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    kdm1a lysine (K)-specific demethylase 1a [ Danio rerio (zebrafish) ]

    Gene ID: 558450, updated on 9-Dec-2024

    Summary

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    Official Symbol
    kdm1aprovided by ZNC
    Official Full Name
    lysine (K)-specific demethylase 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-7828
    See related
    Ensembl:ENSDARG00000060679 AllianceGenome:ZFIN:ZDB-GENE-030131-7828
    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
    Also known as
    aof2; kdm1; wu:fb82e06; wu:fc51a02; wu:fj36a05; wu:fj66b06
    Summary
    Enables histone deacetylase activity. Acts upstream of or within nervous system development; regulation of hemopoiesis; and regulation of retinoic acid biosynthetic process. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in brain; head; intestine; and spinal cord. Used to study myelodysplastic syndrome. Orthologous to human KDM1A (lysine demethylase 1A). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See kdm1a in Genome Data Viewer
    Location:
    chromosome: 17
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 17 NC_007128.7 (28084395..28101982, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 17 NC_007128.6 (28067432..28085042, complement)

    Chromosome 17 - NC_007128.7Genomic Context describing neighboring genes Neighboring gene leucine zipper protein 1 Neighboring gene uncharacterized LOC137488108 Neighboring gene transmembrane protein 30B Neighboring gene 5-hydroxytryptamine (serotonin) receptor 1D, G protein-coupled

    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. Splicing- and demethylase-independent functions of LSD1 in zebrafish primitive hematopoiesis. Tamaoki J, et al. Sci Rep, 2020 May 22. PMID 32444613, Free PMC Article
    2. Trans-2-phenylcyclopropylamine regulates zebrafish lateral line neuromast development mediated by depression of LSD1 activity. He Y, et al. Int J Dev Biol, 2013. PMID 23873368
    3. Lysine-specific demethylase 1 expression in zebrafish during the early stages of neuronal development. Li A, et al. Neural Regen Res, 2012 Dec 5. PMID 25337119, Free PMC Article
    4. ZebraShare: a new venue for rapid dissemination of zebrafish mutant data. DeLaurier A, et al. PeerJ, 2021. PMID 33954026, Free PMC Article
    5. Genetic and epigenetic orchestration of Gfi1aa-Lsd1-cebpa in zebrafish neutrophil development. Wu M, et al. Development, 2021 Sep 1. PMID 34373913

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LSD1 promotes the egress of hematopoietic stem and progenitor cells into the bloodstream during the endothelial-to-hematopoietic transition.
      Title: LSD1 promotes the egress of hematopoietic stem and progenitor cells into the bloodstream during the endothelial-to-hematopoietic transition.
    2. Genetic and epigenetic orchestration of Gfi1aa-Lsd1-cebpa in zebrafish neutrophil development.
      Title: Genetic and epigenetic orchestration of Gfi1aa-Lsd1-cebpa in zebrafish neutrophil development.
    3. LSD1 plays a critical role in hair cell regeneration and might represent a novel biomarker and potential therapeutic approach for the treatment of hearing loss.
      Title: LSD1 is Required for Hair Cell Regeneration in Zebrafish.
    4. results suggest that the LSD1-dependent shutdown of Etv2 gene expression may be a significant event required for hemangioblasts to initiate hematopoietic differentiation
      Title: LSD1/KDM1A promotes hematopoietic commitment of hemangioblasts through downregulation of Etv2.
    5. Results indicate that LSD1 demethylase activity is required for neuromast development in zebrafish larvae.
      Title: Trans-2-phenylcyclopropylamine regulates zebrafish lateral line neuromast development mediated by depression of LSD1 activity.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0601

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables FAD-dependent H3K4me/H3K4me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables FAD-dependent H3K4me/H3K4me3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables flavin adenine dinucleotide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables flavin adenine dinucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone deacetylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in epigenetic regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of hemopoiesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of retinoic acid biosynthetic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific histone demethylase 1A
    Names
    amine oxidase (flavin containing) domain 2
    lsd1
    lysine (K)-specific demethylase 1
    lysine-specific demethylase 1
    NP_001229924.1
    XP_005158840.1

    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)

    1. NM_001242995.1 → NP_001229924.1  lysine-specific histone demethylase 1A

      Status: PROVISIONAL

      Source sequence(s)
      BC125965
      UniProtKB/TrEMBL
      A0A8M1NYP3, A0JMQ3, F6NIA2
      Related
      ENSDARP00000080193.4, ENSDART00000085758.6
      Conserved Domains (5) summary
      pfam01593
      Location:262 → 805
      Amino_oxidase; Flavin containing amine oxidoreductase
      pfam04433
      Location:151 → 238
      SWIRM; SWIRM domain
      pfam13450
      Location:257 → 315
      NAD_binding_8; NAD(P)-binding Rossmann-like domain
      cl09111
      Location:393 → 494
      Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...
      cl17165
      Location:371 → 441
      SKA2; Spindle and kinetochore-associated protein 2

    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_007128.7 Reference GRCz11 Primary Assembly

      Range
      28084395..28101982 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005158783.5 → XP_005158840.1  lysine-specific histone demethylase 1A isoform X1

      UniProtKB/TrEMBL
      A0A0P0UQI8, A0JMQ3
      Related
      ENSDARP00000150698.1, ENSDART00000180532.1
      Conserved Domains (5) summary
      pfam01593
      Location:259 → 802
      Amino_oxidase; Flavin containing amine oxidoreductase
      pfam04433
      Location:148 → 235
      SWIRM; SWIRM domain
      pfam13450
      Location:254 → 312
      NAD_binding_8; NAD(P)-binding Rossmann-like domain
      cl09111
      Location:390 → 491
      Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...
      cl17165
      Location:368 → 438
      SKA2; Spindle and kinetochore-associated protein 2
    Nucleotide Protein Strain
    Heading Accession and Version

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