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EZ-editor™ Gene Knockout Cell Line Strategy

Tpm1 Gene Knockout Strategy

EZ-editor™ technology (CRISPR based), developed by Ubigene, is more efficient than general CRISPR/Cas9 technology in double-strand breaking and homologous recombination. With EZ-editor™, Ubigene has successfully edited over 10000 genes on more than 500 types of cell lines.
Objective
To create a Human Tpm1 Knockout model in cell line by EZ-editor™-mediated genome engineering.
Target gene info
Official symbol
Tpm1
Gene id
24851
Organism
Rattus norvegicus
Gene type
protein-coding
Official full symbol
tropomyosin 1
Also known as
Alpha-tm, Tma2, Tmsa
Genomic regions
Chromosome 8
Summary
This gene is a member of the tropomyosin family and encodes a protein that heterodimerizes with a beta subunit, binding actin in both muscle and nonmuscle cells. In both smooth and striated muscle cells, it plays a role in calcium dependent-regulation of muscle contraction. In nonmuscle cells, it stabilizes cytoskeleton actin filaments. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.
Strategy Summary
This gene has 28 protein coding transcripts：
Transcript Length(nt) Protein Length(aa) Protein name Transcript type Transcript name ccds
XM_063264927 3072 XP_063120997 281 tropomyosin alpha-1 chain 3 transcript variant X6
XM_006243390 1899 XP_006243452 284 tropomyosin alpha-1 chain 3 transcript variant X2
XM_063264926 2995 XP_063120996 281 tropomyosin alpha-1 chain 3 transcript variant X5
XM_063264928 2995 XP_063120998 281 tropomyosin alpha-1 chain 3 transcript variant X7
XM_063264930 2025 XP_063121000 326 tropomyosin alpha-1 chain 3 transcript variant X11
NM_001034069 1740 NP_001029241 284 tropomyosin alpha-1 chain 3 transcript variant Tpm1.6
NM_001034070 1740 NP_001029242 284 tropomyosin alpha-1 chain 3 transcript variant Tpm1.7
NM_001034071 1740 NP_001029243 284 tropomyosin alpha-1 chain 3 transcript variant Tpm1.3
XM_006243395 2860 XP_006243457 245 tropomyosin alpha-1 chain 3 transcript variant X10
NM_001034073 1677 NP_001029245 248 tropomyosin alpha-1 chain 3 transcript variant Tpm1.8
NM_001034074 1677 NP_001029246 248 tropomyosin alpha-1 chain 3 transcript variant Tpm1.9
NM_001034072 1261 NP_001029244 281 tropomyosin alpha-1 chain 3 transcript variant Tpm1.10
NM_001301736 1188 NP_001288665 245 tropomyosin alpha-1 chain 3 transcript variant Tpm1.12
NM_001034068 1166 NP_001029240 287 tropomyosin alpha-1 chain 3 transcript variant 1
NM_001301336 1235 NP_001288265 284 tropomyosin alpha-1 chain 3 transcript variant Tpm1.1
NM_001301342 1251 NP_001288271 284 tropomyosin alpha-1 chain 3 transcript variant Tpm1.2
XM_063264935 1190 XP_063121005 251 tropomyosin alpha-1 chain 3 transcript variant X16
NM_019131 1103 NP_062004 251 tropomyosin alpha-1 chain 3 transcript variant Tpm1.11
NM_001034075 1182 NP_001029247 248 tropomyosin alpha-1 chain 3 transcript variant Tpm1.13
XM_063264933 1320 XP_063121003 287 tropomyosin alpha-1 chain 3 transcript variant X14
XM_008766207 1399 XP_008764429 284 tropomyosin alpha-1 chain 3 transcript variant X1
XM_063264934 1243 XP_063121004 287 tropomyosin alpha-1 chain 3 transcript variant X15
XM_063264924 1322 XP_063120994 284 tropomyosin alpha-1 chain 3 transcript variant X3
XM_063264929 1187 XP_063120999 248 tropomyosin alpha-1 chain 3 transcript variant X8
XM_063264932 2062 XP_063121002 326 tropomyosin alpha-1 chain 3 transcript variant X13
XM_006243393 1801 XP_006243455 248 tropomyosin alpha-1 chain 3 transcript variant X9
XM_063264925 1130 XP_063120995 284 tropomyosin alpha-1 chain 3 transcript variant X4
XM_063264931 1256 XP_063121001 326 tropomyosin alpha-1 chain 3 transcript variant X12
Frame-shift
Fragment A
Fragment B
Strategy

Project Comprehensive Difficulty Assessment

According to the Red Cotton database: the CRISPR gene-editing strategy design is Unknown.
Knockout project comprehensive difficulty is thus assessed as Unknown.
Red Cotton™ Notes Gene Tpm1 had been KO in hela cell line.
EZ-editor™ Gene Dependency
EZ-editor™ Gene Expression Level
EZ-editor™ Gene Copy Number

EZ-editor™ Gene Dependency

Result

The Tpm1 gene you inquire is evaluated as high risk in 0% cell line. Cell line is not selected, unable to assess the accurate risk level, for reference only.

Gene lethality score

Dependent Cell Lines Gene Dependency 0 0.5 1

Lethality score of Tpm1 in different cells

0.0%>0.5
All cells
0
Non-essential gene
0.5
Boundary score
1
Essential gene
More details

EZ-editor™ Gene Expression Level

Result

In all cell lines, there is 0.1% cells with expression level below cutoff, 9.9% cells with low expression level, 78.8% cells with medium expression level, 11.1% cells with high expression level of Tpm1 gene. Cell line is not selected, unable to assess the accurate expression level, for reference only.

Gene Expression

Cell Lines Frequency log2(TPM+1) 0 2 4 6 8 10 12

TPM of Tpm1 in different cells

0.1%9.9%78.8%11.1%
All cells
0~0.5
Below cutoff
0.5~10
Low
10~1000
Medium
>1000
High
More details

EZ-editor™ Gene Copy Number

Result

In all cell lines, there is 64.9% cells with low copy number, 31.5% cells with medium copy number, 3.6% cells with high copy number of Tpm1 gene. Cell line is not selected, unable to assess the accurate copy number, for reference only.

Gene Copy Number

Copy number 0 1 2 3 4 5 6 7 0 100 200 300 400 500 600Cell Lines

Copy number of Tpm1 in different cells

64.9%31.5%3.6%
All cells
0~2
Low
2~4
Medium
>4
High
More details
Work flow
Ubigene Red Cotton Workflow

Ubigene - Make genome editing easier

Ubigene is an international high-technology enterprise focused on gene-editing cells. Our exclusive EZ-editor™ technology has 10-20 times more efficient editing than traditional methods, easily achieving gene knockout, point mutation, and knock-in. Based on EZ-editor™ technology, Ubigene has accumulated over 6000 successful gene-editing cases from more than 300 cell lines including iPSC and ESC, and has established a KO Cell Line Bank with 5000+ KO cell lines and Red Cotton™ gRNA Plasmid Bank with 10000+ gRNA plasmids available in stock.

Ubigene focuses on technological innovation and product development, of which EZ-editor™ series products that cover the whole workflow of gene-editing keep improving. Ubigene will move on toward our goal of "Make genome editing easier" and we won't stop!

Cell products

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红棉系统新技能上线啦！基因风险评估：“火眼金睛”辨基因，致死风险一秒知。评估结果可在Red Cotton Assessment模块查看哦。

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