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SLC39A1 (solute carrier family 39 (zinc transporter), member 1)

Written2011-10Renty B Franklin, Leslie C Costello
Department of Oncology, Diagnostic Sciences, Dental School, The Greenebaum Cancer Center, University of Maryland, Baltimore, MD, 21201, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_namesZIRTL
zinc/iron regulated transporter-like
solute carrier family 39 (zinc transporter), member 1
Alias_symbol (synonym)ZIP1
Other alias
HGNC (Hugo) SLC39A1
LocusID (NCBI) 27173
Atlas_Id 46571
Location 1q21.3  [Link to chromosome band 1q21]
Location_base_pair Starts at 153959099 and ends at 153963368 bp from pter ( according to hg19-Feb_2009)  [Mapping SLC39A1.png]
Fusion genes
(updated 2016)
HSD11B2 (16q22.1) / SLC39A1 (1q21.3)SLC39A1 (1q21.3) / BLK (8p23.1)SLC39A1 (1q21.3) / CRTC2 (1q21.3)
SLC39A1 (1q21.3) / PARD3 (10p11.22)SLC39A1 (1q21.3) / RAB13 (1q21.3)

DNA/RNA

Description The SLC39A1 gene contains 5 exons, three of which are coding. The length of the gene is 8600 base pairs according to the Entrez Gene database. Several transcripts have been reported containing either 3, 4, or 5 exons. However, the coding sequence for SLC39A1 is the same for all reported transcripts.
Transcription Only a single isoform has been reported; mRNA 2445 bases in length; coding region of 975 bases.
Pseudogene None reported.

Protein

Description SLC39A1 encodes Zrt/Irt-like protein family member 1 (ZIP1).
ZIP1 is a 35 kDa molecular weight protein consisting of 324 amino acids. The protein contains 8 transmembrane spanning domains and shows the characteristics of a zinc transporter (Gaither and Eide, 2001).
Expression ZIP1 is ubiquitously expressed in mammalian cells (Gaither and Eide, 2001). Expression is down regulated in prostate malignancy (Franklin et al., 2005). Its constitutive expression is reported to be regulated by SP and CREB1 (Makhov et al., 2009). Down regulation of expression in prostate malignancy is reported due to transcription repression by ras response element binding protein-1 (RREB-1) (Milon et al., 2010).
Localisation ZIP1 is located at the cell membrane.
Function ZIP1 is a facilitated zinc uptake transporter (Franklin et al., 2003). Activity of the transporter results in the intracellular accumulation of zinc. ZIP1 is involved in apoptosis induction in prostate cancer cells.
Homology Mus musculus Slc39a1; Rattus norvegicus Slc39a1; Bos taurus Slc39a1; Danio rerio slc39a1.

Mutations

Note No diseases related to mutation are reported.

Implicated in

Note
  
Entity Prostate cancer
Note SLC39A1 is down regulated in prostate cancer (Franklin et al., 2005). Knockdown of the SLC39A1 expression decreases cellular zinc and increases growth of PC-3 cells (Franklin et al., 2003). Over expression of SLC39A1 inhibits prostate tumor growth in a xenograft model (Golovine et al., 2008).
  

Bibliography

hZIP1 zinc uptake transporter down regulation and zinc depletion in prostate cancer.
Franklin RB, Feng P, Milon B, Desouki MM, Singh KK, Kajdacsy-Balla A, Bagasra O, Costello LC.
Mol Cancer. 2005 Sep 9;4:32.
PMID 16153295
 
The human ZIP1 transporter mediates zinc uptake in human K562 erythroleukemia cells.
Gaither LA, Eide DJ.
J Biol Chem. 2001 Jun 22;276(25):22258-64. Epub 2001 Apr 11.
PMID 11301334
 
Overexpression of the zinc uptake transporter hZIP1 inhibits nuclear factor-kappaB and reduces the malignant potential of prostate cancer cells in vitro and in vivo.
Golovine K, Makhov P, Uzzo RG, Shaw T, Kunkle D, Kolenko VM.
Clin Cancer Res. 2008 Sep 1;14(17):5376-84.
PMID 18765529
 
Transcriptional regulation of the major zinc uptake protein hZip1 in prostate cancer cells.
Makhov P, Golovine K, Uzzo RG, Wuestefeld T, Scoll BJ, Kolenko VM.
Gene. 2009 Feb 15;431(1-2):39-46. Epub 2008 Nov 5.
PMID 19026724
 
Ras responsive element binding protein-1 (RREB-1) down-regulates hZIP1 expression in prostate cancer cells.
Milon BC, Agyapong A, Bautista R, Costello LC, Franklin RB.
Prostate. 2010 Feb 15;70(3):288-96.
PMID 19802870
 

Citation

This paper should be referenced as such :
Franklin, RB ; Costello, LC
SLC39A1 (solute carrier family 39 (zinc transporter), member 1)
Atlas Genet Cytogenet Oncol Haematol. 2012;16(3):218-219.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SLC39A1ID46571ch1q21.html


