Human Gene ZDHHC9 (ENST00000357166.11) from GENCODE V44
  Description: Homo sapiens zinc finger DHHC-type palmitoyltransferase 9 (ZDHHC9), transcript variant 1, mRNA. (from RefSeq NM_016032)
RefSeq Summary (NM_016032): This gene encodes an integral membrane protein that is a member of the zinc finger DHHC domain-containing protein family. The encoded protein forms a complex with golgin subfamily A member 7 and functions as a palmitoyltransferase. This protein specifically palmitoylates HRAS and NRAS. Mutations in this gene are associated with X-linked cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, May 2010].
Gencode Transcript: ENST00000357166.11
Gencode Gene: ENSG00000188706.13
Transcript (Including UTRs)
   Position: hg38 chrX:129,803,288-129,843,886 Size: 40,599 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chrX:129,806,370-129,841,945 Size: 35,576 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:129,803,288-129,843,886)mRNA (may differ from genome)Protein (364 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZDHC9_HUMAN
DESCRIPTION: RecName: Full=Palmitoyltransferase ZDHHC9; EC=2.3.1.-; AltName: Full=Zinc finger DHHC domain-containing protein 9; Short=DHHC-9; Short=DHHC9; AltName: Full=Zinc finger protein 379; AltName: Full=Zinc finger protein 380;
FUNCTION: The ZDHHC9-GOLGA7 complex is a palmitoyltransferase specific for HRAS and NRAS.
CATALYTIC ACTIVITY: Palmitoyl-CoA + protein-cysteine = S-palmitoyl protein + CoA.
SUBUNIT: Interacts with GOLGA7.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Highly expressed in kidney, skeletal muscle, brain, lung and liver. Absent in thymus, spleen and leukocytes.
DOMAIN: The DHHC domain is required for palmitoyltransferase activity.
DISEASE: Defects in ZDHHC9 are the cause of mental retardation syndromic X-linked ZDHHC9-related (MRXSZ) [MIM:300799]. A disorder characterized by significantly sub-average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. Some patients have marfanoid habitus as an additional feature.
SIMILARITY: Belongs to the DHHC palmitoyltransferase family. ERF2/ZDHHC9 subfamily.
SIMILARITY: Contains 1 DHHC-type zinc finger.
SEQUENCE CAUTION: Sequence=AAD34084.1; Type=Erroneous initiation; Sequence=BAA91683.1; Type=Erroneous initiation; Sequence=BAD93044.1; Type=Erroneous initiation; Sequence=CAB82308.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ZDHHC9
Diseases sorted by gene-association score: mental retardation, x-linked syndromic, raymond type* (1300), lujan-fryns syndrome (11), fryns syndrome (10), benign epilepsy with centrotemporal spikes (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.81 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 446.08 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -158.70394-0.403 Picture PostScript Text
3' UTR -980.903082-0.318 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001594 - Znf_DHHC_palmitoyltrfase

Pfam Domains:
PF01529 - DHHC palmitoyltransferase

ModBase Predicted Comparative 3D Structure on Q9Y397
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0016409 palmitoyltransferase activity
GO:0016740 transferase activity
GO:0016746 transferase activity, transferring acyl groups
GO:0019706 protein-cysteine S-palmitoyltransferase activity
GO:0043849 Ras palmitoyltransferase activity

Biological Process:
GO:0018230 peptidyl-L-cysteine S-palmitoylation
GO:0018345 protein palmitoylation

Cellular Component:
GO:0000139 Golgi membrane
GO:0002178 palmitoyltransferase complex
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031228 intrinsic component of Golgi membrane


