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    Slit2 slit guidance ligand 2 [ Mus musculus (house mouse) ]

    Gene ID: 20563, updated on 9-Dec-2024

    Summary

    Official Symbol
    Slit2provided by MGI
    Official Full Name
    slit guidance ligand 2provided by MGI
    Primary source
    MGI:MGI:1315205
    See related
    Ensembl:ENSMUSG00000031558 AllianceGenome:MGI:1315205
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Slil3; Drad-1; slit-2; mKIAA4141; b2b1200.1Clo; E030015M03Rik; E130320P19Rik
    Summary
    The protein encoded by this gene is a member of the Slit family of secreted glycoproteins, which function as ligands for the Robo family of immunoglobulin receptors. Slit proteins play highly conserved roles in axon guidance and neuronal migration and may also have functions during other cell migration processes including leukocyte migration. In mammals, members of the slit family are characterized by an N-terminal signal peptide, four leucine-rich repeats, nine epidermal growth factor repeats, and a C-terminal cysteine knot. Mice deficient for this gene exhibit abnormal axonal projections in the embryonic forebrain and develop supernumerary uretic buds that maintain improper connections to the nephric duct. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
    Expression
    Broad expression in CNS E11.5 (RPKM 6.3), limb E14.5 (RPKM 5.2) and 18 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Slit2 in Genome Data Viewer
    Location:
    5 B3; 5 26.05 cM
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (48138633..48465077)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (47981291..48307735)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene ribosomal protein L7A pseudogene Neighboring gene calmodulin 2 pseudogene Neighboring gene STARR-seq mESC enhancer starr_13022 Neighboring gene STARR-seq mESC enhancer starr_13023 Neighboring gene STARR-seq mESC enhancer starr_13024 Neighboring gene microRNA 218-1 Neighboring gene STARR-seq mESC enhancer starr_13026 Neighboring gene STARR-positive B cell enhancer ABC_E4755 Neighboring gene RIKEN cDNA 5730480H06 gene Neighboring gene PARK2 co-regulated-like Neighboring gene Kv channel interacting protein 4

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Chemically induced (ENU) (1) 
    • Endonuclease-mediated (3) 
    • Targeted (2)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA4141

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables GTPase inhibitor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables Roundabout binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables Roundabout binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables chemorepellent activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables heparan sulfate proteoglycan binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables heparin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables heparin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables heparin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables laminin-1 binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables proteoglycan binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables signaling receptor binding TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Roundabout signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in aortic valve morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in axon extension involved in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within axon guidance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within axonogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within axonogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in branching morphogenesis of an epithelial tube ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell migration involved in sprouting angiogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cell-cell adhesion IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within cell-cell adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to heparin ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chemorepulsion involved in postnatal olfactory bulb interneuron migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in corticospinal neuron axon guidance through spinal cord ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within dorsal/ventral axon guidance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within dorsal/ventral axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within in utero embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in induction of negative chemotaxis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within kidney development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within mammary duct terminal end bud growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within mammary gland duct morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within mammary gland duct morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within metanephros development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in motor neuron axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within negative chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative chemotaxis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of actin filament polymerization ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of axon extension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell growth IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of cell growth ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of cell population proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of cellular response to growth factor stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of chemokine-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of endothelial cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of gene expression IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of lamellipodium assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of leukocyte chemotaxis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of monocyte chemotaxis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of mononuclear cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of neutrophil chemotaxis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of protein phosphorylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of retinal ganglion cell axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of small GTPase mediated signal transduction ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of smooth muscle cell chemotaxis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of smooth muscle cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of vascular permeability ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in neuron projection extension ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neuron projection morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within neuron projection morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within olfactory bulb development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of synapse assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in pulmonary valve morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in retinal ganglion cell axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within retinal ganglion cell axon guidance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within retinal ganglion cell axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in retinal ganglion cell axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within telencephalon cell migration IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in ureteric bud development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ventricular septum morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cell body ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cell projection ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
     
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
     
    located_in extracellular space HDA PubMed 
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
     
    located_in neuronal cell body ISO
    Inferred from Sequence Orthology
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    slit homolog 2 protein
    Names
    downregulated during adipocyte differentiation-1
    neurogenic extracellular slit protein

