https://www.alphaknockout.com
Mouse Rabgap1 Knockout Project (CRISPR/Cas9)
Objective: To create a Rabgap1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Rabgap1 gene (NCBI Reference Sequence: NM_146121 ; Ensembl: ENSMUSG00000035437 ) is located on Mouse chromosome 2. 26 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 26 (Transcript: ENSMUST00000061179). Exon 2~5 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 2~5 covers 23.5% of the coding region. The size of effective KO region: ~6090 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 26
Legends Exon of mouse Rabgap1 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. 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 Exon 5 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(28.0% 560) | C(17.25% 345) | T(36.05% 721) | G(18.7% 374)
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(23.2% 464) | C(22.5% 450) | T(34.15% 683) | G(20.15% 403)
Note: The 2000 bp section downstream of Exon 5 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 + 37467428 37469427 2000 browser details YourSeq 102 780 1295 2000 74.9% chr6 - 134607591 134608062 472 browser details YourSeq 101 710 874 2000 80.2% chr12 - 51881590 51881737 148 browser details YourSeq 94 620 869 2000 89.8% chr2 + 181329469 181329739 271 browser details YourSeq 88 735 874 2000 82.3% chr15 + 84660836 84660975 140 browser details YourSeq 87 35 177 2000 94.0% chr9 - 37149800 37150115 316 browser details YourSeq 84 779 1086 2000 79.4% chr11 + 19032410 19032639 230 browser details YourSeq 83 631 869 2000 89.6% chr9 + 58293114 58293352 239 browser details YourSeq 83 779 1202 2000 92.8% chr1 + 161045850 161180416 134567 browser details YourSeq 75 25 117 2000 90.4% chr11 + 81155702 81155794 93 browser details YourSeq 74 24 119 2000 84.4% chr19 - 6326461 6326543 83 browser details YourSeq 74 551 874 2000 74.5% chr16 + 41816244 41816398 155 browser details YourSeq 73 779 869 2000 91.9% chr7 + 123138502 123138592 91 browser details YourSeq 72 782 874 2000 91.6% chr11 - 52297043 52297134 92 browser details YourSeq 71 631 866 2000 91.9% chr15 - 12105916 12200999 95084 browser details YourSeq 71 780 1197 2000 87.4% chr11 + 6423874 6424296 423 browser details YourSeq 70 35 118 2000 91.7% chr8 - 77629782 77629865 84 browser details YourSeq 70 779 874 2000 91.3% chr15 - 62100318 62100412 95 browser details YourSeq 70 27 108 2000 92.7% chr3 + 72850289 72850370 82 browser details YourSeq 69 779 868 2000 94.9% chr13 - 38830041 38830344 304
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% chr2 + 37475468 37477467 2000 browser details YourSeq 950 612 1988 2000 87.1% chr18 + 11662799 11664186 1388 browser details YourSeq 906 614 1993 2000 86.7% chr15 + 25259012 25260415 1404 browser details YourSeq 896 685 1990 2000 86.5% chr4 - 147817398 147818701 1304 browser details YourSeq 891 629 1989 2000 88.0% chr18 - 5129625 5130987 1363 browser details YourSeq 889 623 1990 2000 86.1% chr7 + 130924547 130925937 1391 browser details YourSeq 870 635 1989 2000 86.1% chr3 + 82750577 82751944 1368 browser details YourSeq 864 648 1990 2000 87.7% chr16 + 33642921 33644296 1376 browser details YourSeq 851 588 1990 2000 87.0% chr3 - 116709251 116710654 1404 browser details YourSeq 851 618 1990 2000 88.0% chr9 + 77861652 77863043 1392 browser details YourSeq 850 615 1990 2000 85.8% chr14 + 73807594 73808999 1406 browser details YourSeq 849 616 1990 2000 85.6% chr1 + 95371549 95372948 1400 browser details YourSeq 845 633 1990 2000 88.0% chr10 - 74872765 74874121 1357 browser details YourSeq 844 690 1990 2000 86.3% chr8 - 82290260 82291580 1321 browser details YourSeq 844 612 1986 2000 86.8% chr6 - 43112414 43113799 1386 browser details YourSeq 841 619 1990 2000 85.1% chr14 + 9406624 9408025 1402 browser details YourSeq 840 614 1990 2000 87.5% chr7 - 46695191 46696576 1386 browser details YourSeq 834 607 1925 2000 87.9% chr3 + 135716185 135717522 1338 browser details YourSeq 833 619 1980 2000 86.6% chr19 - 32421396 32422765 1370 browser details YourSeq 831 614 1990 2000 86.9% chr6 + 140859315 140860719 1405