-  Descriptions from all associated GenBank mRNAs
  LF211467 - JP 2014500723-A/18970: Polycomb-Associated Non-Coding RNAs.
MA447044 - JP 2018138019-A/18970: Polycomb-Associated Non-Coding RNAs.
JD021216 - Sequence 2240 from Patent EP1572962.
JD028721 - Sequence 9745 from Patent EP1572962.
JD035957 - Sequence 16981 from Patent EP1572962.
LF379989 - JP 2014500723-A/187492: Polycomb-Associated Non-Coding RNAs.
MA615566 - JP 2018138019-A/187492: Polycomb-Associated Non-Coding RNAs.
JD019055 - Sequence 79 from Patent EP1572962.
JD033571 - Sequence 14595 from Patent EP1572962.
JD031395 - Sequence 12419 from Patent EP1572962.
JD021133 - Sequence 2157 from Patent EP1572962.
JD033336 - Sequence 14360 from Patent EP1572962.
JD028543 - Sequence 9567 from Patent EP1572962.
LF211468 - JP 2014500723-A/18971: Polycomb-Associated Non-Coding RNAs.
MA447045 - JP 2018138019-A/18971: Polycomb-Associated Non-Coding RNAs.
AY952881 - Homo sapiens antigen MMSA-1 mRNA, complete cds.
AY358558 - Homo sapiens clone DNA39975 ZDHHC9 (UNQ261) mRNA, complete cds.
AK001424 - Homo sapiens cDNA FLJ10562 fis, clone NT2RP2002701.
AL161962 - Homo sapiens mRNA; cDNA DKFZp761E1347 (from clone DKFZp761E1347); partial cds.
BC000035 - Homo sapiens zinc finger, DHHC-type containing 9, mRNA (cDNA clone MGC:845 IMAGE:3506601), complete cds.
BC006200 - Homo sapiens zinc finger, DHHC-type containing 9, mRNA (cDNA clone MGC:2823 IMAGE:2964425), complete cds.
BC012826 - Homo sapiens zinc finger, DHHC-type containing 9, mRNA (cDNA clone MGC:4496 IMAGE:2964425), complete cds.
BC003128 - Homo sapiens zinc finger, DHHC-type containing 9, mRNA (cDNA clone MGC:3355 IMAGE:2957911), complete cds.
AB209807 - Homo sapiens mRNA for zinc finger, DHHC domain containing 9 variant protein.
AK096967 - Homo sapiens cDNA FLJ39648 fis, clone SMINT2004891, highly similar to Palmitoyltransferase ZDHHC9 (EC 2.3.1.-).
AK001112 - Homo sapiens cDNA FLJ10250 fis, clone HEMBB1000763, highly similar to Palmitoyltransferase ZDHHC9 (EC 2.3.1.-).
AK001524 - Homo sapiens cDNA FLJ10662 fis, clone NT2RP2006141.
LF379990 - JP 2014500723-A/187493: Polycomb-Associated Non-Coding RNAs.
MA615567 - JP 2018138019-A/187493: Polycomb-Associated Non-Coding RNAs.
LF379991 - JP 2014500723-A/187494: Polycomb-Associated Non-Coding RNAs.
MA615568 - JP 2018138019-A/187494: Polycomb-Associated Non-Coding RNAs.
AF151847 - Homo sapiens CGI-89 protein mRNA, complete cds.
JD020510 - Sequence 1534 from Patent EP1572962.
JD035913 - Sequence 16937 from Patent EP1572962.
JD492105 - Sequence 473129 from Patent EP1572962.
JD322424 - Sequence 303448 from Patent EP1572962.
JD078926 - Sequence 59950 from Patent EP1572962.
LF379992 - JP 2014500723-A/187495: Polycomb-Associated Non-Coding RNAs.
MA615569 - JP 2018138019-A/187495: Polycomb-Associated Non-Coding RNAs.
EU831584 - Synthetic construct Homo sapiens clone HAIB:100066613; DKFZo007A0319 zinc finger, DHHC-type containing 9 protein (ZDHHC9) gene, encodes complete protein.
EU831669 - Synthetic construct Homo sapiens clone HAIB:100066698; DKFZo003A0320 zinc finger, DHHC-type containing 9 protein (ZDHHC9) gene, encodes complete protein.
KJ893819 - Synthetic construct Homo sapiens clone ccsbBroadEn_03213 ZDHHC9 gene, encodes complete protein.
KR709805 - Synthetic construct Homo sapiens clone CCSBHm_00006216 ZDHHC9 (ZDHHC9) mRNA, encodes complete protein.
KR709806 - Synthetic construct Homo sapiens clone CCSBHm_00006217 ZDHHC9 (ZDHHC9) mRNA, encodes complete protein.
LF379997 - JP 2014500723-A/187500: Polycomb-Associated Non-Coding RNAs.
MA615574 - JP 2018138019-A/187500: Polycomb-Associated Non-Coding RNAs.
LF379998 - JP 2014500723-A/187501: Polycomb-Associated Non-Coding RNAs.
MA615575 - JP 2018138019-A/187501: Polycomb-Associated Non-Coding RNAs.
LF380001 - JP 2014500723-A/187504: Polycomb-Associated Non-Coding RNAs.
MA615578 - JP 2018138019-A/187504: Polycomb-Associated Non-Coding RNAs.
LF380002 - JP 2014500723-A/187505: Polycomb-Associated Non-Coding RNAs.
MA615579 - JP 2018138019-A/187505: Polycomb-Associated Non-Coding RNAs.
LF380004 - JP 2014500723-A/187507: Polycomb-Associated Non-Coding RNAs.
MA615581 - JP 2018138019-A/187507: Polycomb-Associated Non-Coding RNAs.
JD024713 - Sequence 5737 from Patent EP1572962.
JD030359 - Sequence 11383 from Patent EP1572962.
JD029660 - Sequence 10684 from Patent EP1572962.
JD336733 - Sequence 317757 from Patent EP1572962.
JD407734 - Sequence 388758 from Patent EP1572962.
JD499959 - Sequence 480983 from Patent EP1572962.
JD232027 - Sequence 213051 from Patent EP1572962.
JD393291 - Sequence 374315 from Patent EP1572962.
JD027706 - Sequence 8730 from Patent EP1572962.
JD020636 - Sequence 1660 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4F6G2, CGI-89, CXorf11, D3DTF9, ENST00000357166.1, ENST00000357166.10, ENST00000357166.2, ENST00000357166.3, ENST00000357166.4, ENST00000357166.5, ENST00000357166.6, ENST00000357166.7, ENST00000357166.8, ENST00000357166.9, NM_016032, Q59EK4, Q5JSW5, Q8WWS7, Q9BPY4, Q9NSP0, Q9NVL0, Q9NVR6, Q9Y397, uc004euw.1, uc004euw.2, uc004euw.3, uc004euw.4, uc004euw.5, UNQ261/PRO298, ZDHC9_HUMAN, ZDHHC10, ZNF379, ZNF380
UCSC ID: ENST00000357166.11
RefSeq Accession: NM_016032
Protein: Q9Y397 (aka ZDHC9_HUMAN or ZDH9_HUMAN)
CCDS: CCDS35395.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.