SPTY2D1 SPT2 chromatin protein domain containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPTY2D1provided by HGNC
Official Full Name: SPT2 chromatin protein domain containing 1provided by HGNC
Primary source: HGNC:HGNC:26818
See related: Ensembl:ENSG00000179119 AllianceGenome:HGNC:26818
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: Spt2
Summary: Enables DNA binding activity and histone binding activity. Involved in nucleosome organization; regulation of chromatin assembly; and regulation of transcription, DNA-templated. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in bone marrow (RPKM 18.4), gall bladder (RPKM 8.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p15.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (18606403..18634342, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (18704496..18732445, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (18627950..18655889, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The role of histone chaperone spty2d1 in human colorectal cancer.
Title: The role of histone chaperone spty2d1 in human colorectal cancer.
Results from a study on gene expression variability markers in early-stage human embryos shows that SPTY2D1 is a putative expression variability marker for the 3-day, 8-cell embryo stage.
Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
there may be a racial/ethnic- and/or sex-specific association between the SPTY2D1 rs17579600 single nucleotide polymorphism and serum lipid parameters in some ethnic groups.
Title: Association of the SPT2 chromatin protein domain containing 1 gene rs17579600 polymorphism and serum lipid traits.
These findings suggest that the association between the SPTY2D1 rs7934205 SNP and serum lipid levels might have ethnic- and/or sex-specificity.
Title: Sex-specific association of the SPTY2D1 rs7934205 polymorphism and serum lipid levels.
Spt2 is a novel histone chaperone with a separate DNA-binding domain that facilitates ribosomal DNA transcription through chromatin remodeling during transcription.
Title: Vertebrate Spt2 is a novel nucleolar histone chaperone that assists in ribosomal DNA transcription.

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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
Biological, clinical and population relevance of 95 loci for blood lipids. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

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

RH16432 (e-PCR)
- UniSTS:84252

D8S2279 (e-PCR)
- UniSTS:473907

STS-R07743 (e-PCR)
- UniSTS:68934

D15S1477 (e-PCR)
- UniSTS:474482

RH94100 (e-PCR)
- UniSTS:83833

D11S3114 (e-PCR)
- UniSTS:152207

RH80031 (e-PCR)
- UniSTS:91103

D11S2378 (e-PCR)
- UniSTS:245

STS-H94880 (e-PCR)
- UniSTS:22266

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase I core binding	ISS Inferred from Sequence or Structural Similarity more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables histone chaperone activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleosome assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in nucleosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription by RNA polymerase I	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: protein SPT2 homolog

Names: SPT2 domain-containing protein 1; SPT2, Suppressor of Ty, domain containing 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.