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    H1-9P H1.9 linker histone, pseudogene [ Homo sapiens (human) ]

    Gene ID: 373861, updated on 2-Nov-2024

    Summary

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    Official Symbol
    H1-9Pprovided by HGNC
    Official Full Name
    H1.9 linker histone, pseudogeneprovided by HGNC
    Primary source
    HGNC:HGNC:30616
    See related
    Ensembl:ENSG00000253730 MIM:608101; AllianceGenome:HGNC:30616
    Gene type
    pseudo
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    H1-9; H1.9; HILS1
    Summary
    This locus is the ortholog of a mouse protein-coding gene that displays characteristics of a linker histone and is expressed in nuclei of late maturing spermatids. The human locus is expressed; however, the open reading frame has been disrupted by a frameshift so it is unlikely to encode a functional protein. [provided by RefSeq, Oct 2008]
    Expression
    Biased expression in testis (RPKM 4.3), heart (RPKM 1.0) and 6 other tissues See more
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    Genomic context

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    See H1-9P in Genome Data Viewer
    Location:
    17q21.33
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (50171428..50172476, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (51038500..51039548, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (48248789..48249837, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:48210517-48211258 Neighboring gene protein phosphatase 1 regulatory subunit 9B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48223652-48224322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48224323-48224991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12379 Neighboring gene uncharacterized LOC124904025 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8683 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8684 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8686 Neighboring gene Sharpr-MPRA regulatory region 5931 Neighboring gene CRISPRi-validated cis-regulatory element chr17.3603 Neighboring gene uncharacterized LOC105371818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8687 Neighboring gene Sharpr-MPRA regulatory region 13843 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48240960-48241460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48252214-48252815 Neighboring gene sarcoglycan alpha Neighboring gene Sharpr-MPRA regulatory region 9980 Neighboring gene Sharpr-MPRA regulatory region 10059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48259283-48260178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48261754-48262744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48266067-48266622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48266623-48267176 Neighboring gene collagen type I alpha 1 chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:48273702-48274901 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8690 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48283085-48283586 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:48287195-48287760 Neighboring gene TGF-beta induced lncRNA activating myofibroblasts

    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
    • 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. Rapid evolution of the mammalian HILS1 gene and the nuclear condensation process during mammalian spermiogenesis. Su Y, et al. J Genet Genomics, 2013 Jan 20. PMID 23357345
    2. Histone gene expression profile during spermatogenesis. Teng YN, et al. Fertil Steril, 2010 May 1. PMID 19896661
    3. Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements. Mishra LN, et al. Epigenetics Chromatin, 2018 Aug 1. PMID 30068355, Free PMC Article
    4. Mapping of post-translational modifications of spermatid-specific linker histone H1-like protein, HILS1. Mishra LN, et al. J Proteomics, 2015 Oct 14. PMID 26257145
    5. Quantitative assessment of transition proteins 1, 2 spermatid-specific linker histone H1-like protein transcripts in spermatozoa from normozoospermic and asthenozoospermic men. Jedrzejczak P, et al. Arch Androl, 2007 Jul-Aug. PMID 17852044

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. We found significantly lower levels of HILS1, TNP1, and TNP2 transcripts in spermatozoa from asthenozoospermic men compared to normozoospermic men.
      Title: Quantitative assessment of transition proteins 1, 2 spermatid-specific linker histone H1-like protein transcripts in spermatozoa from normozoospermic and asthenozoospermic men.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Other Names

    • histone linker H1 domain, spermatid-specific 1 (pseudogene)
    • spermatid-specific linker histone H1-like protein

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nucleic acid binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nucleosomal DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in chromosome condensation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromosome condensation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in germ cell development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in heterochromatin formation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nucleosome assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in spermatogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in male germ cell nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of nucleosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    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.

    RNA

    1. NR_024192.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal segment, compared to variant 1. Neither variant is likely to express a functional protein.
      Source sequence(s)
      AY286318, BC033456

    2. NR_024193.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Neither variant is likely to express a functional protein.
      Source sequence(s)
      AC015909, AY286318, BC033456, BC109047
      Related
      ENST00000751803.1

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      50171428..50172476 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      51038500..51039548 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_194072.1: Suppressed sequence

      Description
      NM_194072.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P60008.1 GenPept UniProtKB/Swiss-Prot:P60008

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials