Mouse Gene Slit1 (ENSMUST00000025993.9) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus slit guidance ligand 1 (Slit1), mRNA. (from RefSeq NM_015748)
Gencode Transcript: ENSMUST00000025993.9
Gencode Gene: ENSMUSG00000025020.11
Transcript (Including UTRs)
   Position: mm10 chr19:41,600,259-41,743,665 Size: 143,407 Total Exon Count: 37 Strand: -
Coding Region
   Position: mm10 chr19:41,600,451-41,743,408 Size: 142,958 Coding Exon Count: 37 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:41,600,259-41,743,665)mRNA (may differ from genome)Protein (1531 aa)
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BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SLIT1_MOUSE
DESCRIPTION: RecName: Full=Slit homolog 1 protein; Short=Slit-1; Flags: Precursor;
FUNCTION: Thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions (By similarity). SLIT1 and SLIT2 together seem to be essential for midline guidance in the forebrain by acting as repulsive signal preventing inappropriate midline crossing by axons projecting from the olfactory bulb.
SUBUNIT: Interacts with GREM1 (By similarity) and ROBO1.
SUBCELLULAR LOCATION: Secreted (By similarity).
DEVELOPMENTAL STAGE: During retinal development, is expressed at E12.5 in the dorsocentral region of the retina, and at E17.5 is only very weakly expressed. In the developing optic chiasm is expressed at E12.5 around the junction of the optic nerve and the brain, with strongest expression dorsal to the site at which the optic stalk joins the diencephalon, and also weakly in a subset of the CD44/SSEA neurons. In the more dorsal region of the developing optic chiasm, is expressed in some distance posterior to the axons. However, more ventrally, is expressed in a region directly adjacent to the path taken by the RGC axons. By E17.5 is not longer be detected at the junction of the brain and optic nerve and is only weakly expressed by the CD44/SSEA neurons. Outside the developing brain detected at between E8.5 and E9.5 in the primordiun of the branchial arches, between E9.5 and 10.5 in the posterior dermamyotome. By E11.5 the expression pattern along somite boundaries was most prominent caudally. Weak expression was also observed in the nasal pit at E11.5. From E13.5 to E17.5 expression was observed in the trigeminal ganglion, in the olfactory epithelium, and in the neural layer of the retina in the developing eye (with strongest expression in the inner nuclear layer).
DISRUPTION PHENOTYPE: Mice show significant axon guidance errors in a variety of pathways, including corticofugal, callosal and thalamocortical tracts. Mice double-deficient in SLIT1 and SLIT2 show retinal axon guidance defects and a disorganized lateral olfactory tract (LOT).
SIMILARITY: Contains 1 CTCK (C-terminal cystine knot-like) domain.
SIMILARITY: Contains 9 EGF-like domains.
SIMILARITY: Contains 1 laminin G-like domain.
SIMILARITY: Contains 20 LRR (leucine-rich) repeats.
SIMILARITY: Contains 4 LRRCT domains.
SIMILARITY: Contains 4 LRRNT domains.
SEQUENCE CAUTION: Sequence=BAC65658.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -100.70257-0.392 Picture PostScript Text
3' UTR -79.60192-0.415 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR000483 - Cys-rich_flank_reg_C
IPR006207 - Cys_knot_C
IPR000742 - EG-like_dom
IPR001881 - EGF-like_Ca-bd
IPR013032 - EGF-like_CS
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR018097 - EGF_Ca-bd_CS
IPR003645 - Fol_N
IPR001791 - Laminin_G
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp
IPR000372 - LRR-contain_N

Pfam Domains:
PF00008 - EGF-like domain
PF00054 - Laminin G domain
PF01462 - Leucine rich repeat N-terminal domain
PF01463 - Leucine rich repeat C-terminal domain
PF02210 - Laminin G domain
PF12661 - Human growth factor-like EGF
PF13306 - Leucine rich repeats (6 copies)
PF13855 - Leucine rich repeat

SCOP Domains:
49899 - Concanavalin A-like lectins/glucanases
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1
56436 - C-type lectin-like
57196 - EGF/Laminin
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on Q80TR4
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
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Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005509 calcium ion binding
GO:0043395 heparan sulfate proteoglycan binding
GO:0048495 Roundabout binding

Biological Process:
GO:0007097 nuclear migration
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0007409 axonogenesis
GO:0007411 axon guidance
GO:0008045 motor neuron axon guidance
GO:0021772 olfactory bulb development
GO:0022028 tangential migration from the subventricular zone to the olfactory bulb
GO:0022029 telencephalon cell migration
GO:0030154 cell differentiation
GO:0031290 retinal ganglion cell axon guidance
GO:0033563 dorsal/ventral axon guidance
GO:0048812 neuron projection morphogenesis
GO:0048843 negative regulation of axon extension involved in axon guidance
GO:0048846 axon extension involved in axon guidance
GO:0050919 negative chemotaxis
GO:0051964 negative regulation of synapse assembly

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005622 intracellular
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  BC057131 - Mus musculus slit homolog 1 (Drosophila), mRNA (cDNA clone MGC:63234 IMAGE:6827560), complete cds.
BC062091 - Mus musculus slit homolog 1 (Drosophila), mRNA (cDNA clone MGC:67195 IMAGE:6827560), complete cds.
AK122376 - Mus musculus mRNA for mKIAA0813 protein.
AF144627 - Mus musculus SLIT1 (Slit1) mRNA, complete cds.
AB345128 - Mus musculus non-coding RNA, oocyte_clustered_small_RNA10329, complete sequence.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04360 - Axon guidance

Reactome (by CSHL, EBI, and GO)

Protein Q80TR4 (Reactome details) participates in the following event(s):

R-MMU-8985829 Slit1 binds Robo1,(Robo2)
R-MMU-8985822 Nck2 binds to Robo1,(Robo2)
R-MMU-9010235 Robo1 binds Flrt3

-  Other Names for This Gene
  Alternate Gene Symbols: Kiaa0813, NM_015748, Q80TR4, Q9WVB5, SLIT1_MOUSE, uc008hmf.1, uc008hmf.2, uc008hmf.3
UCSC ID: uc008hmf.3
RefSeq Accession: NM_015748
Protein: Q80TR4 (aka SLIT1_MOUSE or SLT1_MOUSE)
CCDS: CCDS29812.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.