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SLC39A1 Gene

protein-coding   GIFtS: 55
GCID: GC01M153931

Solute Carrier Family 39 (Zinc Transporter), Member 1

(Previous name: zinc/iron regulated transporter-like)
(Previous symbol: ZIRTL)
  See SLC39A1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Solute Carrier Family 39 (Zinc Transporter), Member 11 2     Zinc Transporter ZIP12
ZIRTL1 2 3 5     IRT13
Zrt- And Irt-Like Protein 12 3     ZIP-13
ZIP12 3     hZIP13
Zinc/Iron Regulated Transporter-Like1     Solute Carrier Family 39 Member 13
Solute Carrier Family 39 (Zinc Transporter), Member 32     Zinc-Iron-Regulated Transporter-Like3

External Ids:    HGNC: 128761   Entrez Gene: 271732   Ensembl: ENSG000001435707   OMIM: 6047405   UniProtKB: Q9NY263   

Export aliases for SLC39A1 gene to outside databases

Previous GC identifers: GC01M151748 GC01M149662 GC01M150706 GC01M151148 GC01M150744 GC01M152198 GC01M125294


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SLC39A1 Gene:
This gene encodes a member of the zinc-iron permease family. The encoded protein is localized to the cell membrane
and acts as a zinc uptake transporter. This gene has been linked to prostate cancer, breast cancer, and
Alzheimer's disease. Alternative splicing results in multiple transcript variants. (provided by RefSeq, Dec 2012)

GeneCards Summary for SLC39A1 Gene:
SLC39A1 (solute carrier family 39 (zinc transporter), member 1) is a protein-coding gene. Diseases associated with SLC39A1 include acrodermatitis enteropathica, and enteropathica. GO annotations related to this gene include inorganic cation transmembrane transporter activity and receptor binding. An important paralog of this gene is SLC39A3.

UniProtKB/Swiss-Prot: S39A1_HUMAN, Q9NY26
Function: Mediates zinc uptake. May function as a major endogenous zinc uptake transporter in many cells of the
body. Responsible for the rapid uptake and accumulation of physiologically effective zinc in prostate cells

Gene Wiki entry for SLC39A1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NT_004487.20  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SLC39A1 gene promoter:
         Tal-1beta   CREB   PPAR-gamma1   POU2F1   POU2F1a   deltaCREB   PPAR-gamma2   ITF-2   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SLC39A1 promoter sequence
   Search Chromatin IP Primers for SLC39A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC39A1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q21   Ensembl cytogenetic band:  1q21.3   HGNC cytogenetic band: 1q21

SLC39A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC39A1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M153931:  view genomic region     (about GC identifiers)

Start:
153,931,575 bp from pter      End:
153,940,188 bp from pter
Size:
8,614 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: S39A1_HUMAN, Q9NY26 (See protein sequence)
Recommended Name: Zinc transporter ZIP1  
Size: 324 amino acids; 34250 Da
Miscellaneous: Inhibited by Ni(2+) ions. Fe(2+) ions do not inhibit zinc uptake
Sequence caution: Sequence=AAD27717.1; Type=Frameshift; Positions=16, 40;
Secondary accessions: Q5T4K1 Q8N2H7 Q9BTV0 Q9UBI7 Q9Y2Z7 Q9Y380

Explore the universe of human proteins at neXtProt for SLC39A1: NX_Q9NY26

Explore proteomics data for SLC39A1 at MOPED


See SLC39A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (6 alternative transcripts): 
NP_001258886.1  NP_001258887.1  NP_001258888.1  NP_001258889.1  NP_001258890.1  NP_055252.2  

ENSEMBL proteins: 
 ENSP00000348535   ENSP00000357612   ENSP00000357610   ENSP00000309710   ENSP00000392950  
 ENSP00000392229   ENSP00000407717   ENSP00000443632  
Reactome Protein details: Q9NY26

SLC39A1 Human Recombinant Protein Products:

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Novus Biologicals SLC39A1 Protein
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Browse Proteins at Cloud-Clone Corp.

