Slc39a6 solute carrier family 39 member 6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Slc39a6provided by RGD
Official Full Name: solute carrier family 39 member 6provided by RGD
Primary source: RGD:1304664
See related: EnsemblRapid:ENSRNOG00000028703 AllianceGenome:RGD:1304664
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable monoatomic cation:bicarbonate symporter activity and zinc ion transmembrane transporter activity. Predicted to be involved in several processes, including T cell receptor signaling pathway; intracellular zinc ion homeostasis; and zinc ion import across plasma membrane. Located in apical plasma membrane. Orthologous to human SLC39A6 (solute carrier family 39 member 6). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 81.5), Testes (RPKM 73.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 18p12

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	18	NC_086036.1 (16139621..16160163, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	18	NC_051353.1 (15864874..15885417, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	18	NC_005117.4 (16523450..16543992, complement)

Chromosome 18 - NC_086036.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Liv-1 (SLC39A6)is localized to the plasma membrane in neurons, suggesting that it plays a role in Zn uptake into neurons
Title: Zinc deficiency is associated with increased brain zinc import and LIV-1 expression and decreased ZnT-1 expression in neonatal rats.

Submit: New GeneRIF Correction

General gene information

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Markers

AI502079 (e-PCR)
- UniSTS:226235

RH129896 (e-PCR)
- UniSTS:213184

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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	ISO Inferred from Sequence Orthology more info
enables zinc ion transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in T cell receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in T cell receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in bicarbonate transport	IEA Inferred from Electronic Annotation more info
involved_in epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
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
involved_in intracellular zinc ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in lymphocyte activation	ISO Inferred from Sequence Orthology more info
involved_in lymphocyte activation	ISS Inferred from Sequence or Structural Similarity 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	ISO Inferred from Sequence Orthology more info
involved_in zinc ion import across plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in zinc ion transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in zinc ion transmembrane transport	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in lamellipodium membrane	ISO Inferred from Sequence Orthology more info
located_in lamellipodium membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane raft	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology 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 ZIP6

Names: ZIP-6; solute carrier family 39 (metal ion transporter), member 6; 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_001024745.1 → NP_001019916.1 zinc transporter ZIP6 precursor

See identical proteins and their annotated locations for NP_001019916.1

Status: PROVISIONAL

Source sequence(s)

BC097493

UniProtKB/Swiss-Prot

Q4V887

UniProtKB/TrEMBL

A6J2K7

Related

ENSRNOP00000034256.4, ENSRNOT00000036306.6

Conserved Domains (2) summary

pfam02535
Location:309 → 728

Zip; ZIP Zinc transporter

cl00262
Location:77 → 123

TroA-like; Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between ...