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CRISPR-U™ Gene Knockout Cell Line Strategy

HDAC6 Gene Knockout Strategy

CRISPR-U™ technology (CRISPR based), developed by Ubigene, is more efficient than general CRISPR/Cas9 technology in double-strand breaking and homologous recombination. With CRISPR-U™, Ubigene has successfully edited over 3000 genes on more than 200 types of cell lines.
Objective
To create a Human HDAC6 Knockout model in cell line by CRISPR-U™-mediated genome engineering.
Target gene info
Official symbol
HDAC6
Gene id
10013
Organism
Homo sapiens
Gene type
protein-coding
Official full symbol
histone deacetylase 6
Also known as
CPBHM, HD6, JM21, PPP1R90
Genomic regions
Chromosome X
Summary
Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to class II of the histone deacetylase/acuc/apha family. It contains an internal duplication of two catalytic domains which appear to function independently of each other. This protein possesses histone deacetylase activity and represses transcription.
Strategy Summary
This gene has 26 protein coding transcripts:
Transcript ID Name bp Protein Biotype CCDS UniProt Match RefSeq Match Flags
ENST00000334136.11 HDAC6-201 4118 1215aa Protein coding CCDS14306 Q9UBN7-1 NM_006044.4 MANE Select, Ensembl Canonical, GENCODE basic, APPRIS P2, TSL:1,
ENST00000443563.6 HDAC6-210 4431 1215aa Protein coding CCDS14306 Q9UBN7-1 - GENCODE basic, APPRIS P2, TSL:4,
ENST00000376619.7 HDAC6-203 4197 1215aa Protein coding CCDS14306 Q9UBN7-1 - GENCODE basic, APPRIS P2, TSL:1,
ENST00000423941.6 HDAC6-205 4158 1215aa Protein coding CCDS14306 Q9UBN7-1 - GENCODE basic, APPRIS P2, TSL:4,
ENST00000644068.1 HDAC6-236 4147 1215aa Protein coding CCDS14306 Q9UBN7-1 - GENCODE basic, APPRIS P2,
ENST00000440653.2 HDAC6-208 4145 1215aa Protein coding CCDS14306 Q9UBN7-1 - GENCODE basic, APPRIS P2, TSL:4,
ENST00000643374.2 HDAC6-233 4110 1215aa Protein coding CCDS14306 Q9UBN7-1 - GENCODE basic, APPRIS P2,
ENST00000697349.1 HDAC6-256 4108 1211aa Protein coding A0A8V8TKY7 - GENCODE basic,
ENST00000376610.7 HDAC6-202 4107 1215aa Protein coding CCDS14306 Q9UBN7-1 - GENCODE basic, APPRIS P2, TSL:5,
ENST00000376643.7 HDAC6-204 4067 1215aa Protein coding CCDS14306 Q9UBN7-1 - GENCODE basic, APPRIS P2, TSL:5,
ENST00000469223.6 HDAC6-215 4061 1160aa Protein coding A0A2R8YDE6 - GENCODE basic, APPRIS ALT2, TSL:5,
ENST00000643934.1 HDAC6-235 3987 1160aa Protein coding A0A2R8YDE6 - GENCODE basic, APPRIS ALT2,
ENST00000697320.1 HDAC6-249 3985 1160aa Protein coding A0A2R8YDE6 - GENCODE basic, APPRIS ALT2,
ENST00000697368.1 HDAC6-257 3948 1166aa Protein coding A0A8V8TL08 - GENCODE basic,
ENST00000642405.2 HDAC6-232 3933 1192aa Protein coding A0A2R8Y559 - GENCODE basic,
ENST00000697328.1 HDAC6-251 3769 1108aa Protein coding A0A8V8TMA5 - GENCODE basic,
ENST00000477561.6 HDAC6-219 3662 1160aa Protein coding A0A2R8YDE6 - GENCODE basic, APPRIS ALT2, TSL:5,
ENST00000646703.2 HDAC6-239 2771 893aa Protein coding A0A2R8YCS4 - GENCODE basic,
ENST00000438518.6 HDAC6-207 2172 146aa Protein coding CCDS87740 Q9BRX7 - GENCODE basic, TSL:4,
ENST00000462730.5 HDAC6-212 1999 146aa Protein coding CCDS87740 Q9BRX7 - GENCODE basic, TSL:1,
ENST00000697348.1 HDAC6-255 1821 146aa Protein coding CCDS87740 Q9BRX7 - GENCODE basic,
ENST00000465269.6 HDAC6-213 1152 146aa Protein coding CCDS87740 Q9BRX7 - GENCODE basic, TSL:1,
ENST00000476625.5 HDAC6-217 967 91aa Protein coding A0A2R8Y5Z4 - GENCODE basic, TSL:3,
ENST00000461608.2 HDAC6-211 954 211aa Protein coding A0A2R8Y758 - GENCODE basic, TSL:2,
ENST00000441703.6 HDAC6-209 591 146aa Protein coding CCDS87740 Q9BRX7 - GENCODE basic, TSL:3,
ENST00000489352.5 HDAC6-228 585 91aa Protein coding A0A2R8Y5Z4 - GENCODE basic, TSL:4,
ENST00000647398.2 HDAC6-240 3926 146aa Nonsense mediated decay CCDS87740 Q9BRX7 - -
ENST00000697886.1 HDAC6-274 3903 701aa Nonsense mediated decay A0A8V8TLA9 - -
ENST00000498808.7 HDAC6-231 3450 921aa Nonsense mediated decay A0A8V8TM63 - TSL:5,
ENST00000480525.6 HDAC6-220 3305 669aa Nonsense mediated decay A0A2R8Y6Z9 - TSL:3,
ENST00000488543.2 HDAC6-226 5807 No protein Retained intron - - TSL:2,
ENST00000697347.1 HDAC6-254 5794 No protein Retained intron - - -
ENST00000697893.1 HDAC6-281 5373 No protein Retained intron - - -
ENST00000697417.2 HDAC6-267 5336 No protein Retained intron - - -
ENST00000697389.1 HDAC6-266 5266 No protein Retained intron - - -
ENST00000643659.1 HDAC6-234 5249 No protein Retained intron - - -
