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

Gene ID: 6586, updated on 7-Apr-2024

Summary

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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
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Genomic context

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See SLIT3 in Genome Data Viewer
Location:
5q34-q35.1
Exon count:
37
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (168661740..169301139, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (169196497..169836714, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (168088745..168728143, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23591 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:168006261-168006804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16599 Neighboring gene NANOG hESC enhancer GRCh37_chr5:168027313-168027855 Neighboring gene microRNA 103a-1 Neighboring gene microRNA 103b-1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:168064510-168065010 Neighboring gene pantothenate kinase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:168098339-168098914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:168110883-168111382 Neighboring gene ribosomal protein L10 pseudogene 9 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:168139117-168140316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:168148006-168148550 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:168173006-168173578 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:168173579-168174150 Neighboring gene SLIT3 antisense RNA 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:168180411-168180912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:168180913-168181412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:168182248-168183075 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:168212567-168213766 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:168249557-168250756 Neighboring gene microRNA 218-2 Neighboring gene uncharacterized LOC105377713 Neighboring gene uncharacterized LOC107986472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16600 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:168411250-168411831 Neighboring gene uncharacterized LOC124901130 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:168433635-168434834 Neighboring gene SLIT3 antisense RNA 1 Neighboring gene uncharacterized LOC105377712 Neighboring gene NANOG hESC enhancer GRCh37_chr5:168554345-168554846 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:168568788-168568956 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:168590816-168591682 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:168591683-168592547 Neighboring gene microRNA 585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:168800883-168801384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23592 Neighboring gene uncharacterized LOC124901131 Neighboring gene uncharacterized LOC105377714 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:168884987-168885782 Neighboring gene uncharacterized LOC105377715 Neighboring gene RNA, U6 small nuclear 477, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Abnormal expression of SLIT3 induces intravillous vascularization dysplasia in ectopic pregnancy. Zhu Q, et al. PeerJ, 2023. PMID 36793891, Free PMC Article
  2. Isolated congenital diaphragm hernia associated with homozygous SLIT3 gene variant in dizygous twins. Kaya TB, et al. Eur J Med Genet, 2021 Jul. PMID 33933663
  3. Single-nucleotide polymorphism rs10036727 in the SLIT3 gene is associated with osteoporosis at the femoral neck in older Mexican postmenopausal women. Hidalgo-Bravo A, et al. Gynecol Endocrinol, 2020 Dec. PMID 32762475
  4. Gingival crevicular fluid levels of SLIT3 are increased in periodontal disease. Zhong W, et al. Oral Dis, 2020 Jan. PMID 31696592
  5. Suppression of Slit3 induces tumor proliferation and chemoresistance in hepatocellular carcinoma through activation of GSK3β/β-catenin pathway. Ng L, et al. BMC Cancer, 2018 Jun 1. PMID 29859044, Free PMC Article

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Abnormal expression of SLIT3 induces intravillous vascularization dysplasia in ectopic pregnancy.
    Title: Abnormal expression of SLIT3 induces intravillous vascularization dysplasia in ectopic pregnancy.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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].
  10. High genetic risk scores of SLIT3, PLEKHA5 and PPP2R2C variants increase susceptibility to increased insulin resistance by 50% and its risk may be exacerbated by consuming more than 10 cups coffee/week or 220 mg caffeine/day.
    Title: High genetic risk scores of SLIT3, PLEKHA5 and PPP2R2C variants increased insulin resistance and interacted with coffee and caffeine consumption in middle-aged adults.
Submit: New GeneRIF Correction See all GeneRIFs (33)

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
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10764

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

  1. NG_033081.2 RefSeqGene

    Range
    5000..644399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    168661740..169301139 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009779.1 → XP_016865268.1  slit homolog 3 protein isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    169196497..169836714 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054353256.1 → XP_054209231.1  slit homolog 3 protein isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75094.3 GenPept UniProtKB/Swiss-Prot:O75094

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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