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

Gene ID: 373861, updated on 23-Nov-2023

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
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_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (50171428..50172476, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (51038500..51039548, complement)
105.20220307 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 long intergenic non-protein coding RNA 1969

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)

Genotypes

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
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Research Materials
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