 
Search eBioscience for Proteins for SLC39A1 

SLC39A1 Antibody Products:

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Search eBioscience for ELISAs for SLC39A1 


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
SLC: Solute carriers

IUPHAR Guide to PHARMACOLOGY protein family classification: Zinc transporter 1
SLC39 family of metal ion transporters

1 InterPro protein domain:
 IPR003689 ZIP

Graphical View of Domain Structure for InterPro Entry Q9NY26

ProtoNet protein and cluster: Q9NY26

1 Blocks protein domain: IPB003689 Zinc transporter ZIP

UniProtKB/Swiss-Prot: S39A1_HUMAN, Q9NY26
Similarity: Belongs to the ZIP transporter (TC 2.A.5) family


Find genes that share domains with SLC39A1           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: S39A1_HUMAN, Q9NY26
Function: Mediates zinc uptake. May function as a major endogenous zinc uptake transporter in many cells of the
body. Responsible for the rapid uptake and accumulation of physiologically effective zinc in prostate cells

     Gene Ontology (GO): 4 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005102receptor binding IEA--
GO:0005385zinc ion transmembrane transporter activity IEA--
GO:0022890inorganic cation transmembrane transporter activity TAS10610721
GO:0046873metal ion transmembrane transporter activity ----
     
Find genes that share ontologies with SLC39A1           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for SLC39A1:
 Increased G1 DNA content 

     5 MGI mutant phenotypes (inferred from 1 allele(MGI details for Slc39a1):
 craniofacial  embryogenesis  growth/size/body  integument  limbs/digits/tail 

Find genes that share phenotypes with SLC39A1           About GenesLikeMe

Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SLC39A1
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   genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SLC39A1
   genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SLC39A1

miRNA
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miRTarBase miRNAs that target SLC39A1:
hsa-mir-96-5p (MIRT027938), hsa-mir-30c-5p (MIRT047939), hsa-mir-215-5p (MIRT024724), hsa-mir-877-5p (MIRT037329), hsa-mir-192-5p (MIRT026105)

Block miRNA regulation of human, mouse, rat SLC39A1 using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate SLC39A1 (see all 20):
hsa-miR-146a hsa-miR-1271 hsa-miR-218 hsa-miR-223 hsa-miR-133a hsa-miR-4274 hsa-miR-376a* hsa-miR-3121-3p
SwitchGear 3'UTR luciferase reporter plasmidSLC39A1 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat SLC39A1

Gene Editing
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GenScript: all cDNA clones in your preferred vector (see all 4): SLC39A1 (NM_015359)
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SLC39A1

Cell Line
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Browse ESI BIO Cell Lines and PureStem Progenitors for SLC39A1 
In Situ Assay
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC39A1


(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
S39A1_HUMAN, Q9NY26: Cell membrane; Multi-pass membrane protein. Endoplasmic reticulum membrane; Multi-pass
membrane protein. Note=Shows a vesicular localization corresponding partially to the endoplasmic reticulum in
several epithelial cell lines
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
endoplasmic reticulum5
plasma membrane5

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005789endoplasmic reticulum membrane IEA--
GO:0005886plasma membrane TAS--
GO:0016020membrane TAS10610721
GO:0016021integral component of membrane IEA--

Find genes that share ontologies with SLC39A1           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for SLC39A1 About    
See pathways by source

SuperPathContained pathways About
1Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
SLC-mediated transmembrane transport0.47
Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds0.38
Transmembrane transport of small molecules0.47
2Metal ion SLC transporters
Metal ion SLC transporters
Zinc influx into cells by the SLC39 gene family0.00
Zinc transporters0.00
3Senescence and Autophagy
Senescence and Autophagy


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Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways


1 BioSystems Pathway for SLC39A1
    Senescence and Autophagy

1 Reactome Pathway for SLC39A1
    Zinc influx into cells by the SLC39 gene family


    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SLC39A1
Interactions:

