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

    Gene ID: 6585, updated on 9-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLIT1 in Genome Data Viewer
    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_000010.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr10.3525 Neighboring gene uncharacterized LOC102723665 Neighboring gene H3K27ac hESC enhancers GRCh37_chr10:98591864-98592578 and GRCh37_chr10:98592579-98593294 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:98593295-98594008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98597029-98597529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98599567-98600066 Neighboring gene Sharpr-MPRA regulatory region 4280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98602601-98603100 Neighboring gene ligand dependent nuclear receptor corepressor Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 35 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:98744001-98744502 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:98744503-98745002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98761702-98762390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98780664-98781497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98790940-98791510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98791511-98792081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:98794025-98794781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98797839-98798339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2666 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:98829552-98830751 Neighboring gene Sharpr-MPRA regulatory region 3512 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:98839846-98840622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98850461-98851078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98860158-98861022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98861023-98861885 Neighboring gene SLIT1 antisense RNA 1 Neighboring gene MPRA-validated peak1061 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98890534-98891034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98900602-98901342 Neighboring gene ARHGAP19-SLIT1 readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:98922776-98923310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:98923311-98923844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98923845-98924378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98945560-98946060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:98946061-98946561 Neighboring gene uncharacterized LOC112268065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2668 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:98962904-98963503 Neighboring gene uncharacterized LOC105378447 Neighboring gene Rho GTPase activating protein 19

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough ARHGAP19-SLIT1

    Readthrough gene: ARHGAP19-SLIT1, Included gene: ARHGAP19

    Clone Names

    • MGC164811

    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

    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)

    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.

    mRNA and Protein(s)

    1. NM_003061.3NP_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:3364
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:866915
      LRRCT; Leucine rich repeat C-terminal domain
      smart00282
      Location:11891322
      LamG; Laminin G domain
      cd00054
      Location:10851119
      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:87220
      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:4362
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:334373
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:590649
      LRR_8; Leucine rich repeat
      cl15307
      Location:439469
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like 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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      96998038..97185959 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      97878923..98066822 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)