SLIT1 slit guidance ligand 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLIT1provided by HGNC
Official Full Name: slit guidance ligand 1provided by HGNC
Primary source: HGNC:HGNC:11085
See related: Ensembl:ENSG00000187122 MIM:603742; AllianceGenome:HGNC:11085
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MEGF4; SLIL1; SLIT3; SLIT-1
Summary: Enables Roundabout binding activity. Involved in axon extension involved in axon guidance; motor neuron axon guidance; and negative chemotaxis. Predicted to be located in several cellular components, including endoplasmic reticulum membrane; extracellular region; and focal adhesion. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in brain (RPKM 15.8) and thyroid (RPKM 1.3) See more
Orthologs: mouse all
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Genomic context

Location:: 10q24.1

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (96998038..97185959, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (97878923..98066822, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (98757795..98945716, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Micro RNA-640 Targeting SLIT1 Enhances Glioma Radiosensitivity by Restraining the Activation of Wnt/beta-Catenin Signaling Pathway.
Title: Micro RNA-640 Targeting SLIT1 Enhances Glioma Radiosensitivity by Restraining the Activation of Wnt/β-Catenin Signaling Pathway.
SLIT1-mutated hematopoietic stem cells have a role in clonal hematopoiesis in acquired aplastic anemia
Title: Clonal hematopoiesis by SLIT1-mutated hematopoietic stem cells due to a breakdown of the autocrine loop involving Slit1 in acquired aplastic anemia.
Findings show that SLIT1 is a direct target of SUV39H2 which binds to its promoter and catalyzes H3K9 tri-methylation to silence SLIT1 expression.
Title: SUV39H2 promotes colorectal cancer proliferation and metastasis via tri-methylation of the SLIT1 promoter.
Observational study of gene-disease association. (HuGE Navigator)
Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
Slits are negative regulators of Sdf1 and Cxcr4 in breast cancer cells.
Title: SLITs suppress tumor growth in vivo by silencing Sdf1/Cxcr4 within breast epithelium.
heparin/HS is an integral component of the minimal Slit-Robo signaling complex and serves to stabilize the relatively weak Slit-Robo interaction
Title: A molecular mechanism for the heparan sulfate dependence of slit-robo signaling.
Analysis of alternative splicing and conserved domains in human and mouse slit genes
Title: Conserved modularity and potential for alternate splicing in mouse and human Slit genes.
evidence showing that Slit1 and Slit2 proteins are selective inhibitors and repellents for dorsally projecting, but not for ventrally projecting, cranial motor axons
Title: Slit-mediated repulsion is a key regulator of motor axon pathfinding in the hindbrain.
In fetal and embryonic stem cell cultures Slit-1 inhibited neurite outgrowth.
Title: Axonal growth regulation of fetal and embryonic stem cell-derived dopaminergic neurons by Netrin-1 and Slits.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Gene-alcohol interactions identify several novel blood pressure loci including a promising locus near SLC16A9. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp160, precursor	env	HIV-1 gp160 interacts with SLIT1; predicted interaction to be relevant to viral egress at plasma membrane/extracellular matrix	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH94174 (e-PCR)
- UniSTS:90114

SHGC-156107 (e-PCR)
- UniSTS:182323

D10S1157 (e-PCR)
- UniSTS:5689

RH46480 (e-PCR)
- UniSTS:33087

G32476 (e-PCR)
- UniSTS:117061

D10S1210 (e-PCR)
- UniSTS:57159

G60317 (e-PCR)
- UniSTS:137573

RH66322 (e-PCR)
- UniSTS:76403

D10S1758 (e-PCR), detects polymorphism
- UniSTS:17298

WI-13377 (e-PCR)
- UniSTS:57760

WI-15882 (e-PCR)
- UniSTS:69095

A009E24 (e-PCR)
- UniSTS:3564

RH92281 (e-PCR)
- UniSTS:88305

Readthrough ARHGAP19-SLIT1

Readthrough gene: ARHGAP19-SLIT1, Included gene: ARHGAP19

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables Roundabout binding	IBA Inferred from Biological aspect of Ancestor more info
enables Roundabout binding	IPI Inferred from Physical Interaction more info	PubMed
enables calcium ion binding	NAS Non-traceable Author Statement more info	PubMed
enables heparan sulfate proteoglycan binding	IEA Inferred from Electronic Annotation more info
enables heparin 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 axon extension involved in axon guidance	IDA Inferred from Direct Assay more info	PubMed
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in axon guidance	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration	IDA Inferred from Direct Assay more info	PubMed
involved_in dorsal/ventral axon guidance	IEA Inferred from Electronic Annotation more info
involved_in forebrain morphogenesis	NAS Non-traceable Author Statement more info	PubMed
involved_in motor neuron axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of axon extension involved in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in nuclear migration	IEA Inferred from Electronic Annotation more info
involved_in retinal ganglion cell axon guidance	IEA Inferred from Electronic Annotation more info
involved_in spinal cord development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: slit homolog 1 protein

Names: multiple EGF like domains 4; multiple EGF-like domains protein 4; multiple epidermal growth factor-like domains protein 4; slit homolog 1

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_003061.3 → NP_003052.2 slit homolog 1 protein precursor

See identical proteins and their annotated locations for NP_003052.2

Status: VALIDATED

Source sequence(s)

AL512424, BC028105, BC146761, CD671648

Consensus CDS

CCDS7453.1

UniProtKB/Swiss-Prot

O75093, Q5T0V1, Q8WWZ2, Q9UIL7

UniProtKB/TrEMBL

A6H8V1

Related

ENSP00000266058.4, ENST00000266058.9

Conserved Domains (9) summary

smart00013
Location:33 → 64

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:866 → 915

LRRCT; Leucine rich repeat C-terminal domain

smart00282
Location:1189 → 1322

LamG; Laminin G domain

cd00054
Location:1085 → 1119

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd00116
Location:87 → 220

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:43 → 62

LRR_RI; leucine-rich repeat [structural motif]

pfam12799
Location:334 → 373

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:590 → 649

LRR_8; Leucine rich repeat

cl15307
Location:439 → 469

TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain