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

Summary

Official Symbol: Slit1provided by RGD
Official Full Name: slit guidance ligand 1provided by RGD
Primary source: RGD:69307
See related: Ensembl:ENSRNOG00000026065 AllianceGenome:RGD:69307
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: Enables heparan sulfate proteoglycan binding activity. Involved in brain development; negative regulation of axon extension involved in axon guidance; and spinal cord development. Located in extracellular space. Orthologous to human SLIT1 (slit guidance ligand 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 62.4), Kidney (RPKM 4.4) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 1q54

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (250358917..250507476, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (240409559..240558127, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (260843481..260992366, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expression of Slit and Robo during remodeling of corticospinal tract in cervical spinal cord in middle cerebral artery occlusion rats.
Title: Expression of Slit and Robo during remodeling of corticospinal tract in cervical spinal cord in middle cerebral artery occlusion rats.
These findings indicate that Slit1/Robo2 signaling may have a role in regulating peripheral nerve regeneration.
Title: Slit1 promotes regenerative neurite outgrowth of adult dorsal root ganglion neurons in vitro via binding to the Robo receptor.
The difference in expression pattern of Slit family mRNA in the neurons during peripheral nerve regeneration suggests that it plays a different role in axonal regeneration after axotomy of peripheral nerves
Title: mRNA expression changes of slit proteins following peripheral nerve injury in the rat model.
The novel splicing product, Slit1alpha, arises through alternative splicing at the C-terminus of Slit1, causing defects in the cysteine knot domain.
Title: Expression and function of Slit1alpha, a novel alternative splicing product for slit1.
Ig domains 1 and 2 of Robo1 are important for Robo-Slit interaction and provide functional data using the Slit-mediated olfactory bulb repulsion assay.
Title: Extracellular Ig domains 1 and 2 of Robo are important for ligand (Slit) binding.

Submit: New GeneRIF Correction

General gene information

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Markers

D1Mco5 (e-PCR)
- UniSTS:240396

AU048769 (e-PCR)
- UniSTS:145219

D1Rat449 (e-PCR), detects polymorphism
- UniSTS:227231

D1Got241 (e-PCR)
- UniSTS:112865

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables Roundabout binding	IBA Inferred from Biological aspect of Ancestor more info
enables Roundabout binding	IEA Inferred from Electronic Annotation more info
enables Roundabout binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables heparan sulfate proteoglycan binding	IDA Inferred from Direct Assay more info	PubMed
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in axon extension involved in axon guidance	IEA Inferred from Electronic Annotation more info
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
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
NOT involved_in chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration	ISO Inferred from Sequence Orthology more info
involved_in dorsal/ventral axon guidance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dorsal/ventral axon guidance	ISO Inferred from Sequence Orthology more info
involved_in motor neuron axon guidance	IEA Inferred from Electronic Annotation more info
involved_in motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative chemotaxis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in negative chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of axon extension involved in axon guidance	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuron projection morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in nuclear migration	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within nuclear migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within olfactory bulb development	ISO Inferred from Sequence Orthology more info
involved_in retinal ganglion cell axon guidance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within retinal ganglion cell axon guidance	ISO Inferred from Sequence Orthology more info
involved_in spinal cord development	IEP Inferred from Expression Pattern more info	PubMed
involved_in tangential migration from the subventricular zone to the olfactory bulb	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within tangential migration from the subventricular zone to the olfactory bulb	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within telencephalon cell migration	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	IEA Inferred from Electronic Annotation more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info

General protein information

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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)

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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)

NM_022953.2 → NP_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, Q8CJG8, Q8CJG9, Q8CJH0, Q9QWL1, Q9WUG5

UniProtKB/TrEMBL

A6JH83, F1LS74

Related

ENSRNOP00000035315.5, ENSRNOT00000034758.7

Conserved Domains (9) summary

smart00013
Location:33 → 64

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:866 → 915

LRRCT; Leucine rich repeat C-terminal domain

smart00282
Location:1186 → 1319

LamG; Laminin G domain

cd00054
Location:1085 → 1119

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:87 → 275

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:43 → 62

LRR_RI; leucine-rich repeat [structural motif]

pfam12799
Location:334 → 373

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:589 → 649

LRR_8; Leucine rich repeat

cl21545
Location:1494 → 1529

GHB_like; Glycoprotein hormone beta chain homologues