    GeneGlobe Interaction Network for SLC39A1

STRING Interaction Network Preview (showing 5 interactants - click image to see 13)

Selected Interacting proteins for SLC39A1 (Q9NY263 ENSP000003097104) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
InteractantInteraction Details
GeneCardExternal ID(s)
PLEKHM2Q8IWE53, ENSP000003649564I2D: score=3 STRING: ENSP00000364956
KCNAB1Q147223, ENSP000004199524I2D: score=1 STRING: ENSP00000419952
PRKCZQ055133, ENSP000003678304I2D: score=1 STRING: ENSP00000367830
SLC39A2Q9NP943, ENSP000002986814I2D: score=1 STRING: ENSP00000298681
KCNAB2Q133033, ENSP000001642474I2D: score=1 STRING: ENSP00000164247
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Gene Ontology (GO): 5 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006812cation transport TAS10610721
GO:0006829zinc ion transport ----
GO:0030001metal ion transport ----
GO:0055085transmembrane transport TAS--
GO:0071577zinc ion transmembrane transport IMP11301334

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for SLC39A1 (S39A1)

3 Novoseek inferred chemical compound relationships for SLC39A1 gene    About this table
Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
zinc 67.9 53 16153295 (6), 11301334 (4), 17550612 (4), 14525987 (2) (see all 15)
iron 31.7 11 12805609 (4), 14526117 (4), 18397377 (1)
cadmium 24.9 1 14526117 (1)



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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for SLC39A1 gene (6 alternative transcripts): 
NM_001271957.1  NM_001271958.1  NM_001271959.1  NM_001271960.1  NM_001271961.1  NM_014437.4  

Unigene Cluster for SLC39A1:

Solute carrier family 39 (zinc transporter), member 1
Hs.7854  [show with all ESTs]
Unigene Representative Sequence: BC047288
9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000356205(uc001fdk.3 uc010pee.2) ENST00000368623(uc001fdj.3)
ENST00000368621(uc001fdi.3) ENST00000310483(uc001fdl.3) ENST00000429040
ENST00000413622 ENST00000417348 ENST00000461071 ENST00000537590
miRNA
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Block miRNA regulation of human, mouse, rat SLC39A1 using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate SLC39A1 (see all 20):
hsa-miR-146a hsa-miR-1271 hsa-miR-218 hsa-miR-223 hsa-miR-133a hsa-miR-4274 hsa-miR-376a* hsa-miR-3121-3p
SwitchGear 3'UTR luciferase reporter plasmidSLC39A1 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat SLC39A1
Clone
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OriGene ORF clones in mouse, rat for SLC39A1
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
GenScript: all cDNA clones in your preferred vector (see all 4): SLC39A1 (NM_015359)
DNA2.0 Custom Codon Optimized Gene Synthesis Service for SLC39A1
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SLC39A1
Primer
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OriGene qPCR primer pairs and template standards for SLC39A1
OriGene qSTAR qPCR primer pairs in human, mouse for SLC39A1
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SLC39A1
  QuantiTect SYBR Green Assays in human, mouse, rat SLC39A1
  QuantiFast Probe-based Assays in human, mouse, rat SLC39A1

Additional mRNA sequence: 

AF132942.1 AF151829.1 AJ243649.1 AJ271671.1 AK074943.1 AK075257.1 AK293389.1 AK297983.1 
AK300244.1 BC002563.2 BC003152.2 BC007886.2 BC014303.2 BC047288.1 BC069261.1 CR457217.1 

Selected DOTS entries (see all 48):

DT.92452611  DT.99950147  DT.100804939  DT.100670050  DT.100670043  DT.95070646  DT.100670055  DT.100670051 
DT.95070643  DT.121436483  DT.121436419  DT.100670047  DT.100876689  DT.121436521  DT.91935800  DT.100670049 
DT.92452610  DT.100804343  DT.121436477  DT.121436480  DT.92452619  DT.100835652  DT.100846585  DT.100670045 

