browser details YourSeq 32 360 505 913 97.1% chr11 - 101933771 101933918 148 browser details YourSeq 32 277 452 913 92.2% chr5 + 142594689 142594892 204 browser details YourSeq 31 272 310 913 89.8% chr13 - 73947383 73947421 39 browser details YourSeq 31 275 309 913 94.3% chr9 + 47882968 47883002 35 browser details YourSeq 31 454 506 913 75.6% chr1 + 123108528 123108577 50
Note: The 913 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: Rab11fip2 RAB11 family interacting protein 2 (class I) [ Mus musculus (house mouse) ] Gene ID: 74998, updated on 12-Aug-2019
Gene summary
Official Symbol Rab11fip2 provided by MGI Official Full Name RAB11 family interacting protein 2 (class I) provided by MGI Primary source MGI:MGI:1922248 See related Ensembl:ENSMUSG00000040022 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 Nrip11; AW558126; 4930470G04Rik; A830046J09Rik Expression Broad expression in cortex adult (RPKM 5.3), CNS E18 (RPKM 5.1) and 25 other tissues See more Orthologs human all
Genomic context
Location: 19; 19 D3 See Rab11fip2 in Genome Data Viewer Exon count: 8
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (59893502..59943656, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 19 NC_000085.5 (59978787..60019557, complement)
Chromosome 19 - NC_000085.6
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Transcript information: This gene has 3 transcripts
Gene: Rab11fip2 ENSMUSG00000040022
Description RAB11 family interacting protein 2 (class I) [Source:MGI Symbol;Acc:MGI:1922248] Gene Synonyms 4930470G04Rik, A830046J09Rik, Rab11-FIP2, nRip11 Location Chromosome 19: 59,902,884-59,943,654 reverse strand. GRCm38:CM001012.2 About this gene This gene has 3 transcripts (splice variants), 197 orthologues, 2 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Rab11fip2-203 ENSMUST00000171986.7 5363 370aa ENSMUSP00000128813.1 Protein coding CCDS50482 G3UW57 TSL:1 GENCODE basic
Rab11fip2-201 ENSMUST00000051996.12 4482 529aa ENSMUSP00000059978.6 Protein coding CCDS38033 G3XA57 TSL:1 GENCODE basic
Rab11fip2-202 ENSMUST00000170819.1 1539 512aa ENSMUSP00000133151.1 Protein coding - G3XA57 TSL:5 GENCODE basic APPRIS P1
60.77 kb Forward strand 59.90Mb 59.91Mb 59.92Mb 59.93Mb 59.94Mb 59.95Mb Genes Gm4219-201 >lncRNA (Comprehensive set...