Gene Page:SLC39A1

Summary?
GeneID 27173
Symbol SLC39A1
Synonyms ZIP1|ZIRTL
Description solute carrier family 39 member 1
Reference MIM: 604740|HGNC:HGNC:12876|Ensembl:ENSG00000143570|HPRD:11984|Vega:OTTHUMG00000037158
Gene type protein-coding
Map location 1q21
Sherlock p-value 0.383
Fetal beta -0.022
DMG 1 (# studies)
eGene Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
GSMA_I Genome scan meta-analysis Psr: 0.0235
GSMA_IIA Genome scan meta-analysis (All samples) Psr: 0.00814

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg14747580 1 153936275 SLC39A1 2.15E-8 -0.006 7.29E-6 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs4501739 chrX 35960848 SLC39A1 27173 0.14 trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
死神:胎儿(13 - 26所示postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
UNC119 0.92 0.91
TBCB 0.91 0.91
EBP 0.90 0.91
DALRD3 0.90 0.91
RNF25 0.90 0.91
DGUOK 0.89 0.89
FNDC4 0.89 0.91
ITPA 0.89 0.91
STK19 0.89 0.91
EMD 0.89 0.88
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.8 -0.74 -0.77
AF347015.27 -0.73 -0.76
AF347015.26 -0.72 -0.80
MT-CYB -0.72 -0.77
AF347015.33 -0.72 -0.76
MT-CO2 -0.72 -0.73
AF347015.15 -0.71 -0.77
AF347015.2 -0.71 -0.78
AF347015.31 -0.69 -0.72
MT-ATP8 -0.66 -0.79

Section III. Gene Ontology annotation

Molecular function 去的术语 Evidence Neuro keywords PubMed ID
GO:0005385 zinc ion transmembrane transporter activity IEA -
GO:0008270 zinc ion binding IEA -
GO:0046873 metal ion transmembrane transporter activity IEA -
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0030001 metal ion transport IEA -
GO:0006829 zinc ion transport IEA -
GO:0006811 ion transport IEA -
去:0015674 di-, tri-valent inorganic cation transport TAS 10610721
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0005789 endoplasmic reticulum membrane IEA -
GO:0005624 membrane fraction TAS 10610721
GO:0005783 endoplasmic reticulum IEA -
GO:0016020 membrane IEA -
GO:0016021 integral to membrane TAS 10610721
GO:0005886 plasma membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 413 270 All SZGR 2.0 genes in this pathway
REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT 241 157 All SZGR 2.0 genes in this pathway
REACTOME TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 89 54 All SZGR 2.0 genes in this pathway
REACTOME ZINC TRANSPORTERS 15 9 All SZGR 2.0 genes in this pathway
REACTOME METAL ION SLC TRANSPORTERS 22 13 All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 1 UP 276 165 All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 2 UP 139 83 All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 UP 341 197 All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747 453 All SZGR 2.0 genes in this pathway
LOCKWOOD AMPLIFIED IN LUNG CANCER 214 139 All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734 436 All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215 893 528 All SZGR 2.0 genes in this pathway
ZHOU TNF SIGNALING 30MIN 54 36 All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED 1229 713 All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D UP 210 124 All SZGR 2.0 genes in this pathway
MCCABE BOUND BY HOXC6 469 239 All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863 514 All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A 770 480 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-182 815 821 1A hsa-miR-182 UUUGGCAAUGGUAGAACUCACA
hsa-miR-182 UUUGGCAAUGGUAGAACUCACA
miR-218 605 611 m8 hsa-miR-218brain UUGUGCUUGAUCUAACCAUGU
miR-223 939 945 m8 hsa-miR-223 UGUCAGUUUGUCAAAUACCCC
miR-96 575 582 1A,m8 hsa-miR-96brain UUUGGCACUAGCACAUUUUUGC
hsa-miR-96brain UUUGGCACUAGCACAUUUUUGC