Human Gene ZACN (ENST00000334586.10) from GENCODE V44
  Description: Homo sapiens zinc activated ion channel (ZACN), mRNA. (from RefSeq NM_180990)
RefSeq Summary (NM_180990): LGICZ1 is a zinc-activated ligand-gated ion channel that defines a new subgroup of the cysteine-loop superfamily of ligand-gated ion channels (Davies et al., 2003 [PubMed 12381728]).[supplied by OMIM, Mar 2008].
Gencode Transcript: ENST00000334586.10
Gencode Gene: ENSG00000186919.13
Transcript (Including UTRs)
   Position: hg38 chr17:76,079,182-76,082,806 Size: 3,625 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr17:76,079,265-76,082,653 Size: 3,389 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:76,079,182-76,082,806)mRNA (may differ from genome)Protein (412 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZACN_HUMAN
DESCRIPTION: RecName: Full=Zinc-activated ligand-gated ion channel; AltName: Full=Ligand-gated ion channel zinc-activated 1; AltName: Full=Ligand-gated ion-channel receptor L2; Flags: Precursor;
FUNCTION: Zinc-activated ligand-gated ion channel.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Detected in pancreas, brain, liver, placenta, trachea, kidney, spinal cord, stomach and fetal brain. In the adult brain region expression is detected in the hippocampus, striatum, amygdala and thalamus.
PTM: Glycosylated.
MISCELLANEOUS: The mouse and rat orthologous proteins do not exist.
SIMILARITY: Belongs to the ligand-gated ion channel (TC 1.A.9) family.
CAUTION: It is uncertain whether Met-1 or Met-2 is the initiator.
SEQUENCE CAUTION: Sequence=AAI10598.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAO20969.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=EAW89365.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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


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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.70 RPKM in Colon - Sigmoid
Total median expression: 1.44 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 -29.2083-0.352 Picture PostScript Text
3' UTR -47.50153-0.310 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
IPR006202 - Neur_chan_lig-bd
IPR006201 - Neur_channel
IPR006029 - Neurotrans-gated_channel_TM
IPR018000 - Neurotransmitter_ion_chnl_CS

Pfam Domains:
PF02931 - Neurotransmitter-gated ion-channel ligand binding domain

ModBase Predicted Comparative 3D Structure on Q401N2
FrontTopSide
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005216 ion channel activity
GO:0005230 extracellular ligand-gated ion channel activity
GO:0008270 zinc ion binding
GO:0015276 ligand-gated ion channel activity
GO:0022850 serotonin-gated cation channel activity

Biological Process:
GO:0006811 ion transport
GO:0007165 signal transduction
GO:0007210 serotonin receptor signaling pathway
GO:0010043 response to zinc ion
GO:0034220 ion transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK122638 - Homo sapiens cDNA FLJ16063 fis, clone THYMU2027497.
JD074531 - Sequence 55555 from Patent EP1572962.
AF512521 - Homo sapiens ligand-gated ion channel subunit (LGICZ) mRNA, complete cds.
BC110596 - Homo sapiens zinc activated ligand-gated ion channel, mRNA (cDNA clone IMAGE:40023954).
BC110597 - Homo sapiens zinc activated ligand-gated ion channel, mRNA (cDNA clone MGC:129841 IMAGE:40023955), complete cds.
KJ901091 - Synthetic construct Homo sapiens clone ccsbBroadEn_10485 ZACN gene, encodes complete protein.
AB223030 - Homo sapiens LGICZ mRNA for ligand-gated ion-channel receptor L2, complete cds.
BC075850 - Homo sapiens cDNA clone IMAGE:6087213, with apparent retained intron.
CU677224 - Synthetic construct Homo sapiens gateway clone IMAGE:100016850 3' read EXOC7 mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000334586.1, ENST00000334586.2, ENST00000334586.3, ENST00000334586.4, ENST00000334586.5, ENST00000334586.6, ENST00000334586.7, ENST00000334586.8, ENST00000334586.9, L2, LGICZ, LGICZ1, NM_180990, Q2TB29, Q401N2, Q6ZWK3, Q86YW4, uc002jqn.1, uc002jqn.2, uc002jqn.3, uc002jqn.4, ZAC, ZACN_HUMAN
UCSC ID: ENST00000334586.10
RefSeq Accession: NM_180990
Protein: Q401N2 (aka ZACN_HUMAN)
CCDS: CCDS11740.2

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