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NTN4 netrin 4 [ Homo sapiens (human) ]

Gene ID: 59277, updated on 11-Sep-2019

Summary

Official Symbol
NTN4provided by HGNC
Official Full Name
netrin 4provided by HGNC
Primary source
HGNC:HGNC:13658
See related
Ensembl:ENSG00000074527 MIM:610401
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PRO3091
Summary
This gene encodes a member of the netrin family of proteins, which function in various biological processes including axon guidance, tumorogenesis, and angiogenesis. Netrins are laminin-related proteins that have an N-terminal laminin-type domain, epidermal growth factor-like repeat domain, and a positively charged heparin-binding domain at the C-terminus. The protein encoded by this gene is involved in processes including neurite growth and migration, angiogenesis and mural cell adhesion to endothelial cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
Expression
Broad expression in spleen (RPKM 88.7), kidney (RPKM 62.7) and 20 other tissues See more
Orthologs

Genomic context

See NTN4 in Genome Data Viewer
Location:
12q22
Exon count:
12
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (95657807..95791155, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (96051583..96184565, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene methionyl aminopeptidase 2 Neighboring gene ubiquitin specific peptidase 44 Neighboring gene phosphoglycerate mutase 1 pseudogene 5 Neighboring gene uncharacterized LOC105369919 Neighboring gene uncharacterized LOC105369921 Neighboring gene RNA, U6 small nuclear 247, pseudogene Neighboring gene long intergenic non-protein coding RNA 2410

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study in Koreans identifies susceptibility loci for allergic nickel dermatitis.
NHGRI GWA Catalog
Genome-wide association studies identify four ER negative-specific breast cancer risk loci.
NHGRI GWA Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
NHGRI GWA Catalog

Pathways from BioSystems

  • Axon guidance, organism-specific biosystem (from KEGG)
    Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, conserved biosystem (from KEGG)
    Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, organism-specific biosystem (from REACTOME)
    Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Netrin-1 signaling, organism-specific biosystem (from REACTOME)
    Netrin-1 signaling, organism-specific biosystemNetrins are secreted proteins that play a crucial role in neuronal migration and in axon guidance during the development of the nervous system. To date, several Netrins have been described in mouse a...
  • Non-integrin membrane-ECM interactions, organism-specific biosystem (from REACTOME)
    Non-integrin membrane-ECM interactions, organism-specific biosystemSeveral non-integrin membrane proteins interact with extracellular matrix proteins. Transmembrane proteoglycans may associate with integrins and growth factor receptors to influence their function, o...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ23180

Gene Ontology Provided by GOA

Function Evidence Code Pubs
laminin-1 binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
animal organ morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon guidance TAS
Traceable Author Statement
more info
 
basement membrane assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron remodeling IEA
Inferred from Electronic Annotation
more info
 
regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling IEA
Inferred from Electronic Annotation
more info
 
substrate adhesion-dependent cell spreading IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tissue development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
laminin complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
netrin-4
Names
beta-netrin
hepar-derived netrin-like protein

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_051252.1 RefSeqGene

    Range
    5443..138400
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001329700.2NP_001316629.1  netrin-4 isoform 2 precursor

    Status: REVIEWED

    Source sequence(s)
    AK290591, AK315796, AL137540, AY330211, BI549738, DB473670
    Consensus CDS
    CCDS86325.1
    UniProtKB/Swiss-Prot
    Q9HB63
    UniProtKB/TrEMBL
    A8K3H6, B2RE43
    Related
    ENSP00000447292.1, ENST00000553059.1
    Conserved Domains (5) summary
    smart00180
    Location:395446
    EGF_Lam; Laminin-type epidermal growth factor-like domai
    cd00055
    Location:261320
    EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
    pfam00053
    Location:332392
    Laminin_EGF; Laminin EGF domain
    pfam00055
    Location:43260
    Laminin_N; Laminin N-terminal (Domain VI)
    cl02512
    Location:504603
    NTR_like; NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the ...
  2. NM_001329701.2NP_001316630.1  netrin-4 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AF297711, AK290591, AL137540, BP232567
    Consensus CDS
    CCDS86324.1
    UniProtKB/Swiss-Prot
    Q9HB63
    UniProtKB/TrEMBL
    A8K3H6
    Related
    ENSP00000444432.1, ENST00000538383.5
  3. NM_001329702.1NP_001316631.1  netrin-4 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC008128, AC090001, AL137540
    Consensus CDS
    CCDS86324.1
    UniProtKB/Swiss-Prot
    Q9HB63
  4. NM_021229.4NP_067052.2  netrin-4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_067052.2

    Status: REVIEWED

    Source sequence(s)
    AC090001, AF297711, AL833767, BC013591, BI549738
    Consensus CDS
    CCDS9054.1
    UniProtKB/Swiss-Prot
    Q9HB63
    Related
    ENSP00000340998.4, ENST00000343702.9
    Conserved Domains (5) summary
    smart00180
    Location:395446
    EGF_Lam; Laminin-type epidermal growth factor-like domai
    cd00055
    Location:261320
    EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
    cd03578
    Location:516626
    NTR_netrin-4_like; NTR domain, Netrin-4-like subfamily; composed of the C-terminal NTR domains of netrin-4 (beta netrin) and similar proteins. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration during neural ...
    pfam00053
    Location:332392
    Laminin_EGF; Laminin EGF domain
    pfam00055
    Location:43260
    Laminin_N; Laminin N-terminal (Domain VI)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    95657807..95791155 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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