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slit1b slit homolog 1b (Drosophila) [ Danio rerio (zebrafish) ]

Gene ID: 561685, updated on 2-Nov-2024

Summary

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Official Symbol
slit1bprovided by ZNC
Official Full Name
slit homolog 1b (Drosophila)provided by ZNC
Primary source
ZFIN:ZDB-GENE-030722-4
See related
Ensembl:ENSDARG00000099446 AllianceGenome:ZFIN:ZDB-GENE-030722-4
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Summary
Predicted to enable calcium ion binding activity. Acts upstream of or within cranial nerve morphogenesis. Predicted to be located in extracellular region. Predicted to be active in plasma membrane. Is expressed in central nervous system; forebrain; hindbrain; hindbrain nucleus; and retinal inner nuclear layer. Orthologous to human SLIT1 (slit guidance ligand 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
all
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Genomic context

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See slit1b in Genome Data Viewer
Location:
chromosome: 22
Exon count:
37
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (34843275..34937531, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (34867219..34961817, complement)

Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene 4-hydroxy-2-oxoglutarate aldolase 1 Neighboring gene ligand dependent nuclear receptor corepressor Neighboring gene Rho GTPase activating protein 19 Neighboring gene Kv channel interacting protein 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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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Related articles in PubMed

  1. Two divergent slit1 genes in zebrafish. Hutson LD, et al. Dev Dyn, 2003 Nov. PMID 14579375
  2. Slit1b-Robo3 signaling and N-cadherin regulate apical process retraction in developing retinal ganglion cells. Wong GK, et al. J Neurosci, 2012 Jan 4. PMID 22219284, Free PMC Article
  3. Robo2 is required for establishment of a precise glomerular map in the zebrafish olfactory system. Miyasaka N, et al. Development, 2005 Mar. PMID 15716341
  4. Analysis of the astray/robo2 zebrafish mutant reveals that degenerating tracts do not provide strong guidance cues for regenerating optic axons. Wyatt C, et al. J Neurosci, 2010 Oct 13. PMID 20943924, Free PMC Article
  5. Stromal cell-derived factor-1 antagonizes slit/robo signaling in vivo. Chalasani SH, et al. J Neurosci, 2007 Jan 31. PMID 17267551, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. slit1a and slit1b are both expressed in the midline, hypochord, telencephalon, and hindbrain.
    Title: Two divergent slit1 genes in zebrafish.
  2. Slit-Robo signaling downregulates N-cadherin activity to allow apical retraction in newly generated retinal ganglion cells.
    Title: Slit1b-Robo3 signaling and N-cadherin regulate apical process retraction in developing retinal ganglion cells.
Submit: New GeneRIF Correction

General gene information

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Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within axon guidance NAS
Non-traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cranial nerve morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
slit homolog 1b
Names
chunp9742

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)

  1. NM_001034975.1 → NP_001030147.1  slit homolog 1b precursor

    See identical proteins and their annotated locations for NP_001030147.1

    Status: PROVISIONAL

    Source sequence(s)
    DQ153065
    UniProtKB/TrEMBL
    Q3Y6S4
    Related
    ENSDARP00000150065.1, ENSDART00000188330.1
    Conserved Domains (9) summary
    smart00013
    Location:732 → 764
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:668 → 717
    LRRCT; Leucine rich repeat C-terminal domain
    cd00054
    Location:1082 → 1118
    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 ...
    cd00110
    Location:1160 → 1314
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    cd00116
    Location:84 → 217
    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:60 → 83
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:329 → 369
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:306 → 365
    LRR_8; Leucine rich repeat
    cl15307
    Location:435 → 465
    TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007133.7 Reference GRCz11 Primary Assembly

    Range
    34843275..34937531 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009296502.4 → XP_009294777.1  slit homolog 1b isoform X1

    UniProtKB/TrEMBL
    A0A0R4IU60, A0A8M3ANA1
    Related
    ENSDARP00000139567.1, ENSDART00000169217.3
    Conserved Domains (9) summary
    smart00013
    Location:509 → 540
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:212 → 260
    LRRCT; Leucine rich repeat C-terminal domain
    cd00054
    Location:1081 → 1117
    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 ...
    cd00110
    Location:1159 → 1313
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    cd00116
    Location:84 → 217
    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:60 → 83
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:329 → 369
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:306 → 365
    LRR_8; Leucine rich repeat
    cl15307
    Location:435 → 465
    TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

RNA

  1. XR_011008164.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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