https://www.alphaknockout.com
Mouse Gltp Knockout Project (CRISPR/Cas9)
Objective: To create a Gltp knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Gltp gene (NCBI Reference Sequence: NM_019821 ; Ensembl: ENSMUSG00000011884 ) is located on Mouse chromosome 5. 5 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 5 (Transcript: ENSMUST00000012028). Exon 2~4 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 about 16.59% of the coding region. Exon 2~4 covers 54.86% of the coding region. The size of effective KO region: ~3626 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
Legends Exon of mouse Gltp 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 2000 bp section downstream of Exon 4 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(21.95% 439) | C(28.7% 574) | T(21.65% 433) | G(27.7% 554)
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(19.05% 381) | C(21.7% 434) | T(28.3% 566) | G(30.95% 619)
Note: The 2000 bp section downstream of Exon 4 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.
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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 - 114677680 114679679 2000 browser details YourSeq 42 702 781 2000 87.5% chr5 - 131179873 131179950 78 browser details YourSeq 39 697 778 2000 88.4% chr5 - 106209272 106209351 80 browser details YourSeq 38 695 758 2000 97.6% chr7 + 44365845 44366205 361 browser details YourSeq 33 702 778 2000 68.5% chr1 + 45961981 45962056 76 browser details YourSeq 32 394 437 2000 97.1% chr17 + 65775784 65776059 276 browser details YourSeq 32 699 758 2000 91.2% chr1 + 17049104 17049162 59 browser details YourSeq 31 689 723 2000 88.3% chr8 + 82810263 82810296 34 browser details YourSeq 31 701 792 2000 97.0% chr17 + 84030634 84030726 93 browser details YourSeq 30 679 719 2000 96.9% chr9 - 123375074 123375118 45 browser details YourSeq 30 698 732 2000 87.5% chr10 - 61795015 61795047 33 browser details YourSeq 30 703 774 2000 85.8% chr1 + 174880834 174880906 73 browser details YourSeq 28 679 721 2000 69.0% chr8 - 105236736 105236764 29 browser details YourSeq 28 699 730 2000 87.1% chr5 - 128633398 128633428 31 browser details YourSeq 27 697 725 2000 89.3% chr1 - 151317959 151317986 28 browser details YourSeq 25 702 732 2000 89.3% chr1 + 10077016 10077045 30 browser details YourSeq 24 1225 1253 2000 93.2% chr7 + 115405861 115405891 31 browser details YourSeq 23 697 719 2000 100.0% chr9 - 119791794 119791816 23 browser details YourSeq 23 391 413 2000 100.0% chr5 + 119569121 119569143 23 browser details YourSeq 23 381 408 2000 96.0% chr5 + 114712511 114712539 29
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% chr5 - 114672054 114674053 2000 browser details YourSeq 681 1308 2000 2000 99.3% chr5 - 114671778 114672535 758 browser details YourSeq 678 1308 2000 2000 99.2% chr5 - 114671504 114672405 902 browser details YourSeq 675 1308 2000 2000 98.9% chr5 - 114671573 114672474 902 browser details YourSeq 595 1329 2000 2000 97.4% chr5 - 114671916 114672526 611 browser details YourSeq 545 1308 1992 2000 98.8% chr5 - 114671102 114672198 1097 browser details YourSeq 528 1321 1861 2000 98.9% chr5 - 114671642 114672396 755 browser details YourSeq 476 1450 2000 2000 96.1% chr5 - 114672261 114672746 486 browser details YourSeq 465 1308 1786 2000 99.0% chr5 - 114671302 114672129 828 browser details YourSeq 458 1308 1781 2000 98.6% chr5 - 114671516 114672060 545 browser details YourSeq 404 1308 1723 2000 99.1% chr5 - 114671364 114671991 628 browser details YourSeq 393 1308 1717 2000 98.3% chr5 - 114671302 114671922 621 browser details YourSeq 390 1381 2000 2000 99.5% chr5 - 114671985 114672746 762 browser details YourSeq 350 1580 2000 2000 97.8% chr5 - 114672330 114672746 417 browser details YourSeq 344 1354 1717 2000 98.1% chr5 - 114671438 114671811 374 browser details YourSeq 310 1536 1999 2000 99.1% chr5 - 114671642 114672173 532 browser details YourSeq 83 1571 1777 2000 87.1% chr6 - 116093328 116093687 360 browser details YourSeq 79 1441 1639 2000 85.8% chr6 - 116093328 116093687 360 browser details YourSeq 75 1468 1639 2000 83.0% chr10 + 20143099 20143253 155 browser details YourSeq 74 1461 1647 2000 94.2% chr14 + 99116170 99116410 241
Note: The 2000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Gltp glycolipid transfer protein [ Mus musculus (house mouse) ] Gene ID: 56356, updated on 12-Aug-2019
Gene summary
Official Symbol Gltp provided by MGI Official Full Name glycolipid transfer protein provided by MGI Primary source MGI:MGI:1929253 See related Ensembl:ENSMUSG00000011884 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 C76925; C77564; 1110001F24Rik Expression Ubiquitous expression in stomach adult (RPKM 119.7), lung adult (RPKM 84.5) and 26 other tissues See more Orthologs human all
Genomic context
Location: 5; 5 F See Gltp in Genome Data Viewer Exon count: 5
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (114669490..114690935, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (115119499..115140944, complement)
Chromosome 5 - NC_000071.6
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Transcript information: This gene has 3 transcripts
Gene: Gltp ENSMUSG00000011884
Description glycolipid transfer protein [Source:MGI Symbol;Acc:MGI:1929253] Gene Synonyms 1110001F24Rik Location Chromosome 5: 114,669,398-114,690,984 reverse strand. GRCm38:CM000998.2 About this gene This gene has 3 transcripts (splice variants), 212 orthologues, 5 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Gltp-201 ENSMUST00000012028.13 1762 209aa ENSMUSP00000012028.7 Protein coding CCDS19569 Q9JL62 TSL:1 GENCODE basic APPRIS P1
Gltp-203 ENSMUST00000112214.7 944 179aa ENSMUSP00000107833.1 Protein coding - D3Z1H8 TSL:3 GENCODE basic
Gltp-202 ENSMUST00000112212.1 799 190aa ENSMUSP00000107831.1 Protein coding - D3Z1H9 TSL:5 GENCODE basic
41.59 kb Forward strand 114.66Mb 114.67Mb 114.68Mb 114.69Mb 114.70Mb Contigs < AC124228.16 AC087330.6 > Genes (Comprehensive set... < Gltp-201protein coding
< Gltp-203protein coding
< Gltp-202protein coding
Regulatory Build
114.66Mb 114.67Mb 114.68Mb 114.69Mb 114.70Mb Reverse strand 41.59 kb
Regulation Legend
CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
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Transcript: ENSMUST00000012028
< Gltp-201protein coding
Reverse strand 21.59 kb
ENSMUSP00000012... Superfamily Glycolipid transfer protein superfamily
Pfam Glycolipid transfer protein domain
PANTHER PTHR10219:SF74
PTHR10219 Gene3D Glycolipid transfer protein superfamily
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant synonymous variant
Scale bar 0 20 40 60 80 100 120 140 160 180 209
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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