Aliases for SPTY2D1 Gene

Aliases for SPTY2D1 Gene

  • SPT2 Chromatin Protein Domain Containing 1 2 3 5
  • SPT2 Domain-Containing Protein 1 3 4
  • Protein SPT2 Homolog 3 4
  • SPT2, Suppressor Of Ty, Domain Containing 1 (S. Cerevisiae) 2
  • SPT2, Suppressor Of Ty, Domain Containing 1 3
  • Protein KU002155 4
  • Spt2 3

External Ids for SPTY2D1 Gene

Previous GeneCards Identifiers for SPTY2D1 Gene

  • GC11M018585
  • GC11M018312

Summaries for SPTY2D1 Gene

GeneCards Summary for SPTY2D1 Gene

SPTY2D1 (SPT2 Chromatin Protein Domain Containing 1) is a Protein Coding gene. An important paralog of this gene is CCDC61.

UniProtKB/Swiss-Prot Summary for SPTY2D1 Gene

  • Histone chaperone that stabilizes pre-existing histone tetramers and regulates replication-independent histone exchange on chromatin (PubMed:26109053). Required for normal chromatin refolding in the coding region of transcribed genes, and for the suppression of spurious transcription (PubMed:26109053). Binds DNA and histones and promotes nucleosome assembly (in vitro) (PubMed:23378026, PubMed:26109053). Facilitates formation of tetrameric histone complexes containing histone H3 and H4 (PubMed:26109053). Modulates RNA polymerase 1-mediated transcription (By similarity). Binds DNA, with a preference for branched DNA species, such as Y-form DNA and Holliday junction DNA (PubMed:23378026).

Additional gene information for SPTY2D1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPTY2D1 Gene

Genomics for SPTY2D1 Gene

GeneHancer (GH) Regulatory Elements for SPTY2D1 Gene

Promoters and enhancers for SPTY2D1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPTY2D1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SPTY2D1 gene promoter:
  • ARP-1
  • C/EBPalpha
  • C/EBPbeta
  • CHOP-10
  • Hlf
  • STAT3
  • STAT5A
  • STAT5B

Genomic Locations for SPTY2D1 Gene

Genomic Locations for SPTY2D1 Gene
chr11:18,606,401-18,634,791
(GRCh38/hg38)
Size:
28,391 bases
Orientation:
Minus strand
chr11:18,627,948-18,656,338
(GRCh37/hg19)
Size:
28,391 bases
Orientation:
Minus strand

Genomic View for SPTY2D1 Gene

Genes around SPTY2D1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPTY2D1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPTY2D1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPTY2D1 Gene

Proteins for SPTY2D1 Gene

  • Protein details for SPTY2D1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q68D10-SPT2_HUMAN
    Recommended name:
    Protein SPT2 homolog
    Protein Accession:
    Q68D10
    Secondary Accessions:
    • Q6AWA5
    • Q6MZI5
    • Q7Z390
    • Q7Z470
    • Q86VG8
    • Q8N3E7
    • Q8N417
    • Q8N8I3

    Protein attributes for SPTY2D1 Gene

    Size:
    685 amino acids
    Molecular mass:
    75599 Da
    Quaternary structure:
    • Interacts with histones (PubMed:23378026). Interacts with a heterotetrameric complex formed by histone H3 and H4, especially when the histone tetramer is not bound to DNA (PubMed:26109053).
    Miscellaneous:
    • The histone binding domain can functionally complement the yeast ortholog in regulating histone exchange and suppression of spurious transcription.
    SequenceCaution:
    • Sequence=AAP13351.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SPTY2D1 Gene

    Alternative splice isoforms for SPTY2D1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPTY2D1 Gene

Post-translational modifications for SPTY2D1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SPTY2D1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SPTY2D1 Gene

Domains & Families for SPTY2D1 Gene

Gene Families for SPTY2D1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SPTY2D1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SPTY2D1 Gene

GenScript: Design optimal peptide antigens:
  • SPT2 domain-containing protein 1 (SPT2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q68D10

UniProtKB/Swiss-Prot:

SPT2_HUMAN :
  • The acidic C-terminal domain mediates interaction with histone H3/H4 complexes.
  • Belongs to the SPT2 family.
Domain:
  • The acidic C-terminal domain mediates interaction with histone H3/H4 complexes.
Family:
  • Belongs to the SPT2 family.
genes like me logo Genes that share domains with SPTY2D1: view

Function for SPTY2D1 Gene

Molecular function for SPTY2D1 Gene

UniProtKB/Swiss-Prot Function:
Histone chaperone that stabilizes pre-existing histone tetramers and regulates replication-independent histone exchange on chromatin (PubMed:26109053). Required for normal chromatin refolding in the coding region of transcribed genes, and for the suppression of spurious transcription (PubMed:26109053). Binds DNA and histones and promotes nucleosome assembly (in vitro) (PubMed:23378026, PubMed:26109053). Facilitates formation of tetrameric histone complexes containing histone H3 and H4 (PubMed:26109053). Modulates RNA polymerase 1-mediated transcription (By similarity). Binds DNA, with a preference for branched DNA species, such as Y-form DNA and Holliday junction DNA (PubMed:23378026).

