SLIT3 slit guidance ligand 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLIT3provided by HGNC
Official Full Name: slit guidance ligand 3provided by HGNC
Primary source: HGNC:HGNC:11087
See related: Ensembl:ENSG00000184347 MIM:603745; AllianceGenome:HGNC:11087
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: MEGF5; SLIL2; SLIT1; slit2; Slit-3
Summary: The protein encoded by this gene is secreted, likely interacting with roundabout homolog receptors to effect cell migration. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
Expression: Broad expression in fat (RPKM 23.0), gall bladder (RPKM 21.4) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q34-q35.1

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (168661740..169301139, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (169196497..169836714, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (168088745..168728143, complement)

Chromosome 5 - NC_000005.10 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Role of SLIT3-ROBO4 Signaling in Endoplasmic Reticulum Stress-Induced Delayed Corneal Epithelial and Nerve Regeneration.
Title: The Role of SLIT3-ROBO4 Signaling in Endoplasmic Reticulum Stress-Induced Delayed Corneal Epithelial and Nerve Regeneration.
Stromal Cell-SLIT3/Cardiomyocyte-ROBO1 Axis Regulates Pressure Overload-Induced Cardiac Hypertrophy.
Title: Stromal Cell-SLIT3/Cardiomyocyte-ROBO1 Axis Regulates Pressure Overload-Induced Cardiac Hypertrophy.
Abnormal expression of SLIT3 induces intravillous vascularization dysplasia in ectopic pregnancy.
Title: Abnormal expression of SLIT3 induces intravillous vascularization dysplasia in ectopic pregnancy.
LncRNA PGM5-AS1 Inhibits the Progression of Bladder Cancer by Regulating miR-587/SLIT3 Axis.
Title: LncRNA PGM5-AS1 Inhibits the Progression of Bladder Cancer by Regulating miR-587/SLIT3 Axis.
LncRNA ubiquitin-binding protein domain protein 10 antisense RNA 1 inhibits colon adenocarcinoma progression via the miR-515-5p/slit guidance ligand 3 axis.
Title: LncRNA ubiquitin-binding protein domain protein 10 antisense RNA 1 inhibits colon adenocarcinoma progression via the miR-515-5p/slit guidance ligand 3 axis.
Single-nucleotide polymorphism rs10036727 in the SLIT3 gene is associated with osteoporosis at the femoral neck in older Mexican postmenopausal women.
Title: Single-nucleotide polymorphism rs10036727 in the SLIT3 gene is associated with osteoporosis at the femoral neck in older Mexican postmenopausal women.
Isolated congenital diaphragm hernia associated with homozygous SLIT3 gene variant in dizygous twins.
Title: Isolated congenital diaphragm hernia associated with homozygous SLIT3 gene variant in dizygous twins.
Identification of slit3 as a locus affecting nicotine preference in zebrafish and human smoking behaviour.
Title: Identification of slit3 as a locus affecting nicotine preference in zebrafish and human smoking behaviour.
the level of gingival crevicular fluid SLIT3 was higher in patients with periodontitis than in healthy individuals and was closely associated with clinical attachment loss and radiographic bone loss
Title: Gingival crevicular fluid levels of SLIT3 are increased in periodontal disease.
SLIT3 and SPARCL1 can be regulated by DNA methylation and down-regulated in lung adenocarcinoma
Title: [Expression and prognosis effect of methylation-regulated SLIT3 and SPARCL1 genes in smoking-related lung adenocarcinoma].

Submit: New GeneRIF Correction See all GeneRIFs (34)

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
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-143393 (e-PCR)
- UniSTS:184065