Selected AceView cDNA sequences (see all 822):

BC047288 BM803217 BQ932828 BU172782 CB154271 AA922287 BU175207 CR599760 
BM786617 CR616553 CR613217 BG831757 BQ067116 CR615172 BX363529 BI755149 
AA357049 BG752491 BM556000 AF289574 AL555096 BX384222 CR614937 CR593791 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for SLC39A1 (see all 10)    About this scheme

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b · 9c · 9d · 9e · 9f · 9g ·
SP1:                                -     -     -     -     -     -     -     -     -     -                                                                     
SP2:                    -           -     -     -     -     -     -     -     -     -     -                                                                     
SP3:        -     -     -           -     -     -     -     -     -     -     -     -     -                                                                     
SP4:                                            -     -     -     -     -     -     -     -                                                                     
SP5:                                                  -     -     -     -     -     -     -                                                                     

ExUns: 9h
SP1:      
SP2:      
SP3:      
SP4:      
SP5:      


ECgene alternative splicing isoforms for SLC39A1

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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SLC39A1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CCCAGATGAT
SLC39A1 Expression
About this image


SLC39A1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 6) fully expand
 
 Brain (Nervous System)    fully expand to see all 7 entries
         Mature Choroid Plexus Cells Choroid Plexus
         Cerebral Cortex
 
 Neural Tube (Nervous System)    fully expand to see all 3 entries
         Metencephalon
 
 Thymus (Hematopoietic System)
         Thymus
 
 Epithelial Cells
         Mature Choroid Plexus Cells Choroid Plexus
 
 Gall Bladder (Hepatobiliary System)
SLC39A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SLC39A1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.7854

UniProtKB/Swiss-Prot: S39A1_HUMAN, Q9NY26
Tissue specificity: Ubiquitous. Expressed in most adult and fetal tissues including the epidermis

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QuantiFast Probe-based Assays in human, mouse, rat SLC39A1
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC39A1

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for SLC39A1 gene from Selected species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Slc39a11 , 5 solute carrier family 39 (zinc transporter), member more1, 5 86.93(n)1
93.83(a)1
  3 (39.21 cM)5
307911  NM_013901.21  NP_038929.21 
 902481725 
lizard
(Anolis carolinensis)
Reptilia SLC39A16
solute carrier family 39 (zinc transporter), membe...
46(a)
1 ↔ 1
AAWZ02040249(1048-3180)
African clawed frog
(Xenopus laevis)
Amphibia BU910435.12   -- 70.84(n)    BU910435.1 
zebrafish
(Danio rerio)
Actinopterygii slc39a36
solute carrier family 39 (zinc transporter), membe...
34(a)
1 ↔ 1
16(54805838-54807761) ENSDARG00000016145
fruit fly
(Drosophila melanogaster)
Insecta CG94306
--
24(a)
many ↔ many
2R(2605785-2607038)
worm
(Caenorhabditis elegans)
Secernentea F31C3.46
Protein F31C3.4 (F31C3.4) mRNA, complete cds
29(a)
1 → many
I(15050797-15052420) WBGene00009286


ENSEMBL Gene Tree for SLC39A1 (if available)
TreeFam Gene Tree for SLC39A1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SLC39A1 gene
SLC39A32  SLC39A22  
2 SIMAP similar genes for SLC39A1 using alignment to 7 protein entries:     S39A1_HUMAN (see all proteins):
SLC39A2    SLC39A3

