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Aliases for SON Gene

Aliases for SON Gene

  • SON DNA Binding Protein 2 3 5
  • Negative Regulatory Element-Binding Protein 2 3 4
  • Bax Antagonist Selected In Saccharomyces 1 2 3 4
  • NRE-Binding Protein 2 3 4
  • C21orf50 3 4
  • BASS1 3 4
  • NREBP 3 4
  • SON3 3 4
  • Protein DBP-5 4
  • Protein SON 3
  • KIAA1019 4
  • TOKIMS 3
  • DBP-5 3
  • DBP5 4

External Ids for SON Gene

Previous HGNC Symbols for SON Gene

  • C21orf50

Previous GeneCards Identifiers for SON Gene

  • GC21P031492
  • GC21P031575
  • GC21P033835
  • GC21P033837
  • GC21P034914
  • GC21P020393

Summaries for SON Gene

Entrez Gene Summary for SON Gene

  • This gene encodes a protein that contains multiple simple repeats. The encoded protein binds RNA and promotes pre-mRNA splicing, particularly of transcripts with poor splice sites. The protein also recognizes a specific DNA sequence found in the human hepatitis B virus (HBV) and represses HBV core promoter activity. There is a pseudogene for this gene on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

GeneCards Summary for SON Gene

SON (SON DNA Binding Protein) is a Protein Coding gene. Diseases associated with SON include Zttk Syndrome and Blue Color Blindness. GO annotations related to this gene include nucleic acid binding and RNA binding.

UniProtKB/Swiss-Prot for SON Gene

  • RNA-binding protein that acts as a mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. Specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Probably acts by facilitating the interaction between Serine/arginine-rich proteins such as SRSF2 and the RNA polymerase II. Also binds to DNA; binds to the consensus DNA sequence: 5-GA[GT]AN[CG][AG]CC-3. May indirectly repress hepatitis B virus (HBV) core promoter activity and transcription of HBV genes and production of HBV virions. Essential for correct RNA splicing of multiple genes critical for brain development, neuronal migration and metabolism, including TUBG1, FLNA, PNKP, WDR62, PSMD3, PCK2, PFKL, IDH2, and ACY1 (PubMed:27545680).

Gene Wiki entry for SON Gene

Additional gene information for SON Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SON Gene

Genomics for SON Gene

Regulatory Elements for SON Gene

Enhancers for SON 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
GH21H032769 1.2 ENCODE 128.3 -771.3 -771265 3.9 FEZF1 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 SP3 NFYC ZC3H11A ZFP41 PAXBP1 TMEM50B SON DONSON C21orf59 EVA1C URB1 MIS18A-AS1 MIS18A GART
GH21H033539 1.4 ENCODE dbSUPER 106.7 +0.4 390 6.5 DMAP1 YY1 ZNF143 SP3 NFYC ZC3H11A MEF2D SSRP1 ZNF610 GLIS1 SON PAXBP1 TMEM50B GART DONSON C21orf140 C21orf59 PAXBP1-AS1 DNAJC28 ENSG00000231355
GH21H033201 1.9 FANTOM5 Ensembl ENCODE dbSUPER 77.2 -338.7 -338657 4.5 HDGF PKNOX1 SIN3A DMAP1 ZNF48 YY1 FOS ATF7 ZNF548 RUNX3 SON PAXBP1 TMEM50B EVA1C GART DONSON IFNAR2 IFNGR2 URB1 C21orf59
GH21H032611 1.2 ENCODE 85.5 -930.0 -929980 2.5 PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 CBX5 SCAF4 PAXBP1 SON TMEM50B EVA1C GART C21orf59 MIS18A DONSON MIS18A-AS1
GH21H033323 1.4 ENCODE dbSUPER 61.5 -217.4 -217442 2.4 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF766 PAXBP1 SON TMEM50B EVA1C GART LINC01548 ENSG00000226433 ENSG00000238220 OR7E23P IFNAR1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SON on UCSC Golden Path with GeneCards custom track

