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NTN1 netrin 1 [ Homo sapiens (human) ]

Gene ID: 9423, updated on 18-Sep-2024

Summary

Official Symbol
NTN1provided by HGNC
Official Full Name
netrin 1provided by HGNC
Primary source
HGNC:HGNC:8029
See related
Ensembl:ENSG00000065320 MIM:601614; AllianceGenome:HGNC:8029
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
NET1; MRMV4; NTN1L
Summary
Netrin is included in a family of laminin-related secreted proteins. The function of this gene has not yet been defined; however, netrin is thought to be involved in axon guidance and cell migration during development. Mutations and loss of expression of netrin suggest that variation in netrin may be involved in cancer development. [provided by RefSeq, Jul 2008]
Expression
Broad expression in heart (RPKM 20.8), esophagus (RPKM 16.8) and 17 other tissues See more
Orthologs
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Genomic context

See NTN1 in Genome Data Viewer
Location:
17p13.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (9003087..9244000)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (8910268..9150998)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (8924827..9147317)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11717 Neighboring gene phosphoinositide-3-kinase regulatory subunit 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8857999-8858500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8858501-8859000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8191 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11721 Neighboring gene PIK3R5 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8193 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:8907139-8907768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8924225-8924768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8936035-8936534 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:8954033-8954690 and GRCh37_chr17:8954691-8955350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:8955351-8956008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:8956741-8957362 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:8957363-8957982 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:8957983-8958603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8990973-8991474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8991475-8991974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9041579-9042287 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9054043-9054886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9058975-9059476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9059477-9059976 Neighboring gene uncharacterized LOC101928266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9083413-9083914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9086141-9086640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9099203-9100124 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:9124521-9125720 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9128413-9128964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9129517-9130068 Neighboring gene uncharacterized LOC124903923 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9130069-9130619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9131120-9131620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9133199-9133700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8197 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9161269-9161860 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:9176317-9176818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11724 Neighboring gene NANOG hESC enhancer GRCh37_chr17:9225613-9226114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9232495-9233000 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:9233001-9233506 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:9233507-9234012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:9234013-9234518 Neighboring gene syntaxin 8 Neighboring gene Sharpr-MPRA regulatory region 2542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:9377307-9377808 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9409688-9410556 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:9410557-9411424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11727 Neighboring gene ribosomal protein L19 pseudogene 18 Neighboring gene cilia and flagella associated protein 52

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

Associated conditions

Description Tests
Mirror movements 4
MedGen: C4748869 OMIM: 618264 GeneReviews: Congenital Mirror Movements
Compare labs

EBI GWAS Catalog

Description
Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
EBI GWAS Catalog
Identification of inherited genetic variations influencing prognosis in early-onset breast cancer.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of netrin 1 (NTN1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in Cdc42 protein signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in Ras protein signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in anterior/posterior axon guidance IEA
Inferred from Electronic Annotation
more info
 
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
 
involved_in chemorepulsion of axon ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in glial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in inner ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in mammary gland duct morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in motor neuron migration IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of axon extension IEA
Inferred from Electronic Annotation
more info
 
involved_in nuclear migration IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of axon extension ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of cell motility ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of glial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of glial cell migration IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of synapse assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in substrate-dependent cell migration, cell extension ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in actin cytoskeleton IDA
Inferred from Direct Assay
more info
 
located_in basement membrane IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in extracellular region IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
 
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
netrin-1
Names
epididymis tissue protein Li 131P
netrin 1, mouse, homolog of

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)

  1. NM_004822.3NP_004813.2  netrin-1 precursor

    See identical proteins and their annotated locations for NP_004813.2

    Status: REVIEWED

    Source sequence(s)
    AC005695, AC090610, U75586
    Consensus CDS
    CCDS11148.1
    UniProtKB/Swiss-Prot
    E9KL51, O95631
    Related
    ENSP00000173229.2, ENST00000173229.7
    Conserved Domains (4) summary
    smart00136
    Location:46283
    LamNT; Laminin N-terminal domain (domain VI)
    cd00055
    Location:284329
    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 ...
    cd03579
    Location:487601
    NTR_netrin-1_like; NTR domain, Netrin-1-like subfamily; The C-terminal NTR domain of netrins is also called domain C in the context of C. elegans netrin UNC-6. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration ...
    pfam00053
    Location:404441
    Laminin_EGF; Laminin EGF domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    9003087..9244000
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047437096.1XP_047293052.1  netrin-1 isoform X1

    UniProtKB/Swiss-Prot
    E9KL51, O95631
  2. XM_006721595.4XP_006721658.1  netrin-1 isoform X1

    See identical proteins and their annotated locations for XP_006721658.1

    UniProtKB/Swiss-Prot
    E9KL51, O95631
    Conserved Domains (4) summary
    smart00136
    Location:46283
    LamNT; Laminin N-terminal domain (domain VI)
    cd00055
    Location:284329
    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 ...
    cd03579
    Location:487601
    NTR_netrin-1_like; NTR domain, Netrin-1-like subfamily; The C-terminal NTR domain of netrins is also called domain C in the context of C. elegans netrin UNC-6. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration ...
    pfam00053
    Location:404441
    Laminin_EGF; Laminin EGF domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    8910268..9150998
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054317835.1XP_054173810.1  netrin-1 isoform X1

    UniProtKB/Swiss-Prot
    E9KL51, O95631
  2. XM_054317834.1XP_054173809.1  netrin-1 isoform X1

    UniProtKB/Swiss-Prot
    E9KL51, O95631