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    slit2 slit homolog 2 (Drosophila) [ Danio rerio (zebrafish) ]

    Gene ID: 80353, updated on 9-Dec-2024

    Summary

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    Official Symbol
    slit2provided by ZNC
    Official Full Name
    slit homolog 2 (Drosophila)provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-010306-3
    See related
    Ensembl:ENSDARG00000004246 AllianceGenome:ZFIN:ZDB-GENE-010306-3
    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 Roundabout binding activity and heparin binding activity. Acts upstream of or within several processes, including endocardial progenitor cell migration to the midline involved in heart field formation; negative regulation of axon extension; and nervous system development. Predicted to be located in extracellular region. Is expressed in several structures, including axial mesoderm; forebrain neural tube; hypochord; nervous system; and oocyte. Orthologous to human SLIT2 (slit guidance ligand 2). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See slit2 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (23784215..23910040)
    105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (23092978..23219301)

    Chromosome 1 - NC_007112.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108190619 Neighboring gene ligand dependent nuclear receptor corepressor-like Neighboring gene uncharacterized LOC137495490 Neighboring gene microRNA 218a-2 Neighboring gene LPS-responsive vesicle trafficking, beach and anchor containing Neighboring gene mab-21-like 2 Neighboring gene ribosomal protein S3A

    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
    • 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. Focal gene misexpression in zebrafish embryos induced by local heat shock using a modified soldering iron. Hardy ME, et al. Dev Dyn, 2007 Nov. PMID 17907198
    2. Zebrafish Slit2 and Slit3 Act Together to Regulate Retinal Axon Crossing at the Midline. Davison C, et al. J Dev Biol, 2022 Sep 23. PMID 36278546, Free PMC Article
    3. Generating X: formation of the optic chiasm. Rasband K, et al. Neuron, 2003 Sep 11. PMID 12971890
    4. Neuronal NADPH oxidase 2 regulates growth cone guidance downstream of slit2/robo2. Terzi A, et al. Dev Neurobiol, 2021 Jan. PMID 33191581, Free PMC Article
    5. Frizzled-3a and Wnt-8b genetically interact during forebrain commissural formation in embryonic zebrafish. Hofmeister W, et al. Brain Res, 2013 Apr 19. PMID 23438515

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Slit2 is necessary for optic axon organization in the zebrafish ventral midline.
      Title: Slit2 is necessary for optic axon organization in the zebrafish ventral midline.
    2. These data supports a model whereby Wnt signaling through Frizzled-3a attenuates expression of Slit2 in the rostral midline of the forebrain.
      Title: Frizzled-3a and slit2 genetically interact to modulate midline axon crossing in the telencephalon.
    3. In embryonic axon tracts, Robo2 responds to signals from slit2 and slit3.
      Title: Robo2--slit and Dcc--netrin1 coordinate neuron axonal pathfinding within the embryonic axon tracts.
    4. 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.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within anterior/posterior axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within axonal defasciculation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 
    acts_upstream_of_or_within endocardial progenitor cell migration to the midline involved in heart field formation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within morphogenesis of a branching structure IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 
    acts_upstream_of_or_within optic chiasma development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within optic 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
    		  

    General protein information

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    Preferred Names
    slit homolog 2 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)

    1. NM_131735.1 → NP_571810.1  slit homolog 2 protein precursor

      See identical proteins and their annotated locations for NP_571810.1

      Status: PROVISIONAL

      Source sequence(s)
      AF210321
      UniProtKB/TrEMBL
      A0A8M9Q7S9, Q9DE36
      Related
      ENSDARP00000026343.7, ENSDART00000007531.9
      Conserved Domains (11) summary
      smart00013
      Location:710 → 741
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:842 → 891
      LRRCT; Leucine rich repeat C-terminal domain
      cd00054
      Location:1059 → 1095
      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:28 → 223
      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:32 → 49
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00008
      Location:944 → 976
      EGF; EGF-like domain
      pfam02210
      Location:1173 → 1299
      Laminin_G_2; Laminin G domain
      pfam12799
      Location:520 → 558
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:760 → 820
      LRR_8; Leucine rich repeat
      cl15307
      Location:421 → 451
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
      cl21545
      Location:1450 → 1511
      GHB_like; Glycoprotein hormone beta chain homologues

    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_007112.7 Reference GRCz11 Primary Assembly