Phenotypes From GWAS Catalog for SPTY2D1 Gene

Gene Ontology (GO) - Molecular Function for SPTY2D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001042 RNA polymerase I core binding ISS --
GO:0003677 DNA binding IBA,IDA 23378026
GO:0042393 histone binding IDA 23378026
genes like me logo Genes that share ontologies with SPTY2D1: view
genes like me logo Genes that share phenotypes with SPTY2D1: view

Animal Model Products

CRISPR Products

miRNA for SPTY2D1 Gene

miRTarBase miRNAs that target SPTY2D1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SPTY2D1 Gene

Localization for SPTY2D1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTY2D1 Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPTY2D1 gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPTY2D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005634 nucleus IEA --
GO:0005730 nucleolus ISS,IBA --
genes like me logo Genes that share ontologies with SPTY2D1: view

Pathways & Interactions for SPTY2D1 Gene

PathCards logo

SuperPathways for SPTY2D1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SPTY2D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IMP,IBA 23378026
GO:0006355 regulation of transcription, DNA-templated IMP 26109053
GO:0010847 regulation of chromatin assembly IMP,IBA 26109053
GO:0043486 histone exchange IMP 26109053
genes like me logo Genes that share ontologies with SPTY2D1: view

No data available for Pathways by source and SIGNOR curated interactions for SPTY2D1 Gene

Drugs & Compounds for SPTY2D1 Gene

No Compound Related Data Available

Transcripts for SPTY2D1 Gene

mRNA/cDNA for SPTY2D1 Gene

(1) REFSEQ mRNAs :
(14) Additional mRNA sequences :
(93) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SPTY2D1 Gene

No ASD Table

Relevant External Links for SPTY2D1 Gene

GeneLoc Exon Structure for
SPTY2D1
ECgene alternative splicing isoforms for
SPTY2D1

Expression for SPTY2D1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SPTY2D1 Gene

Protein differential expression in normal tissues from HIPED for SPTY2D1 Gene

This gene is overexpressed in Heart (28.3), CD8 Tcells (25.6), and Fetal Liver (9.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPTY2D1 Gene



Protein tissue co-expression partners for SPTY2D1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SPTY2D1 Gene:

SPTY2D1

SOURCE GeneReport for Unigene cluster for SPTY2D1 Gene:

Hs.745113

Evidence on tissue expression from TISSUES for SPTY2D1 Gene

  • Intestine(4.2)
  • Pancreas(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with SPTY2D1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPTY2D1 Gene

Orthologs for SPTY2D1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SPTY2D1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPTY2D1 33 32
  • 99.15 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SPTY2D1 33 32
  • 89.38 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SPTY2D1 33 32
  • 87.42 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Spty2d1 17 33 32
  • 84.39 (n)
rat
(Rattus norvegicus)
Mammalia LOC100365259 32
  • 84.27 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 33
  • 64 (a)
OneToMany
-- 33
  • 62 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SPTY2D1 33
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPTY2D1 33 32
  • 61.31 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SPTY2D1 33
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10782 32
zebrafish
(Danio rerio)
Actinopterygii spty2d1 33
  • 43 (a)
OneToOne
wufb01d08 32
fruit fly
(Drosophila melanogaster)
Insecta CG5815 33
  • 28 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7207 33
  • 35 (a)
OneToOne
Species where no ortholog for SPTY2D1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SPTY2D1 Gene

ENSEMBL:
Gene Tree for SPTY2D1 (if available)
TreeFam:
Gene Tree for SPTY2D1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPTY2D1: view image

Paralogs for SPTY2D1 Gene

Paralogs for SPTY2D1 Gene

genes like me logo Genes that share paralogs with SPTY2D1: view

Variants for SPTY2D1 Gene

Sequence variations from dbSNP and Humsavar for SPTY2D1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000019199 -- 18,634,432(-) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000346679 -- 18,617,979(-) A/G intron_variant
rs1000382959 -- 18,635,154(-) C/A upstream_transcript_variant
rs1000394845 -- 18,631,162(-) C/T intron_variant
rs1000629227 -- 18,612,653(-) A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SPTY2D1 Gene

Variant ID Type Subtype PubMed ID
esv3547393 CNV deletion 23714750
nsv516413 CNV loss 19592680
nsv553633 CNV gain 21841781

Variation tolerance for SPTY2D1 Gene

Residual Variation Intolerance Score: 54.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.44; 77.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPTY2D1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPTY2D1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPTY2D1 Gene

Disorders for SPTY2D1 Gene

Additional Disease Information for SPTY2D1

No disorders were found for SPTY2D1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SPTY2D1 Gene

Publications for SPTY2D1 Gene

  1. Vertebrate Spt2 is a novel nucleolar histone chaperone that assists in ribosomal DNA transcription. (PMID: 23378026) Osakabe A … Kurumizaka H (Journal of cell science 2013) 2 3 4 56
  2. Structure-function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2. (PMID: 26109053) Chen S … Patel DJ (Genes & development 2015) 3 4 56
  3. Biological, clinical and population relevance of 95 loci for blood lipids. (PMID: 20686565) Teslovich TM … Kathiresan S (Nature 2010) 3 43 56
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  5. Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells. (PMID: 29509190) Giurato G … Tarallo R (Scientific data 2018) 3 56

Products for SPTY2D1 Gene

Sources for SPTY2D1 Gene