Find genes that share paralogs with SLC39A1           About GenesLikeMe


1 Pseudogenes.org Pseudogene for SLC39A1
PGOHUM00000246562


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SLC39A1 (see all 98)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1408960561,2
C,F--153933198(+) CCCATG/AGCCAG 12 /A /H /Y syn1 mis11Minor allele frequency- A:0.00NA 3678
rs22809661,2
C,H--153933275(-) GCATCT/GCACTC 6 -- int16Minor allele frequency- G:0.00NS EA NA 424
rs1180920591,2
C,F--153933426(+) GTTACG/ATGTAG 6 -- int11Minor allele frequency- A:0.01EA 120
rs1499717791,2
--153933585(+) TGTCTC/TTACTA 6 -- int10--------
rs1866161481,2
--153933756(+) CAAAAA/GCAAAA 6 -- int10--------
rs1452007621,2
--153933789(+) AAACAC/TTTTGG 6 -- int10--------
rs757509251,2
F--153933946(+) CATTAC/GCAAAT 6 -- int11Minor allele frequency- G:0.02EA 120
rs1491499221,2
--153934008(+) ATACAC/TGAAAA 6 -- int10--------
rs1450413941,2
--153934085(+) TATACA/GCAGTC 6 -- int10--------
rs37911871,2
C,F,A,H--153934203(-) TGGATA/GGTGGG 6 -- int122Minor allele frequency- G:0.25EA NS NA CSA WA 3850

HapMap Linkage Disequilibrium report for SLC39A1 (153931575 - 153940188 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for SLC39A1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv872450CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SLC39A1
DNA2.0 Custom Variant and Variant Library Synthesis for SLC39A1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 604740    OMIM disorders: --

5 diseases for SLC39A1:    
About MalaCards
acrodermatitis enteropathica    enteropathica    acrodermatitis    prostate cancer
breast cancer

1 disease from the University of Copenhagen DISEASES database for SLC39A1:
Acrodermatitis enteropathica

Find genes that share disorders with SLC39A1           About GenesLikeMe

5 Novoseek inferred disease relationships for SLC39A1 gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
zinc deficiency 64.1 1 9618566 (1)
erythroleukemia 49.3 1 11301334 (1)
iron deficiency 39.1 1 14526117 (1)
prostate cancer 38.6 6 17400177 (2), 16153295 (2)
tumors 0 4 17400177 (1), 16700911 (1), 17550612 (1)

Genetic Association Database (GAD): SLC39A1

Export disorders for SLC39A1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for SLC39A1 gene, integrated from 10 sources (see all 48):
(articles sorted by number of sources associating them with SLC39A1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Isolation and characterization of human and mouse ZIRTL, a member of the IRT1 family of transporters, mapping within the epidermal differentiation complex. (PubMed id 10610721)1, 2, 3, 9 Lioumi M.... Ragoussis J. (Genomics 1999)
  2. The human ZIP1 transporter mediates zinc uptake in human K562 erythroleukemia cells. (PubMed id 11301334)1, 2, 9 Gaither L.A. and Eide D.J. (J. Biol. Chem. 2001)
  3. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1, 2 Otsuki T....Isogai T. (DNA Res. 2005)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  6. Human ZIP1 is a major zinc uptake transporter for the accumulation of zinc in prostate cells. (PubMed id 12888280)1, 2 Franklin R.B....Costello L.C. (J. Inorg. Biochem. 2003)
  7. Differential subcellular localization of hZip1 in adherent and non- adherent cells. (PubMed id 11696349)1, 2 Milon B.... Beaumont C. (FEBS Lett. 2001)
  8. Functional expression of the human hZIP2 zinc transporter. (PubMed id 10681536)1, 3 Gaither L.A. and Eide D.J. (J. Biol. Chem. 2000)
  9. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PubMed id 10810093)1, 2 Lai C.-H.... Lin W.-C. (Genome Res. 2000)
  10. A di-leucine sorting signal in ZIP1 (SLC39A1) mediates endocytosis of the protein. (PubMed id 17635580)1, 9 Huang L. and Kirschke C.P. (FEBS J. 2007)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Disorders
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 27173 HGNC: 12876 AceView: SLC39A1andTORC2 Ensembl:ENSG00000143570 euGenes: HUgn27173
ECgene: SLC39A1 H-InvDB: SLC39A1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SLC39A1 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for SLC39A1 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SLC39A1 gene:
Search GeneIP for patents involving SLC39A1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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