Note: The 2000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Rabgap1 RAB GTPase activating protein 1 [ Mus musculus (house mouse) ] Gene ID: 227800, updated on 14-Aug-2019
Gene summary
Official Symbol Rabgap1 provided by MGI Official Full Name RAB GTPase activating protein 1 provided by MGI Primary source MGI:MGI:2385139 See related Ensembl:ENSMUSG00000035437 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 Gapcena; mKIAA4104 Expression Ubiquitous expression in CNS E14 (RPKM 5.5), CNS E18 (RPKM 5.5) and 26 other tissues See more Orthologs human all
Genomic context
Location: 2; 2 B See Rabgap1 in Genome Data Viewer Exon count: 28
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (37443263..37573420)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (37298805..37421957)
Chromosome 2 - NC_000068.7
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Transcript information: This gene has 10 transcripts
Gene: Rabgap1 ENSMUSG00000035437
Description RAB GTPase activating protein 1 [Source:MGI Symbol;Acc:MGI:2385139] Gene Synonyms Gapcena Location Chromosome 2: 37,443,279-37,566,454 forward strand. GRCm38:CM000995.2 About this gene This gene has 10 transcripts (splice variants), 203 orthologues, 32 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Rabgap1- ENSMUST00000061179.11 4967 1064aa ENSMUSP00000061624.5 Protein CCDS16002 A2AWA9 TSL:1 201 coding B2RRC5 GENCODE basic APPRIS P1
Rabgap1- ENSMUST00000112920.1 4847 1064aa ENSMUSP00000108542.1 Protein CCDS16002 A2AWA9 TSL:5 203 coding B2RRC5 GENCODE basic APPRIS P1
Rabgap1- ENSMUST00000066055.9 4247 809aa ENSMUSP00000068835.3 Protein CCDS16003 A2AWA9 TSL:1 202 coding GENCODE basic
Rabgap1- ENSMUST00000133434.7 1594 455aa ENSMUSP00000121963.1 Protein - A2AWA7 CDS 3' 205 coding incomplete TSL:5
Rabgap1- ENSMUST00000148470.7 615 147aa ENSMUSP00000119831.1 Protein - A2AWB0 CDS 3' 206 coding incomplete TSL:3
Rabgap1- ENSMUST00000205186.1 3082 No - Retained - - TSL:NA 210 protein intron
Rabgap1- ENSMUST00000153145.7 1746 No - Retained - - TSL:1 207 protein intron
Rabgap1- ENSMUST00000203470.1 2153 No - lncRNA - - TSL:NA 209 protein
Rabgap1- ENSMUST00000159092.1 1763 No - lncRNA - - TSL:5 208 protein
Rabgap1- ENSMUST00000130601.1 629 No - lncRNA - - TSL:3 204 protein
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143.18 kb Forward strand
37.44Mb 37.46Mb 37.48Mb 37.50Mb 37.52Mb 37.54Mb 37.56Mb Genes (Comprehensive set... Rabgap1-205 >protein coding Gpr21-202 >lncRNA
Rabgap1-201 >protein coding
Rabgap1-207 >retained intron Gm17893-201 >processed pseudogReanbegap1-208 >lncRNA
Rabgap1-209 >lncRNA Rabgap1-210 >retained intron Gpr21-201 >protein coding
Rabgap1-202 >protein coding
Rabgap1-206 >protein coding Rabgap1-204 >lncRNA
Rabgap1-203 >protein coding
Contigs AL953890.7 > Genes < Zbtb6-202protein coding < Strbp-207nonsense mediated decay (Comprehensive set...
< Zbtb26-201protein coding < Strbp-201protein coding
< Zbtb26-202protein coding < Strbp-208lncRNA
< Zbtb26-203lncRNA
Regulatory Build
37.44Mb 37.46Mb 37.48Mb 37.50Mb 37.52Mb 37.54Mb 37.56Mb Reverse strand 143.18 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript RNA gene pseudogene
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Transcript: ENSMUST00000061179
123.15 kb Forward strand
Rabgap1-201 >protein coding
ENSMUSP00000061... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SSF50729 Rab-GTPase-TBC domain superfamily
SMART PTB/PI domain Rab-GTPase-TBC domain
Pfam PTB/PI domain Rab-GTPase-TBC domain
Kinesin-like PROSITE profiles PTB/PI domain Rab-GTPase-TBC domain
PANTHER PTHR22957
Rab GTPase-activating protein 1 Gene3D PH-like domain superfamily 1.10.8.270 1.10.472.80
1.10.10.750 CDD cd01211
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 100 200 300 400 500 600 700 800 900 1064
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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