ENST00000697852.1 HDAC6-272 5151 No protein Retained intron - - -
ENST00000697385.1 HDAC6-262 5089 No protein Retained intron - - -
ENST00000697370.1 HDAC6-259 5079 No protein Retained intron - - -
ENST00000697373.1 HDAC6-261 5060 No protein Retained intron - - -
ENST00000697889.1 HDAC6-277 4949 No protein Retained intron - - -
ENST00000697388.1 HDAC6-265 4941 No protein Retained intron - - -
ENST00000477528.5 HDAC6-218 4832 No protein Retained intron - - TSL:1,
ENST00000697894.1 HDAC6-282 4779 No protein Retained intron - - -
ENST00000486227.5 HDAC6-224 4718 No protein Retained intron - - TSL:2,
ENST00000697281.1 HDAC6-247 4717 No protein Retained intron - - -
ENST00000697552.1 HDAC6-269 4673 No protein Retained intron - - -
ENST00000483656.6 HDAC6-222 4608 No protein Retained intron - - TSL:5,
ENST00000697892.1 HDAC6-280 4605 No protein Retained intron - - -
ENST00000697246.1 HDAC6-241 4601 No protein Retained intron - - -
ENST00000697372.1 HDAC6-260 4597 No protein Retained intron - - -
ENST00000697888.1 HDAC6-276 4573 No protein Retained intron - - -
ENST00000697895.1 HDAC6-283 4544 No protein Retained intron - - -
ENST00000697885.1 HDAC6-273 4476 No protein Retained intron - - -
ENST00000644164.2 HDAC6-237 4441 No protein Retained intron - - -
ENST00000697896.1 HDAC6-284 4436 No protein Retained intron - - -
ENST00000697553.1 HDAC6-270 4424 No protein Retained intron - - -
ENST00000645643.2 HDAC6-238 4415 No protein Retained intron - - -
ENST00000697387.1 HDAC6-264 4412 No protein Retained intron - - -
ENST00000697554.1 HDAC6-271 4407 No protein Retained intron - - -
ENST00000697891.1 HDAC6-279 4351 No protein Retained intron - - -
ENST00000697369.1 HDAC6-258 4295 No protein Retained intron - - -
ENST00000697418.1 HDAC6-268 4293 No protein Retained intron - - -
ENST00000697269.1 HDAC6-246 4241 No protein Retained intron - - -
ENST00000697887.1 HDAC6-275 4235 No protein Retained intron - - -
ENST00000697386.1 HDAC6-263 4175 No protein Retained intron - - -
ENST00000697890.1 HDAC6-278 4171 No protein Retained intron - - -
ENST00000486665.6 HDAC6-225 4044 No protein Retained intron - - TSL:2,
ENST00000697319.1 HDAC6-248 4043 No protein Retained intron - - -
ENST00000430858.2 HDAC6-206 3802 No protein Retained intron - - TSL:3,
ENST00000495515.2 HDAC6-230 3623 No protein Retained intron - - TSL:3,
ENST00000697345.1 HDAC6-252 3195 No protein Retained intron - - -
ENST00000697346.1 HDAC6-253 3186 No protein Retained intron - - -
ENST00000697267.1 HDAC6-244 2748 No protein Retained intron - - -
ENST00000697247.1 HDAC6-242 2647 No protein Retained intron - - -
ENST00000697266.1 HDAC6-243 2541 No protein Retained intron - - -
ENST00000483506.2 HDAC6-221 2376 No protein Retained intron - - TSL:4,
ENST00000697268.1 HDAC6-245 2178 No protein Retained intron - - -
ENST00000697322.1 HDAC6-250 1557 No protein Retained intron - - -
ENST00000489053.2 HDAC6-227 903 No protein Retained intron - - TSL:4,
ENST00000470942.1 HDAC6-216 668 No protein Retained intron - - TSL:3,
ENST00000485102.1 HDAC6-223 667 No protein Retained intron - - TSL:3,
ENST00000468949.1 HDAC6-214 572 No protein Retained intron - - TSL:4,
ENST00000493923.1 HDAC6-229 404 No protein Retained intron - - TSL:3,
Ubigene Red Cotton Transcript
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 HDAC6 had been KO in hela cell line.
EZ-editor™ Gene Dependency
EZ-editor™ Gene Expression Level

EZ-editor™ Gene Dependency

Result

The HDAC6 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 HDAC6 in different cells

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

EZ-editor™ Gene Expression Level

Result

In all cell lines, there is 4.8% cells with low expression level, 95.2% cells with medium expression level of HDAC6 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 HDAC6 in different cells

4.8%95.2%
All cells
0~0.5
Below cutoff
0.5~10
Low
10~1000
Medium
>1000
High
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 CRISPR-U™ technology has 10-20 times more efficient editing than traditional methods, easily achieving gene knockout, point mutation, and knock-in. Based on CRISPR-U™ technology, Ubigene has accumulated over 5000 successful gene-editing cases from more than 200 cell lines including iPSC and ESC, and has established a KO Cell Line Bank with 3500+ 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

温馨提示

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。