slit3 slit homolog 3 (Drosophila) [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: slit3provided by ZNC
Official Full Name: slit homolog 3 (Drosophila)provided by ZNC
Primary source: ZFIN:ZDB-GENE-010306-4
See related: Ensembl:ENSDARG00000034268 AllianceGenome:ZFIN:ZDB-GENE-010306-4
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: zgc:111911
Summary: Predicted to enable Roundabout binding activity and heparin binding activity. Acts upstream of or within central nervous system projection neuron axonogenesis and negative regulation of axon extension. Predicted to be located in extracellular region. Is expressed in several structures, including axial mesoderm; fin; nervous system; pectoral fin bud; and presumptive mesoderm. Orthologous to human SLIT3 (slit guidance ligand 3). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 14

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	14	NC_007125.7 (24491818..24761133, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	14	NC_007125.6 (24194573..24463888, complement)

Chromosome 14 - NC_007125.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of slit3 as a locus affecting nicotine preference in zebrafish and human smoking behaviour.
Title: Identification of slit3 as a locus affecting nicotine preference in zebrafish and human smoking behaviour.
Slit3 (and slit-2) coordinate neuron axonal pathfinding within the embryonic axon tracts along with Robo2 and Dcc-Netrin1.
Title: Robo2--slit and Dcc--netrin1 coordinate neuron axonal pathfinding within the embryonic axon tracts.
Data show that Hedgehog signaling is required for commissure formation, glial bridge formation, and the restricted expression of the guidance molecules slit1a, slit2, slit3 and sema3d.
Title: Hedgehog regulated Slit expression determines commissure and glial cell position in the zebrafish forebrain.

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General gene information

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Markers

G39143 (e-PCR)
- UniSTS:12370

G40293 (e-PCR)
- UniSTS:51941

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables Roundabout binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within central nervous system projection neuron axonogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within central nervous system projection neuron axonogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of axon extension	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of axon extension	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: slit homolog 3 protein

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_131736.3 → NP_571811.3 slit homolog 3 protein precursor

Status: VALIDATED

Source sequence(s)

AL928691, BX323583

UniProtKB/TrEMBL

A0A8M1PC10, F1RCV3

Related

ENSDARP00000112770.1, ENSDART00000146299.3

Conserved Domains (12) summary

smart00369
Location:815 → 838

LRR_TYP; Leucine-rich repeats, typical (most populated) subfamily

smart00013
Location:718 → 749

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:850 → 899

LRRCT; Leucine rich repeat C-terminal domain

cd00054
Location:1067 → 1103

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:78 → 211

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 ...

sd00031
Location:727 → 746

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:55 → 77

LRR_RI; leucine-rich repeat [structural motif]

pfam02210
Location:1182 → 1305

Laminin_G_2; Laminin G domain

pfam12799
Location:323 → 363

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:768 → 828

LRR_8; Leucine rich repeat

cl15307
Location:206 → 255

TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

cl21545
Location:1457 → 1512

GHB_like; Glycoprotein hormone beta chain homologues