Promoters for SON Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000141570 682 4201 DMAP1 YY1 ZNF143 SP3 NFYC ZC3H11A MEF2D SSRP1 ZNF610 GLIS1

Genomic Locations for SON Gene

Genomic Locations for SON Gene
chr21:33,542,618-33,577,514
(GRCh38/hg38)
Size:
34,897 bases
Orientation:
Plus strand
chr21:34,914,924-34,949,812
(GRCh37/hg19)

Genomic View for SON Gene

Genes around SON on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SON Gene

Proteins for SON Gene

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

    Protein Symbol:
    P18583-SON_HUMAN
    Recommended name:
    Protein SON
    Protein Accession:
    P18583
    Secondary Accessions:
    • D3DSF5
    • D3DSF6
    • E7ETE8
    • E7EU67
    • E7EVW3
    • E9PFQ2
    • O14487
    • O95981
    • Q14120
    • Q6PKE0
    • Q9H7B1
    • Q9P070
    • Q9P072
    • Q9UKP9
    • Q9UPY0

    Protein attributes for SON Gene

    Size:
    2426 amino acids
    Molecular mass:
    263830 Da
    Quaternary structure:
    • Interacts with SRSF2. Associates with the spliceosome. Interacts with the AML1-MTG8 (AML1-ETO) fusion protein, possibly leading to trigger signals inhibiting leukemogenesis.
    SequenceCaution:
    • Sequence=AAH02422.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA82971.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAA44793.1; Type=Frameshift; Positions=2315, 2412, 2417; Evidence={ECO:0000305}; Sequence=CAC69885.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part.; Evidence={ECO:0000305};

    Alternative splice isoforms for SON Gene

neXtProt entry for SON Gene

Post-translational modifications for SON Gene

  • Ubiquitination at Lys16, Lys2173, and Lys2382
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SON Gene

Domains & Families for SON Gene

Gene Families for SON Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transporters

Graphical View of Domain Structure for InterPro Entry

P18583

UniProtKB/Swiss-Prot:

SON_HUMAN :
  • Contains 8 types of repeats which are distributed in 3 regions.
Domain:
  • Contains 8 types of repeats which are distributed in 3 regions.
genes like me logo Genes that share domains with SON: view

Function for SON Gene

Molecular function for SON Gene

GENATLAS Biochemistry:
DNA binding protein with some homology to c-mos,ubiquitously expressed,involved in chromatin remodeling
UniProtKB/Swiss-Prot Function:
RNA-binding protein that acts as a mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. Specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Probably acts by facilitating the interaction between Serine/arginine-rich proteins such as SRSF2 and the RNA polymerase II. Also binds to DNA; binds to the consensus DNA sequence: 5-GA[GT]AN[CG][AG]CC-3. May indirectly repress hepatitis B virus (HBV) core promoter activity and transcription of HBV genes and production of HBV virions. Essential for correct RNA splicing of multiple genes critical for brain development, neuronal migration and metabolism, including TUBG1, FLNA, PNKP, WDR62, PSMD3, PCK2, PFKL, IDH2, and ACY1 (PubMed:27545680).

Phenotypes From GWAS Catalog for SON Gene

Gene Ontology (GO) - Molecular Function for SON Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA,IDA 21504830
GO:0005515 protein binding IPI 15324660
GO:0050733 RS domain binding IEA --
genes like me logo Genes that share ontologies with SON: view
genes like me logo Genes that share phenotypes with SON: view

Animal Model Products

CRISPR Products

miRNA for SON Gene

miRTarBase miRNAs that target SON

Inhibitory RNA Products

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

Localization for SON Gene

Subcellular locations from UniProtKB/Swiss-Prot for SON Gene

Nucleus speckle. Note=Colocalizes with the pre-mRNA splicing factor SRSF2.

