SLC39A11 solute carrier family 39 member 11 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC39A11provided by HGNC
Official Full Name: solute carrier family 39 member 11provided by HGNC
Primary source: HGNC:HGNC:14463
See related: Ensembl:ENSG00000133195 MIM:616508; AllianceGenome:HGNC:14463
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ZIP11; ZIP-11; C17orf26
Summary: Predicted to enable zinc ion transmembrane transporter activity. Predicted to be involved in zinc ion transmembrane transport. Predicted to be located in Golgi apparatus; nucleus; and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thyroid (RPKM 5.6), stomach (RPKM 5.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q24.3-q25.1

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (72645949..73092688, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (73518976..73981577, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (70642088..71088827, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Single nucleotide polymorphisms and Zn transport by ZIP11 shape functional phenotypes of HeLa cells.
Title: Single nucleotide polymorphisms and Zn transport by ZIP11 shape functional phenotypes of HeLa cells.
Increased expression of zinc transporter ZIP4, ZIP11, ZnT1, and ZnT6 predicts poor prognosis in pancreatic cancer.
Title: Increased expression of zinc transporter ZIP4, ZIP11, ZnT1, and ZnT6 predicts poor prognosis in pancreatic cancer.
We found 8 different single nucleotide polymorphisms (SNPs) that are significantly different between subjects without gastritis and those with gastritis... In conclusion, we found that zinc transporter gene ZIP11 is associated with chronic gastritis in the Korean population and it may interact with spicy food, which suggests ZIP11 as a therapeutic target for precision nutrition.
Title: Zinc transporter SLC39A11 polymorphisms are associated with chronic gastritis in the Korean population: the possible effect on spicy food intake.
Polymorphisms within ZIP11 gene were significantly associated with bladder cancer risk.
Title: Zinc transporter genes and urological cancers: integrated analysis suggests a role for ZIP11 in bladder cancer.
In glioma tumors, low ZIP11 expression was significantly associated with higher grade. Higher ZIP11 expression was weakly correlated with IDH1 mutation status.
Title: Expression Profile Analysis of Zinc Transporters (ZIP4, ZIP9, ZIP11, ZnT9) in Gliomas and their Correlation with IDH1 Mutation Status.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
This paper describes the genomic region surrounding the SOX9 gene which includes SLC39A11 (C17orf26).
Title: Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Common variants in left/right asymmetry genes and pathways are associated with relative hand skill. EBI GWAS Catalog EBI GWAS CatalogPubMed
Gene-environment interactions and obesity traits among postmenopausal African-American and Hispanic women in the Women's Health Initiative SHARe Study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of liver enzymes in korean children. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of serum selenium concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of smoking behaviours among Bangladeshi adults. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-150922 (e-PCR)
- UniSTS:173585

SHGC-146701 (e-PCR)
- UniSTS:175380

D17S1351 (e-PCR), detects polymorphism
- UniSTS:29216

SHGC-173571 (e-PCR)
- UniSTS:185397

RH118747 (e-PCR)
- UniSTS:138051

RH69804 (e-PCR)
- UniSTS:56412

SHGC-143352 (e-PCR)
- UniSTS:171877

D17S1848 (e-PCR), detects polymorphism
- UniSTS:68971

SHGC-146444 (e-PCR)
- UniSTS:175220

SHGC-110876 (e-PCR)
- UniSTS:168062

D17S692 (e-PCR)
- UniSTS:54663

RH91208 (e-PCR)
- UniSTS:90001

RH78720 (e-PCR)
- UniSTS:69362

STS-D20379 (e-PCR)
- UniSTS:42995

G43511 (e-PCR)
- UniSTS:94968

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables copper ion transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in copper ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in zinc ion import across plasma membrane	IEA Inferred from Electronic Annotation more info
involved_in zinc ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: zinc transporter ZIP11

Names: ZRT/IRT-like protein 11; Zrt- and Irt-like protein 11; solute carrier family 39 (metal ion transporter), member 11; zinc transporter 11

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001159770.2 → NP_001153242.1 zinc transporter ZIP11 isoform 1

See identical proteins and their annotated locations for NP_001153242.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) differs in the 5' UTR and uses an alternate in-frame splice site in the coding region, compared to variant 3. The encoded isoform (1) is longer, compared to isoform 2. Variants 1 and 4 encode the same isoform (1).

Source sequence(s)

AC025198, AC080037, AK095227, BU686998, DA380043

Consensus CDS

CCDS54160.1

UniProtKB/Swiss-Prot

B2R8H7, Q8N1S5, Q8WZ81

Related

ENSP00000445829.2, ENST00000542342.6

Conserved Domains (1) summary

COG0428
Location:6 → 342

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
NM_001352691.2 → NP_001339620.1 zinc transporter ZIP11 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (3) represents the longest transcript but encodes the shorter isoform (2). Variants 2, 3, and 5 encode the same isoform (2).

Source sequence(s)

AC011120, AC025198, AC080037

Consensus CDS

CCDS11690.1

Conserved Domains (1) summary

COG0428
Location:6 → 335

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
NM_001352692.2 → NP_001339621.1 zinc transporter ZIP11 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the coding region, compared to variant 3. The encoded isoform (1) is longer, compared to isoform 2. Variants 1 and 4 encode the same isoform (1).

Source sequence(s)

AC011120, AC025198, AC080037

Consensus CDS

CCDS54160.1

UniProtKB/Swiss-Prot

B2R8H7, Q8N1S5, Q8WZ81

Conserved Domains (1) summary

COG0428
Location:6 → 342

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
NM_001352693.2 → NP_001339622.1 zinc transporter ZIP11 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 3. Variants 2, 3, and 5 encode the same isoform (2).

