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Slit3 slit guidance ligand 3 [ Mus musculus (house mouse) ]

Gene ID: 20564, updated on 18-Apr-2024

Summary

Official Symbol
Slit3provided by MGI
Official Full Name
slit guidance ligand 3provided by MGI
Primary source
MGI:MGI:1315202
See related
Ensembl:ENSMUSG00000056427 AllianceGenome:MGI:1315202
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Slil2; Slit1; b2b2362.1Clo
Summary
Predicted to enable Roundabout binding activity and heparin binding activity. Involved in aortic valve morphogenesis; atrioventricular valve morphogenesis; and ventricular septum morphogenesis. Acts upstream of or within several processes, including axon guidance; negative regulation of cell population proliferation; and negative regulation of gene expression. Located in extracellular space. Is expressed in several structures, including alimentary system; branchial arch; central nervous system; heart; and sensory organ. Used to study congenital diaphragmatic hernia. Orthologous to human SLIT3 (slit guidance ligand 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lung adult (RPKM 31.9), subcutaneous fat pad adult (RPKM 28.2) and 24 other tissues See more
Orthologs
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Genomic context

Location:
11 A4; 11 20.29 cM
Exon count:
36
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (35012283..35599334)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (35121456..35708507)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_29155 Neighboring gene predicted gene, 25799 Neighboring gene predicted gene, 33277 Neighboring gene STARR-seq mESC enhancer starr_29156 Neighboring gene STARR-seq mESC enhancer starr_29157 Neighboring gene STARR-positive B cell enhancer mm9_chr11:34858275-34858576 Neighboring gene STARR-seq mESC enhancer starr_29158 Neighboring gene predicted gene, 26070 Neighboring gene predicted gene, 33453 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:35139747-35139930 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:35137922-35138105 Neighboring gene predicted gene, 46277 Neighboring gene STARR-seq mESC enhancer starr_29166 Neighboring gene STARR-seq mESC enhancer starr_29177 Neighboring gene STARR-seq mESC enhancer starr_29179 Neighboring gene STARR-seq mESC enhancer starr_29180 Neighboring gene predicted gene, 39705 Neighboring gene microRNA 218-2 Neighboring gene predicted gene, 46278 Neighboring gene STARR-positive B cell enhancer ABC_E1137 Neighboring gene microRNA 103-1 Neighboring gene pantothenate kinase 3 Neighboring gene fibrillarin-like 1

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)
  • Gene trapped (1)  1 citation
  • Targeted (5)  1 citation
  • Endonuclease-mediated (6) 
  • Chemically induced (ENU) (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
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 heparin binding IBA
Inferred from Biological aspect of Ancestor
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
 
acts_upstream_of_or_within animal organ morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within animal organ morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in aortic valve morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in atrioventricular 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
 
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within axon guidance IDA
Inferred from Direct Assay
more info
PubMed 
involved_in axon guidance ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
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
 
involved_in negative chemotaxis ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cell growth 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 chemokine-mediated signaling pathway 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 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in ventricular septum morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
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 plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
slit homolog 3 protein
Names
slit-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.

mRNA and Protein(s)

  1. NM_011412.3NP_035542.2  slit homolog 3 protein precursor

    See identical proteins and their annotated locations for NP_035542.2

    Status: VALIDATED

    Source sequence(s)
    AF088902, AK147292, BB645429, BC150780
    Consensus CDS
    CCDS24542.1
    UniProtKB/Swiss-Prot
    B1ATW4, Q9WVB4
    UniProtKB/TrEMBL
    B2RX06
    Related
    ENSMUSP00000066857.4, ENSMUST00000069837.4
    Conserved Domains (12) summary
    smart00013
    Location:725756
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:857906
    LRRCT; Leucine rich repeat C-terminal domain
    cd00054
    Location:10761110
    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:49220
    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:6486
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00008
    Location:11231153
    EGF; EGF-like domain
    pfam01462
    Location:3360
    LRRNT; Leucine rich repeat N-terminal domain
    pfam02210
    Location:11881314
    Laminin_G_2; Laminin G domain
    pfam12799
    Location:331371
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:775835
    LRR_8; Leucine rich repeat
    cl15307
    Location:437467
    TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
    cl21545
    Location:14631519
    GHB_like; Glycoprotein hormone beta chain homologues

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_000077.7 Reference GRCm39 C57BL/6J

    Range
    35012283..35599334
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)