External links

Nomenclature
HGNC (Hugo)SLC39A1   12876
Cards
AtlasSLC39A1ID46571ch1q21
Entrez_Gene (NCBI)SLC39A1  27173  solute carrier family 39 member 1
AliasesZIP1; ZIRTL
GeneCards (Weizmann)SLC39A1
Ensembl hg19 (Hinxton)ENSG00000143570 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000143570 [Gene_View]  chr1:153959099-153963368 [Contig_View]  SLC39A1 [Vega]
ICGC DataPortalENSG00000143570
TCGA cBioPortalSLC39A1
AceView (NCBI)SLC39A1
Genatlas (Paris)SLC39A1
WikiGenes27173
SOURCE (Princeton)SLC39A1
Genetics Home Reference (NIH)SLC39A1
Genomic and cartography
GoldenPath hg38 (UCSC)SLC39A1  -     chr1:153959099-153963368 -  1q21.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SLC39A1  -     1q21.3   [Description]    (hg19-Feb_2009)
EnsemblSLC39A1 - 1q21.3 [CytoView hg19]  SLC39A1 - 1q21.3 [CytoView hg38]
Mapping of homologs : NCBISLC39A1 [Mapview hg19]  SLC39A1 [Mapview hg38]
OMIM604740   
Gene and transcription
Genbank (Entrez)AF132942 AF151829 AJ243649 AJ271671 AK074943
RefSeq transcript (Entrez)NM_001271957 NM_001271958 NM_001271959 NM_001271960 NM_001271961 NM_014437
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SLC39A1
Cluster EST : UnigeneHs.743291 [ NCBI ]
CGAP (NCI)Hs.743291
Alternative Splicing GalleryENSG00000143570
Gene ExpressionSLC39A1 [ NCBI-GEO ]   SLC39A1 [ EBI - ARRAY_EXPRESS ]   SLC39A1 [ SEEK ]   SLC39A1 [ MEM ]
Gene Expression Viewer (FireBrowse)SLC39A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)27173
GTEX Portal (Tissue expression)SLC39A1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NY26   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NY26  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NY26
Splice isoforms : SwissVarQ9NY26
PhosPhoSitePlusQ9NY26
Domains : Interpro (EBI)ZIP   
Domain families : Pfam (Sanger)Zip (PF02535)   
Domain families : Pfam (NCBI)pfam02535   
Conserved Domain (NCBI)SLC39A1
DMDM Disease mutations27173
Blocks (Seattle)SLC39A1
SuperfamilyQ9NY26
Human Protein AtlasENSG00000143570
Peptide AtlasQ9NY26
HPRD11984
IPIIPI00100585   IPI01011934   IPI01011467   IPI00641194   IPI00643494   IPI00644042   
Protein Interaction databases
DIP (DOE-UCLA)Q9NY26
IntAct (EBI)Q9NY26
FunCoupENSG00000143570
BioGRIDSLC39A1
STRING (EMBL)SLC39A1
ZODIACSLC39A1
Ontologies - Pathways
QuickGOQ9NY26
Ontology : AmiGOin utero embryonic development  receptor binding  zinc ion transmembrane transporter activity  endoplasmic reticulum membrane  plasma membrane  plasma membrane  cation transport  membrane  integral component of membrane  inorganic cation transmembrane transporter activity  embryonic cranial skeleton morphogenesis  limb development  zinc II ion transmembrane transport  
Ontology : EGO-EBIin utero embryonic development  receptor binding  zinc ion transmembrane transporter activity  endoplasmic reticulum membrane  plasma membrane  plasma membrane  cation transport  membrane  integral component of membrane  inorganic cation transmembrane transporter activity  embryonic cranial skeleton morphogenesis  limb development  zinc II ion transmembrane transport  
REACTOMEQ9NY26 [protein]
REACTOME PathwaysR-HSA-442380 [pathway]   
NDEx NetworkSLC39A1
Atlas of Cancer Signalling NetworkSLC39A1
Wikipedia pathwaysSLC39A1
Orthology - Evolution
OrthoDB27173
GeneTree (enSembl)ENSG00000143570
Phylogenetic Trees/Animal Genes : TreeFamSLC39A1
HOVERGENQ9NY26
HOGENOMQ9NY26
Homologs : HomoloGeneSLC39A1
Homology/Alignments : Family Browser (UCSC)SLC39A1
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSLC39A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SLC39A1
dbVarSLC39A1
ClinVarSLC39A1
1000_GenomesSLC39A1 
Exome Variant ServerSLC39A1
ExAC (Exome Aggregation Consortium)SLC39A1 (select the gene name)
Genetic variants : HAPMAP27173
Genomic Variants (DGV)SLC39A1 [DGVbeta]
DECIPHERSLC39A1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSLC39A1 
Mutations
ICGC Data PortalSLC39A1 
TCGA Data PortalSLC39A1 
Broad Tumor PortalSLC39A1
OASIS PortalSLC39A1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSLC39A1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSLC39A1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SLC39A1
DgiDB (Drug Gene Interaction Database)SLC39A1
DoCM (Curated mutations)SLC39A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SLC39A1 (select a term)
intoGenSLC39A1
NCG5 (London)SLC39A1
Cancer3DSLC39A1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604740   
Orphanet
MedgenSLC39A1
Genetic Testing Registry SLC39A1
NextProtQ9NY26 [Medical]
TSGene27173
GENETestsSLC39A1
Target ValidationSLC39A1
Huge Navigator SLC39A1 [HugePedia]
snp3D : Map Gene to Disease27173
BioCentury BCIQSLC39A1
ClinGenSLC39A1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD27173
Chemical/Pharm GKB GenePA37465
Clinical trialSLC39A1
Miscellaneous
canSAR (ICR)SLC39A1 (select the gene name)
Probes
Litterature
PubMed38 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSLC39A1
EVEXSLC39A1
GoPubMedSLC39A1
iHOPSLC39A1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Aug 1 17:37:11 CEST 2017

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