slc39a6 solute carrier family 39 member 6 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: slc39a6provided by ZNC
Official Full Name: solute carrier family 39 member 6provided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-3023
See related: Ensembl:ENSDARG00000068143 AllianceGenome:ZFIN:ZDB-GENE-030131-3023
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: liv1; ZIP-6; wu:fc25a09
Summary: Predicted to enable zinc ion transmembrane transporter activity. Acts upstream of or within cell migration involved in gastrulation and epithelial to mesenchymal transition. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. Orthologous to human SLC39A6 (solute carrier family 39 member 6). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (42156286..42174019, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (42306866..42324987, complement)

Chromosome 2 - NC_007113.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The slc39a6 - null mutant zebrafish developed normally during gastrulation. Loss of slc39a6 in zebrafish resulted in significant T lymphocyte reduction and a decrease in intracellular Zn levels. And the slc39a6 deficiency increases caspase-related cell apoptosis in both zebrafish cells and human T cells.
Title: SLC39A6/ZIP6 is essential for zinc homeostasis and T-cell development in zebrafish.
results establish a molecular link between STAT3, LIV1 and Snail in epithelial-mesenchymal transition in gastrula organizer; LIV1 is essential for the nuclear localization of zinc-finger protein Snail
Title: Zinc transporter LIVI controls epithelial-mesenchymal transition in zebrafish gastrula organizer.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables metal ion transmembrane transporter activity	IEA Inferred from Electronic Annotation more info
enables monoatomic cation:bicarbonate symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables zinc ion transmembrane transporter activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within T cell differentiation in thymus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in T cell receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cell migration involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epithelial to mesenchymal transition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelial to mesenchymal transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular monoatomic cation homeostasis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intracellular zinc ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within metal ion transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in zinc ion import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in zinc ion import across plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in zinc ion import across plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within zinc ion transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within zinc ion transport	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane raft	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: zinc transporter ZIP6

Names: ZIP6; estrogen-regulated protein LIV-1; solute carrier family 39 (zinc transporter), member 6; zrt- and Irt-like protein 6

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_001001591.1 → NP_001001591.1 zinc transporter ZIP6

See identical proteins and their annotated locations for NP_001001591.1

Status: PROVISIONAL

Source sequence(s)

AB126260

UniProtKB/Swiss-Prot

Q6L8F3

Related

ENSDARP00000089128.3, ENSDART00000098357.4

Conserved Domains (1) summary

pfam02535
Location:351 → 730

Zip; ZIP Zinc transporter

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007113.7 Reference GRCz11 Primary Assembly

Range

42156286..42174019 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005171365.5 → XP_005171422.1 zinc transporter ZIP6 isoform X1

UniProtKB/TrEMBL

A0A8M2BIS4

Conserved Domains (1) summary

pfam02535
Location:315 → 694

Zip; ZIP Zinc transporter