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

    Gene ID: 6586, updated on 13-May-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
    mouse all
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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. 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.
    2. 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.
    3. Abnormal expression of SLIT3 induces intravillous vascularization dysplasia in ectopic pregnancy.
      Title: Abnormal expression of SLIT3 induces intravillous vascularization dysplasia in ectopic pregnancy.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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
    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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    NEW Try the new Transcript table

    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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