Human Gene SLIT1 (ENST00000266058.9_7) from GENCODE V47lift37
  Description: slit guidance ligand 1 (from RefSeq NM_003061.3)
Gencode Transcript: ENST00000266058.9_7
Gencode Gene: ENSG00000187122.17_11
Transcript (Including UTRs)
   Position: hg19 chr10:98,757,795-98,945,716 Size: 187,922 Total Exon Count: 37 Strand: -
Coding Region
   Position: hg19 chr10:98,760,869-98,945,431 Size: 184,563 Coding Exon Count: 37 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:98,757,795-98,945,716)mRNA (may differ from genome)Protein (1534 aa)
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-  Comments and Description Text from UniProtKB
  ID: SLIT1_HUMAN
DESCRIPTION: RecName: Full=Slit homolog 1 protein; Short=Slit-1; AltName: Full=Multiple epidermal growth factor-like domains protein 4; Short=Multiple EGF-like domains protein 4; 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 ROBO1 and GREM1 (By similarity).
SUBCELLULAR LOCATION: Secreted (By similarity).
TISSUE SPECIFICITY: Predominantly expressed in adult forebrain. Expressed in fetal brain, lung and kidney.
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=BAA32465.3; Type=Erroneous initiation;

-  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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.74 RPKM in Pituitary
Total median expression: 5.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -157.20285-0.552 Picture PostScript Text
3' UTR -1280.003074-0.416 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
IPR025875 - Leu-rich_rpt_2_copies
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 - BspA type Leucine rich repeat region (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
57196 - EGF/Laminin
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on O75093
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion 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:0048846 axon extension involved in axon guidance
GO:0048853 forebrain morphogenesis
GO:0050919 negative chemotaxis
GO:0051964 negative regulation of synapse assembly
GO:0021834 chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005622 intracellular


-  Descriptions from all associated GenBank mRNAs
  AB011537 - Homo sapiens mRNA for MEGF4, partial cds.
BC146761 - Homo sapiens slit homolog 1 (Drosophila), mRNA (cDNA clone MGC:166830 IMAGE:9007200), complete cds.
AB017167 - Homo sapiens mRNA for Slit-1 protein, complete cds.
BC146851 - Homo sapiens slit homolog 1 (Drosophila), mRNA (cDNA clone MGC:181954 IMAGE:9056779), complete cds.
AB383997 - Synthetic construct DNA, clone: pF1KSDA0813, Homo sapiens SLIT1 gene for slit homolog 1 protein precursor, complete cds, without stop codon, in Flexi system.
AY029183 - Homo sapiens SLIT1 isoform B (SLIT1) mRNA, partial cds, alternatively spliced.
BC028105 - Homo sapiens slit homolog 1 (Drosophila), mRNA (cDNA clone IMAGE:5247200), with apparent retained intron.
AK125438 - Homo sapiens cDNA FLJ43449 fis, clone OCBBF2032671.
AY336750 - Homo sapiens putative RhoGAP protein mRNA, complete cds.
JD277827 - Sequence 258851 from Patent EP1572962.
JD151177 - Sequence 132201 from Patent EP1572962.
JD513060 - Sequence 494084 from Patent EP1572962.
JD221824 - Sequence 202848 from Patent EP1572962.
JD370578 - Sequence 351602 from Patent EP1572962.
JD522919 - Sequence 503943 from Patent EP1572962.
JD535297 - Sequence 516321 from Patent EP1572962.
JD190725 - Sequence 171749 from Patent EP1572962.
JD104887 - Sequence 85911 from Patent EP1572962.
JD496100 - Sequence 477124 from Patent EP1572962.
BC139909 - Homo sapiens slit homolog 1 (Drosophila), mRNA (cDNA clone IMAGE:40147578), with apparent retained intron.
JD472114 - Sequence 453138 from Patent EP1572962.
JD452095 - Sequence 433119 from Patent EP1572962.
JD523808 - Sequence 504832 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O75093 (Reactome details) participates in the following event(s):

R-HSA-8985799 SLIT1 binds ROBO1,(ROBO2)
R-HSA-9010396 SLIT1 binds COL4A5
R-HSA-9010231 ROBO1 binds FLRT3
R-HSA-8985812 NCK2 binds to ROBO1,(ROBO2)
R-HSA-373715 DCC interaction with ROBO1
R-HSA-8985801 Regulation of cortical dendrite branching
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-376176 Signaling by ROBO receptors
R-HSA-422475 Axon guidance
R-HSA-373752 Netrin-1 signaling
R-HSA-428542 Regulation of commissural axon pathfinding by SLIT and ROBO
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000266058.1, ENST00000266058.2, ENST00000266058.3, ENST00000266058.4, ENST00000266058.5, ENST00000266058.6, ENST00000266058.7, ENST00000266058.8, KIAA0813, MEGF4, NM_003061, O75093, Q5T0V1, Q8WWZ2, Q9UIL7, SLIL1, SLIT1_HUMAN, uc317iga.1, uc317iga.2
UCSC ID: ENST00000266058.9_7
RefSeq Accession: NM_003061.3
Protein: O75093 (aka SLIT1_HUMAN or SLT1_HUMAN)

-  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.