Source sequence(s)

AC011120, AC025198, AC080037

Consensus CDS

CCDS11690.1

Conserved Domains (1) summary

COG0428
Location:6 → 335

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
NM_139177.4 → NP_631916.2 zinc transporter ZIP11 isoform 2

See identical proteins and their annotated locations for NP_631916.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 3. Variants 2, 3, and 5 encode the same isoform (2).

Source sequence(s)

AC025198, BC035631

Consensus CDS

CCDS11690.1

UniProtKB/Swiss-Prot

Q8N1S5

Related

ENSP00000255559.3, ENST00000255559.8

Conserved Domains (1) summary

COG0428
Location:6 → 335

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

72645949..73092688 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017024335.2 → XP_016879824.1 zinc transporter ZIP11 isoform X8
XM_006721757.3 → XP_006721820.1 zinc transporter ZIP11 isoform X6

Conserved Domains (1) summary

COG0428
Location:6 → 285

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
XM_017024330.2 → XP_016879819.1 zinc transporter ZIP11 isoform X2

UniProtKB/Swiss-Prot

Q8N1S5

Conserved Domains (1) summary

COG0428
Location:6 → 335

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
XM_006721755.3 → XP_006721818.1 zinc transporter ZIP11 isoform X1

See identical proteins and their annotated locations for XP_006721818.1

UniProtKB/Swiss-Prot

B2R8H7, Q8N1S5, Q8WZ81

Conserved Domains (1) summary

COG0428
Location:6 → 342

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
XM_047435571.1 → XP_047291527.1 zinc transporter ZIP11 isoform X8
XM_017024334.3 → XP_016879823.1 zinc transporter ZIP11 isoform X6

Conserved Domains (1) summary

COG0428
Location:6 → 285

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
XM_011524493.2 → XP_011522795.1 zinc transporter ZIP11 isoform X1

See identical proteins and their annotated locations for XP_011522795.1

UniProtKB/Swiss-Prot

B2R8H7, Q8N1S5, Q8WZ81

Conserved Domains (1) summary

COG0428
Location:6 → 342

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
XM_011524494.2 → XP_011522796.1 zinc transporter ZIP11 isoform X1

See identical proteins and their annotated locations for XP_011522796.1

UniProtKB/Swiss-Prot

B2R8H7, Q8N1S5, Q8WZ81

Conserved Domains (1) summary

COG0428
Location:6 → 342

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
XM_017024332.1 → XP_016879821.1 zinc transporter ZIP11 isoform X2

UniProtKB/Swiss-Prot

Q8N1S5

Conserved Domains (1) summary

COG0428
Location:6 → 335

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
XM_017024333.2 → XP_016879822.1 zinc transporter ZIP11 isoform X4
XM_011524495.4 → XP_011522797.1 zinc transporter ZIP11 isoform X7

Conserved Domains (1) summary

COG0428
Location:6 → 218

ZupT; Zinc transporter ZupT [Inorganic ion transport and metabolism]
XM_017024342.2 → XP_016879831.1 zinc transporter ZIP11 isoform X14

UniProtKB/TrEMBL

J3KRX2
XM_006721759.2 → XP_006721822.1 zinc transporter ZIP11 isoform X12

UniProtKB/TrEMBL

J3KRX2

Conserved Domains (1) summary

cl00437
Location:6 → 218

Zip; ZIP Zinc transporter
XM_047435575.1 → XP_047291531.1 zinc transporter ZIP11 isoform X12
XM_047435577.1 → XP_047291533.1 zinc transporter ZIP11 isoform X14

Related

ENSP00000462200.1, ENST00000580557.5
XM_047435578.1 → XP_047291534.1 zinc transporter ZIP11 isoform X15
XM_047435568.1 → XP_047291524.1 zinc transporter ZIP11 isoform X5
XM_006721756.4 → XP_006721819.1 zinc transporter ZIP11 isoform X3

Conserved Domains (1) summary

cl00437
Location:6 → 218

Zip; ZIP Zinc transporter
XM_047435569.1 → XP_047291525.1 zinc transporter ZIP11 isoform X5
XM_047435565.1 → XP_047291521.1 zinc transporter ZIP11 isoform X3
XM_047435570.1 → XP_047291526.1 zinc transporter ZIP11 isoform X5
XM_047435566.1 → XP_047291522.1 zinc transporter ZIP11 isoform X3
XM_011524498.4 → XP_011522800.1 zinc transporter ZIP11 isoform X16

UniProtKB/TrEMBL

J3KRX2

Related

ENSP00000464525.1, ENST00000579732.5

Conserved Domains (1) summary

cl00437
Location:6 → 102

Zip; ZIP Zinc transporter
XM_011524496.3 → XP_011522798.1 zinc transporter ZIP11 isoform X9

Conserved Domains (1) summary

cl00437
Location:6 → 102

Zip; ZIP Zinc transporter
XM_047435572.1 → XP_047291528.1 zinc transporter ZIP11 isoform X10
XM_017024340.3 → XP_016879829.1 zinc transporter ZIP11 isoform X13

UniProtKB/TrEMBL

J3KRX2
XM_006721758.5 → XP_006721821.1 zinc transporter ZIP11 isoform X11

UniProtKB/TrEMBL

J3KRX2

Conserved Domains (1) summary

cl00437
Location:6 → 102

Zip; ZIP Zinc transporter
XM_047435576.1 → XP_047291532.1 zinc transporter ZIP11 isoform X13
XM_017024341.3 → XP_016879830.1 zinc transporter ZIP11 isoform X13

UniProtKB/TrEMBL

J3KRX2
XM_047435574.1 → XP_047291530.1 zinc transporter ZIP11 isoform X11