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

Gene ID: 54665, updated on 10-Oct-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 dioxygenase activity and metal ion binding activity. Predicted to be involved in chromatin organization. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 3.0), ovary (RPKM 2.9) and 25 other tissues See more
Orthologs
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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

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

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 (35) 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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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)

Genotypes

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

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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