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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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