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    RSBN1 round spermatid basic protein 1 [ Homo sapiens (human) ]

    Gene ID: 54665, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RSBN1provided by HGNC
    Official Full Name
    round spermatid basic protein 1provided by HGNC
    Primary source
    HGNC:HGNC:25642
    See related
    Ensembl:ENSG00000081019 MIM:615858; AllianceGenome:HGNC:25642
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    KDM9; ROSBIN
    Summary
    Predicted to enable histone H4K20 demethylase activity and metal ion binding activity. Predicted to be involved in chromatin remodeling. Predicted to be located in endoplasmic reticulum. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 3.0), ovary (RPKM 2.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RSBN1 in Genome Data Viewer
    Location:
    1p13.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (113761832..113812476, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (113773493..113824146, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114304454..114355098, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene membrane associated guanylate kinase, WW and PDZ domain containing 3 Neighboring gene MT-ND5 pseudogene 20 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114181286-114181787 Neighboring gene Sharpr-MPRA regulatory region 12988 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114223507-114224045 Neighboring gene ribosomal protein S2 pseudogene 14 Neighboring gene putative homeodomain transcription factor 1 Neighboring gene Sharpr-MPRA regulatory region 5734 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:114295082-114295283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114299147-114299702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1215 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114301981-114302560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1216 Neighboring gene Sharpr-MPRA regulatory region 4295 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114353909-114354438 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chr1:114354439-114354968 and GRCh37_chr1:114354969-114355498 Neighboring gene AP4B1 antisense RNA 1 Neighboring gene protein tyrosine phosphatase non-receptor type 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1538 Neighboring gene BCL2 like 15

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Dynamic Control of X Chromosome Conformation and Repression by a Histone H4K20 Demethylase. Brejc K, et al. Cell, 2017 Sep 21. PMID 28867287, Free PMC Article
    2. PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes. Smyth DJ, et al. Diabetes, 2008 Jun. PMID 18305142
    3. Rosbin: a novel homeobox-like protein gene expressed exclusively in round spermatids. Takahashi T, et al. Biol Reprod, 2004 May. PMID 14724137
    4. Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis. Prahalad S, et al. Arthritis Rheum, 2009 Jul. PMID 19565500, Free PMC Article
    5. Proteomic analysis of HIV-1 Gag interacting partners using proximity-dependent biotinylation. Le Sage V, et al. Virol J, 2015 Sep 11. PMID 26362536, Free PMC Article

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Novel associations for hypothyroidism include known autoimmune risk loci.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag HIV-1 Gag interacts with RSBN1 as demonstrated by proximity dependent biotinylation proteomics PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp781E21150

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H4K20 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 9

    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_018364.5 → NP_060834.2  lysine-specific demethylase 9

      See identical proteins and their annotated locations for NP_060834.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is the protein-coding transcript.
      Source sequence(s)
      AL137856, AL365321
      Consensus CDS
      CCDS862.1
      UniProtKB/Swiss-Prot
      A8K937, Q5VWQ0, Q6AI21, Q8TC33, Q9HA80, Q9NUP6
      UniProtKB/TrEMBL
      A0A087WWP8
      Related
      ENSP00000261441.5, ENST00000261441.9

    RNA

    1. NR_130896.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate internal exon compared to isoform 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK292552, AL365321, BC026155, N66761

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      113761832..113812476 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001518.3 → XP_016857007.1  lysine-specific demethylase 9 isoform X1

      UniProtKB/TrEMBL
      A0A0C4DH79
      Related
      ENSP00000433256.2, ENST00000476412.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      113773493..113824146 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337162.1 → XP_054193137.1  lysine-specific demethylase 9 isoform X1

      UniProtKB/TrEMBL
      A0A0C4DH79
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VWQ0.2 GenPept UniProtKB/Swiss-Prot:Q5VWQ0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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