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

Gene ID: 20563, updated on 21-Apr-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
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Genomic context

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)
  • Targeted (2)  1 citation
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (3) 

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 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
 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
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
 
acts_upstream_of_or_within chemotaxis IEA
Inferred from Electronic Annotation
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
 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
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
 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
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 region IEA
Inferred from Electronic Annotation
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