Human Gene SLC39A4 (uc003zcp.3)
  Description: Homo sapiens solute carrier family 39 (zinc transporter), member 4 (SLC39A4), transcript variant 1, mRNA.
RefSeq Summary (NM_017767): This gene encodes a member of the zinc/iron-regulated transporter-like protein (ZIP) family. The encoded protein localizes to cell membranes and is required for zinc uptake in the intestine. Mutations in this gene result in acrodermatitis enteropathica. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2013].
Transcript (Including UTRs)
   Position: hg19 chr8:145,637,798-145,641,917 Size: 4,120 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr8:145,637,922-145,641,592 Size: 3,671 Coding Exon Count: 11 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:145,637,798-145,641,917)mRNA (may differ from genome)Protein (622 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC39A4
CDC HuGE Published Literature: SLC39A4

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC39A4
Diseases sorted by gene-association score: acrodermatitis enteropathica* (1737), acrodermatitis (69), enteropathica (62), autosomal recessive disease (7), alopecia (6), metal metabolism disorder (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D015032 Zinc
  • D001564 Benzo(a)pyrene
  • C044387 N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C009505 4,4'-diaminodiphenylmethane
  • D000643 Ammonium Chloride
  • D019256 Cadmium Chloride
  • D002117 Calcitriol
  • D002185 Cannabidiol
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 52.61 RPKM in Small Intestine - Terminal Ileum
Total median expression: 211.11 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 -170.32325-0.524 Picture PostScript Text
3' UTR -13.20124-0.106 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
  Pfam Domains:
PF02535 - ZIP Zinc transporter

ModBase Predicted Comparative 3D Structure on Q6P5W5-2
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK056900 - Homo sapiens cDNA FLJ32338 fis, clone PROST2005919.
LF210336 - JP 2014500723-A/17839: Polycomb-Associated Non-Coding RNAs.
BC001688 - Homo sapiens solute carrier family 39 (zinc transporter), member 4, mRNA (cDNA clone IMAGE:2990059), partial cds.
AK000489 - Homo sapiens cDNA FLJ20482 fis, clone KAT07592.
BC033807 - Homo sapiens solute carrier family 39 (zinc transporter), member 4, mRNA (cDNA clone IMAGE:5185763), with apparent retained intron.
AK000334 - Homo sapiens cDNA FLJ20327 fis, clone HEP10012.
BC062625 - Homo sapiens solute carrier family 39 (zinc transporter), member 4, mRNA (cDNA clone MGC:74741 IMAGE:5203858), complete cds.
AK025537 - Homo sapiens cDNA: FLJ21884 fis, clone HEP02863.
AK290563 - Homo sapiens cDNA FLJ78154 complete cds, highly similar to Homo sapiens solute carrier family 39 (zinc transporter), member 4 (SLC39A4), transcript variant 2, mRNA.
AK000695 - Homo sapiens cDNA FLJ20688 fis, clone KAIA2899.
JD412602 - Sequence 393626 from Patent EP1572962.
JD412603 - Sequence 393627 from Patent EP1572962.
JD174902 - Sequence 155926 from Patent EP1572962.
JD280392 - Sequence 261416 from Patent EP1572962.
KJ899164 - Synthetic construct Homo sapiens clone ccsbBroadEn_08558 SLC39A4 gene, encodes complete protein.
KR711111 - Synthetic construct Homo sapiens clone CCSBHm_00020435 SLC39A4 (SLC39A4) mRNA, encodes complete protein.
KR711112 - Synthetic construct Homo sapiens clone CCSBHm_00020443 SLC39A4 (SLC39A4) mRNA, encodes complete protein.
KU178707 - Homo sapiens solute carrier family 39 member 4 isoform 1 (SLC39A4) mRNA, partial cds.
KU178708 - Homo sapiens solute carrier family 39 member 4 isoform 2 (SLC39A4) mRNA, partial cds, alternatively spliced.
LF337129 - JP 2014500723-A/144632: Polycomb-Associated Non-Coding RNAs.
LF337130 - JP 2014500723-A/144633: Polycomb-Associated Non-Coding RNAs.
JD077345 - Sequence 58369 from Patent EP1572962.
JD324979 - Sequence 306003 from Patent EP1572962.
JD389094 - Sequence 370118 from Patent EP1572962.
JD375231 - Sequence 356255 from Patent EP1572962.
JD051599 - Sequence 32623 from Patent EP1572962.
JD255288 - Sequence 236312 from Patent EP1572962.
JD335148 - Sequence 316172 from Patent EP1572962.
JD324832 - Sequence 305856 from Patent EP1572962.
JD308019 - Sequence 289043 from Patent EP1572962.
JD037332 - Sequence 18356 from Patent EP1572962.
MA445913 - JP 2018138019-A/17839: Polycomb-Associated Non-Coding RNAs.
MA572706 - JP 2018138019-A/144632: Polycomb-Associated Non-Coding RNAs.
MA572707 - JP 2018138019-A/144633: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6P5W5 (Reactome details) participates in the following event(s):

R-HSA-442422 SLC39A1-4 transports Zn2+ from extracellular region to cytosol
R-HSA-442380 Zinc influx into cells by the SLC39 gene family
R-HSA-435354 Zinc transporters
R-HSA-425410 Metal ion SLC transporters
R-HSA-425366 Transport of bile salts and organic acids, metal ions and amine compounds
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: NM_017767, NP_060237, Q6P5W5-2, ZIP4
UCSC ID: uc003zcp.3
RefSeq Accession: NM_017767
Protein: Q6P5W5-2, splice isoform of Q6P5W5 CCDS: CCDS43782.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017767.2
exon count: 11CDS single in 3' UTR: no RNA size: 2342
ORF size: 1869CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 1907.50frame shift in genome: no % Coverage: 98.98
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 442# strange splices: 0
Click here for a detailed description of the fields of the table above.

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