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    Slit1 slit guidance ligand 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 65047, updated on 21-Jul-2018

    Summary

    Official Symbol
    Slit1provided by RGD
    Official Full Name
    slit guidance ligand 1provided by RGD
    Primary source
    RGD:69307
    See related
    Ensembl:ENSRNOG00000026065
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    MEGF4
    Summary
    homolog of Drosophila slit; may play a role in protein-protein interactions during midline formation in the central nervous system; specifically expressed in fetal and adult forebrain neurons [RGD, Feb 2006]
    Annotation information
    Annotation category: suggests misassembly
    Expression
    Biased expression in Brain (RPKM 62.4), Kidney (RPKM 4.4) and 1 other tissue See more
    Orthologs

    Genomic context

    See Slit1 in Genome Data Viewer
    Location:
    1q54
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (260843481..260992366, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 1 NC_005100.3 (268298678..268445090, complement)

    Chromosome 1 - NC_005100.4Genomic Context describing neighboring genes Neighboring gene phosphoinositide-3-kinase adaptor protein 1 Neighboring gene ligand dependent nuclear receptor corepressor Neighboring gene uncharacterized LOC102553433 Neighboring gene Rho GTPase activating protein 19 Neighboring gene uncharacterized LOC102553733

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Axon guidance, organism-specific biosystem (from KEGG)
      Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
    • Axon guidance, conserved biosystem (from KEGG)
      Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
    • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
      Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multi-step process tha...

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    Roundabout binding IEA
    Inferred from Electronic Annotation
    more info
     
    Roundabout binding ISO
    Inferred from Sequence Orthology
    more info
     
    calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    heparan sulfate proteoglycan binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    axon extension involved in axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    axon extension involved in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    axonogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    brain development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    NOT chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration ISO
    Inferred from Sequence Orthology
    more info
     
    dorsal/ventral axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    dorsal/ventral axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    motor neuron axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    motor neuron axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    negative chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    negative chemotaxis ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of axon extension involved in axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    neuron projection morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    nuclear migration IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear migration ISO
    Inferred from Sequence Orthology
    more info
     
    olfactory bulb development ISO
    Inferred from Sequence Orthology
    more info
     
    retinal ganglion cell axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    retinal ganglion cell axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    spinal cord development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    tangential migration from the subventricular zone to the olfactory bulb IEA
    Inferred from Electronic Annotation
    more info
     
    tangential migration from the subventricular zone to the olfactory bulb ISO
    Inferred from Sequence Orthology
    more info
     
    telencephalon cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular space ISO
    Inferred from Sequence Orthology
    more info
     
    intracellular IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    slit homolog 1 protein
    Names
    multiple EGF-like domains protein 4
    multiple epidermal growth factor-like domains 4
    multiple epidermal growth factor-like domains protein 4
    slit-1

    NCBI Reference Sequences (RefSeq)

    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_022953.2NP_075242.1  slit homolog 1 protein precursor

      See identical proteins and their annotated locations for NP_075242.1

      Status: VALIDATED

      Source sequence(s)
      AB011530, BF410201, EV772160
      UniProtKB/Swiss-Prot
      O88279
      Related
      ENSRNOP00000035315.4, ENSRNOT00000034758.6
      Conserved Domains (9) summary
      smart00013
      Location:3364
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:866915
      LRRCT; Leucine rich repeat C-terminal domain
      smart00282
      Location:11861319
      LamG; Laminin G domain
      cd00054
      Location:10851119
      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:87275
      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:4362
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:334373
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:589649
      LRR_8; Leucine rich repeat
      cl21545
      Location:14941529
      GHB_like; Glycoprotein hormone beta chain homologues

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005100.4 Reference Rnor_6.0 Primary Assembly

      Range
      260843481..260992366 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017589694.1XP_017445183.1  slit homolog 1 protein isoform X1

    Alternate Rn_Celera

    Genomic

    1. AC_000069.1 Alternate Rn_Celera

      Range
      236249200..236395640 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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