      Range
      23784215..23910040
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068220869.1 → XP_068076970.1  slit homolog 2 protein isoform X10

      UniProtKB/TrEMBL
      A0A8M9PJA3

    2. XM_021475850.2 → XP_021331525.1  slit homolog 2 protein isoform X1

      UniProtKB/TrEMBL
      A0A8M9Q2G1, A0A8M9QD64
      Conserved Domains (9) summary
      TIGR00864
      Location:635 → 712
      PCC; polycystin cation channel protein
      smart00013
      Location:21 → 51
      LRRNT; Leucine rich repeat N-terminal domain
      cd00054
      Location:1094 → 1130
      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 ...
      sd00033
      Location:32 → 49
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00008
      Location:1011 → 1038
      EGF; EGF-like domain
      pfam02210
      Location:1206 → 1334
      Laminin_G_2; Laminin G domain
      pfam13855
      Location:776 → 835
      LRR_8; Leucine rich repeat
      cl21545
      Location:1485 → 1546
      GHB_like; Glycoprotein hormone beta chain homologues
      cl26018
      Location:694 → 859
      NEL; C-terminal novel E3 ligase, LRR-interacting

    3. XM_068220865.1 → XP_068076966.1  slit homolog 2 protein isoform X4

      UniProtKB/TrEMBL
      A0A8M9PWP8

    4. XM_068220866.1 → XP_068076967.1  slit homolog 2 protein isoform X5

      UniProtKB/TrEMBL
      A0A8M9Q2G6

    5. XM_068220868.1 → XP_068076969.1  slit homolog 2 protein isoform X8

      UniProtKB/TrEMBL
      A0A8M9PWQ2

    6. XM_068220863.1 → XP_068076964.1  slit homolog 2 protein isoform X2

      UniProtKB/TrEMBL
      A0A8M9Q7S3

    7. XM_068220867.1 → XP_068076968.1  slit homolog 2 protein isoform X7

      UniProtKB/TrEMBL
      A0A8M9Q7S7
      Related
      ENSDARP00000155570.1, ENSDART00000188521.1

    8. XM_021475860.2 → XP_021331535.1  slit homolog 2 protein isoform X9

      UniProtKB/TrEMBL
      A0A8M9Q2H0, A0A8M9QD73
      Related
      ENSDARP00000154786.1, ENSDART00000183029.1
      Conserved Domains (8) summary
      TIGR00864
      Location:628 → 705
      PCC; polycystin cation channel protein
      smart00013
      Location:21 → 51
      LRRNT; Leucine rich repeat N-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 ...
      sd00033
      Location:32 → 49
      LRR_RI; leucine-rich repeat [structural motif]
      pfam02210
      Location:1179 → 1307
      Laminin_G_2; Laminin G domain
      pfam13855
      Location:769 → 828
      LRR_8; Leucine rich repeat
      cl21545
      Location:1458 → 1519
      GHB_like; Glycoprotein hormone beta chain homologues
      cl26018
      Location:687 → 852
      NEL; C-terminal novel E3 ligase, LRR-interacting

    9. XM_068220864.1 → XP_068076965.1  slit homolog 2 protein isoform X3

      UniProtKB/TrEMBL
      A0A8M9PJ94

    10. XM_021475857.2 → XP_021331532.1  slit homolog 2 protein isoform X6

      UniProtKB/TrEMBL
      A0A8M9PJA0, A0A8M9QD69
      Conserved Domains (9) summary
      TIGR00864
      Location:620 → 697
      PCC; polycystin cation channel protein
      smart00013
      Location:21 → 51
      LRRNT; Leucine rich repeat N-terminal domain
      cd00054
      Location:1079 → 1115
      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 ...
      sd00033
      Location:32 → 49
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00008
      Location:996 → 1023
      EGF; EGF-like domain
      pfam02210
      Location:1191 → 1319
      Laminin_G_2; Laminin G domain
      pfam13855
      Location:761 → 820
      LRR_8; Leucine rich repeat
      cl21545
      Location:1470 → 1531
      GHB_like; Glycoprotein hormone beta chain homologues
      cl26018
      Location:679 → 844
      NEL; C-terminal novel E3 ligase, LRR-interacting

    Reference GRCz11 ALT_DRER_TU_3

    Genomic

    1. NW_018395373.1 Reference GRCz11 ALT_DRER_TU_3

      Range
      338842..406345
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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