    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_001291227.2NP_001278156.1  slit homolog 2 protein isoform a precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC101004, AC113542, AC157351, AK053182, AW556809, BE944330
      Consensus CDS
      CCDS71586.1
      UniProtKB/TrEMBL
      B2RX05, G3UYX7
      Related
      ENSMUSP00000134263.2, ENSMUST00000174421.8
      Conserved Domains (10) summary
      smart00013
      Location:2758
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:863912
      LRRCT; Leucine rich repeat C-terminal domain
      smart00179
      Location:10021033
      EGF_CA; Calcium-binding EGF-like domain
      smart00282
      Location:11961329
      LamG; Laminin G domain
      cd00054
      Location:10891125
      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:81214
      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:3856
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:328368
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:781841
      LRR_8; Leucine rich repeat
      cl15307
      Location:434464
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
    2. NM_001291228.2NP_001278157.1  slit homolog 2 protein isoform b precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks alternate in-frame exons in the 5' and central coding regions compared to variant 1. It encodes isoform b, which is shorter than isoform a.
      Source sequence(s)
      AC101004, AC113542, AC157351, AK053182, AW556809, BE944330
      Consensus CDS
      CCDS71588.1
      UniProtKB/TrEMBL
      B7ZNW9, G3UY21
      Related
      ENSMUSP00000133912.2, ENSMUST00000174313.8
      Conserved Domains (8) summary
      smart00013
      Location:2758
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:855904
      LRRCT; Leucine rich repeat C-terminal domain
      smart00282
      Location:11791312
      LamG; Laminin G domain
      cd00054
      Location:10721108
      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:81214
      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:3856
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:328368
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:773833
      LRR_8; Leucine rich repeat
    3. NM_178804.5NP_848919.3  slit homolog 2 protein isoform c precursor

      See identical proteins and their annotated locations for NP_848919.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks three alternate in-frame exons compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AC101004, AK033292, AK053182, AW556809, BC079911, BE944330
      Consensus CDS
      CCDS19280.1
      UniProtKB/Swiss-Prot
      E9QKB4, Q9R1B9, Q9Z166
      UniProtKB/TrEMBL
      B7ZNW9
      Related
      ENSMUSP00000133840.3, ENSMUST00000173107.8
      Conserved Domains (8) summary
      smart00013
      Location:2758
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:851900
      LRRCT; Leucine rich repeat C-terminal domain
      smart00282
      Location:11751308
      LamG; Laminin G domain
      cd00054
      Location:10681104
      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:81214
      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:3856
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:324364
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:769829
      LRR_8; Leucine rich repeat

    RNA

    1. NR_111900.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks three internal exons and uses an alternate splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC101004, AC113542, AC157351, AK053182, AW556809, BE944330

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      48138633..48465077
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006503815.4XP_006503878.1  slit homolog 2 protein isoform X3

      UniProtKB/TrEMBL
      A0A140T8T2, B7ZNW9
      Related
      ENSMUSP00000127615.4, ENSMUST00000170109.9
      Conserved Domains (7) summary
      TIGR00864
      Location:8361017
      PCC; polycystin cation channel protein
      smart00013
      Location:2758
      LRRNT; Leucine rich repeat N-terminal domain
      smart00282
      Location:11871320
      LamG; Laminin G domain
      cd00054
      Location:10801116
      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:3856
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:782841
      LRR_8; Leucine rich repeat
      NF033189
      Location:561858
      internalin_A; class 1 internalin InlA
    2. XM_006503814.4XP_006503877.1  slit homolog 2 protein isoform X2

      UniProtKB/TrEMBL
      B2RX05
      Conserved Domains (8) summary
      TIGR00864
      Location:8281009
      PCC; polycystin cation channel protein
      smart00013
      Location:2758
      LRRNT; Leucine rich repeat N-terminal domain
      smart00282
      Location:11881321
      LamG; Laminin G domain
      cd00054
      Location:10811117
      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:3856
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00008
      Location:9981025
      EGF; EGF-like domain
      pfam13855
      Location:774833
      LRR_8; Leucine rich repeat
      NF033189
      Location:553850
      internalin_A; class 1 internalin InlA
    3. XM_006503813.4XP_006503876.1  slit homolog 2 protein isoform X1

      UniProtKB/TrEMBL
      B2RX05
      Conserved Domains (8) summary
      TIGR00864
      Location:8321013
      PCC; polycystin cation channel protein
      smart00013
      Location:2758
      LRRNT; Leucine rich repeat N-terminal domain
      smart00282
      Location:11921325
      LamG; Laminin G domain
      cd00054
      Location:10851121
      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:3856
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00008
      Location:10021029
      EGF; EGF-like domain
      pfam13855
      Location:778837
      LRR_8; Leucine rich repeat
      NF033189
      Location:557854
      internalin_A; class 1 internalin InlA
    4. XM_006503816.4XP_006503879.1  slit homolog 2 protein isoform X4

      UniProtKB/TrEMBL
      B7ZNW9
      Conserved Domains (7) summary
      TIGR00864
      Location:8321013
      PCC; polycystin cation channel protein
      smart00013
      Location:2758
      LRRNT; Leucine rich repeat N-terminal domain
      smart00282
      Location:11831316
      LamG; Laminin G domain
      cd00054
      Location:10761112
      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:3856
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:778837
      LRR_8; Leucine rich repeat
      NF033189
      Location:557854
      internalin_A; class 1 internalin InlA