SHGC-105270 (e-PCR)
- UniSTS:169223

bac51840S (e-PCR)
- UniSTS:181514

bac51858T (e-PCR)
- UniSTS:181516

D5S400 (e-PCR), detects polymorphism
- UniSTS:33557

D5S2075 (e-PCR)
- UniSTS:55578

SHGC-149272 (e-PCR)
- UniSTS:184095

RH92323 (e-PCR)
- UniSTS:88355

AFMa109xa5 (e-PCR)
- UniSTS:52260

SHGC-106334 (e-PCR)
- UniSTS:169765

SGC44608 (e-PCR)
- UniSTS:13865

D5S2045 (e-PCR), detects polymorphism
- UniSTS:25646

WI-17129 (e-PCR)
- UniSTS:48432

RH92760 (e-PCR)
- UniSTS:91441

D5S2559 (e-PCR)
- UniSTS:73012

G16948 (e-PCR)
- UniSTS:3128

Slit3 (e-PCR), detects polymorphism
- UniSTS:463432

D5S2043 (e-PCR), detects polymorphism
- UniSTS:39752

WI-14817 (e-PCR)
- UniSTS:40269

G16886 (e-PCR)
- UniSTS:40271

A003N35 (e-PCR)
- UniSTS:15955

SHGC-147724 (e-PCR)
- UniSTS:175972

SHGC-150783 (e-PCR)
- UniSTS:173670

D5S2052 (e-PCR), detects polymorphism
- UniSTS:61557

SHGC-150624 (e-PCR)
- UniSTS:173174

RH102563 (e-PCR)
- UniSTS:96897

SHGC-145693 (e-PCR)
- UniSTS:174731

SHGC-83613 (e-PCR)
- UniSTS:95897

SHGC-107512 (e-PCR)
- UniSTS:170409

D5S605 (e-PCR)
- UniSTS:426

WI-11149 (e-PCR)
- UniSTS:19882

SHGC-105008 (e-PCR)
- UniSTS:183985

SHGC-144356 (e-PCR)
- UniSTS:172211

SLIT3_8631 (e-PCR)
- UniSTS:467903

SGC32449 (e-PCR)
- UniSTS:25538

STS-R89593 (e-PCR)
- UniSTS:18633

D21S2030 (e-PCR)
- UniSTS:27868

D5S400 (e-PCR), detects polymorphism
- UniSTS:49117

G16910 (e-PCR)
- UniSTS:31969

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 heparin binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in Roundabout signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in aortic valve morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in apoptotic process involved in luteolysis	IEP Inferred from Expression Pattern more info	PubMed
involved_in atrioventricular valve morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
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
involved_in cellular response to hormone stimulus	IEP Inferred from Expression Pattern 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 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 cell growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of chemokine-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in response to cortisol	IEP Inferred from Expression Pattern more info	PubMed
involved_in ventricular septum morphogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: slit homolog 3 protein

Names: multiple EGF like domains 5; multiple EGF-like domains protein 5; multiple epidermal growth factor-like domains protein 5; slit homolog 3

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.

Genomic

NG_033081.2 RefSeqGene

Range

5000..644399

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001271946.2 → NP_001258875.2 slit homolog 3 protein isoform 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC008409, AC008479, AC011365, AC027311, AC094081

Consensus CDS

CCDS64311.1

Related

ENSP00000332164.8, ENST00000332966.8

Conserved Domains (10) summary

TIGR00864
Location:636 → 714

PCC; polycystin cation channel protein

smart00013
Location:33 → 64

LRRNT; Leucine rich repeat N-terminal domain

smart00282
Location:1188 → 1321

LamG; Laminin G domain

COG4886
Location:62 → 220

LRR; Leucine-rich repeat (LRR) protein [Transcription]

cd00054
Location:1081 → 1117

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 ...

sd00033
Location:64 → 86

LRR_RI; leucine-rich repeat [structural motif]

pfam00008
Location:1130 → 1160

EGF; EGF-like domain

pfam13855
Location:776 → 835

LRR_8; Leucine rich repeat

NF033189
Location:107 → 478

internalin_A; class 1 internalin InlA

cl21545
Location:1473 → 1528

GHB_like; Glycoprotein hormone beta chain homologues
NM_003062.4 → NP_003053.2 slit homolog 3 protein isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AC008409, AC008479, AC011365, AC027311, AC094081

Consensus CDS

CCDS4369.1

UniProtKB/Swiss-Prot

A6H8U9, J3KNP3, O75094, O95804, Q9UFH5

Related

ENSP00000430333.2, ENST00000519560.6