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Aliases for SPTY2D1 Gene

Aliases for SPTY2D1 Gene

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

UniProtKB/Swiss-Prot 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).

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SPTY2D1 Gene

Genomics for SPTY2D1 Gene

Regulatory Elements for SPTY2D1 Gene

Enhancers for SPTY2D1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G018633 1.1 ENCODE 39.9 +0.5 545 2.3 HDGF PKNOX1 MLX CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 YY1 SPTY2D1 LDHC YWHABP2 UEVLD TSG101 ENSG00000279837
GH11G018617 0.8 Ensembl ENCODE 33 +16.6 16594 1.7 CBFB SCRT2 FOS ETV6 CREM SPTY2D1 LOC105376579 IGSF22 LDHA UEVLD ENSG00000279837
GH11G018587 1.1 ENCODE 12.6 +45.3 45318 4.8 PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF143 DEK LDHC SPTY2D1 TSG101 SERGEF GC11M018587 UEVLD
GH11G018578 1.2 Ensembl ENCODE 11.3 +55.5 55464 1.3 HDAC1 PKNOX1 FOXA2 ATF1 SIN3A ZNF48 GATA2 ZNF207 FOS RCOR1 LOC100129966 SPTY2D1 TMEM86A LOC105376579 IGSF22 TSG101 SERGEF SPTY2D1-AS1 ENSG00000274589
GH11G018670 1 Ensembl ENCODE 11.4 -34.7 -34707 0.2 PKNOX1 ETV1 CEBPG FOSL1 GATA3 ZNF316 ADNP FOS ZNF652 USF2 TMEM86A SPTY2D1 LOC105376579 IGSF22 LOC100129966 SPTY2D1-AS1 LOC100506569
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SPTY2D1 on UCSC Golden Path with GeneCards custom track

Promoters for SPTY2D1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000037632 591 2001 HDGF PKNOX1 MLX CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 YY1

Genomic Location for SPTY2D1 Gene

Chromosome:
11
Start:
18,606,401 bp from pter
End:
18,634,791 bp from pter
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

Protein Domains for SPTY2D1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SPTY2D1 Gene

GenScript: Design optimal peptide antigens:

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

No data available for Gene Families for SPTY2D1 Gene

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).

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 IDA,IEA 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

Inhibitory RNA Products

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

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 --
genes like me logo Genes that share ontologies with SPTY2D1: view

Pathways & Interactions for SPTY2D1 Gene

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 23378026
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IMP 26109053
GO:0010847 regulation of chromatin assembly IMP 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

Unigene Clusters for SPTY2D1 Gene

SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA 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, PaxDb, 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

Primer Products

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 34 35
  • 99.15 (n)
dog
(Canis familiaris)
Mammalia SPTY2D1 34 35
  • 89.38 (n)
cow
(Bos Taurus)
Mammalia SPTY2D1 34 35
  • 87.42 (n)
mouse
(Mus musculus)
Mammalia Spty2d1 34 16 35
  • 84.39 (n)
rat
(Rattus norvegicus)
Mammalia LOC100365259 34
  • 84.27 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 64 (a)
OneToMany
-- 35
  • 62 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SPTY2D1 35
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPTY2D1 34 35
  • 61.31 (n)
lizard
(Anolis carolinensis)
Reptilia SPTY2D1 35
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10782 34
zebrafish
(Danio rerio)
Actinopterygii spty2d1 35
  • 43 (a)
OneToOne
wufb01d08 34
fruit fly
(Drosophila melanogaster)
Insecta CG5815 35
  • 28 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7207 35
  • 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)

Paralogs for SPTY2D1 Gene

No data available for Paralogs for SPTY2D1 Gene

Variants for SPTY2D1 Gene

Sequence variations from dbSNP and Humsavar for SPTY2D1 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000019199 -- 18,634,432(+) CTCCA(C/T)GGCCT intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs1000346679 -- 18,617,979(+) AGTAA(A/G)TGTAT intron-variant
rs1000382959 -- 18,635,154(+) CTTAG(A/C)AAAAA intron-variant, upstream-variant-2KB
rs1000394845 -- 18,631,162(+) TGATA(C/T)GATAG intron-variant
rs1000629227 -- 18,612,653(+) TATCC(A/C)GAAGG 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)

Relevant External Links 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

Relevant External Links for SPTY2D1

Genetic Association Database (GAD)
SPTY2D1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. (J. Cell. Sci. 2013) 2 3 4 64
  2. Structure-function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2. (PMID: 26109053) Chen S. … Patel D.J. (Genes Dev. 2015) 3 4 64
  3. Biological, clinical and population relevance of 95 loci for blood lipids. (PMID: 20686565) Teslovich T.M. … Kathiresan S. (Nature 2010) 3 46 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. Sex-specific association of the SPTY2D1 rs7934205 polymorphism and serum lipid levels. (PMID: 25755761) Guo T. … Li H. (Int J Clin Exp Pathol 2015) 3 64

Products for SPTY2D1 Gene

Sources for SPTY2D1 Gene

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