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 SON gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SON Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0016607 nuclear speck IDA 21504830
genes like me logo Genes that share ontologies with SON: view

Pathways & Interactions for SON Gene

No Data Available

SIGNOR curated interactions for SON Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SON Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000226 microtubule cytoskeleton organization IMP 21504830
GO:0000281 mitotic cytokinesis IMP 21504830
GO:0006397 mRNA processing IEA,IDA 21504830
GO:0007049 cell cycle IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SON: view

No data available for Pathways by source for SON Gene

Drugs & Compounds for SON Gene

No Compound Related Data Available

Transcripts for SON Gene

Unigene Clusters for SON Gene

SON DNA binding protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b · 13c ^ 14a · 14b ^ 15a · 15b ^ 16 ^ 17a · 17b · 17c ^ 18a ·
SP1: - - - -
SP2: - - - -
SP3: - - -
SP4: -
SP5: -
SP6:
SP7:
SP8:
SP9: -
SP10: -
SP11:
SP12: -
SP13:
SP14:
SP15:

ExUns: 18b · 18c ^ 19 ^ 20 ^ 21a · 21b · 21c · 21d · 21e · 21f · 21g
SP1: - -
SP2: -
SP3: -
SP4: - -
SP5: -
SP6:
SP7:
SP8: -
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for SON Gene

GeneLoc Exon Structure for
SON
ECgene alternative splicing isoforms for
SON

Expression for SON Gene

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

Protein differential expression in normal tissues from HIPED for SON Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.4), Heart (7.3), and Testis (6.9).

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



Protein tissue co-expression partners for SON Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SON Gene:

SON

SOURCE GeneReport for Unigene cluster for SON Gene:

Hs.517262

mRNA Expression by UniProt/SwissProt for SON Gene:

P18583-SON_HUMAN
Tissue specificity: Widely expressed, with the higher expression seen in leukocyte and heart.

Evidence on tissue expression from TISSUES for SON Gene

  • Nervous system(4.9)
  • Liver(4.8)
  • Blood(4.6)
  • Muscle(4.4)
  • Eye(2.9)
  • Lung(2.4)
  • Intestine(2)
  • Spleen(2)
genes like me logo Genes that share expression patterns with SON: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SON Gene

Orthologs for SON Gene

This gene was present in the common ancestor of animals.

Orthologs for SON Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SON 33 34
  • 99.52 (n)
rat
(Rattus norvegicus)
Mammalia Son 33
  • 93.53 (n)
dog
(Canis familiaris)
Mammalia LOC100856585 33
  • 91.61 (n)
-- 34
  • 90 (a)
OneToMany
-- 34
  • 90 (a)
OneToMany
cow
(Bos Taurus)
Mammalia SON 33 34
  • 89.41 (n)
mouse
(Mus musculus)
Mammalia Son 33 16 34
  • 87.54 (n)
oppossum
(Monodelphis domestica)
Mammalia SON 34
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SON 34
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves SON 34
  • 36 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SON 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.16651 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.21268 33
zebrafish
(Danio rerio)
Actinopterygii SON 34
  • 52 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10141 33
fruit fly
(Drosophila melanogaster)
Insecta CG8273 35 34
  • 38 (a)
worm
(Caenorhabditis elegans)
Secernentea D1037.1 35 34
  • 44 (a)
Species where no ortholog for SON was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for SON Gene

ENSEMBL:
Gene Tree for SON (if available)
TreeFam:
Gene Tree for SON (if available)

Paralogs for SON Gene

Pseudogenes.org Pseudogenes for SON Gene

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

No data available for Paralogs for SON Gene

Variants for SON Gene

Sequence variations from dbSNP and Humsavar for SON Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
VAR_077864 ZTTK syndrome (ZTTKS) [MIM:617140]
VAR_077865 ZTTK syndrome (ZTTKS) [MIM:617140]
rs886039773 Pathogenic 33,554,984(+) GACAG(-/TTAG)AGCTC intron-variant, nc-transcript-variant, reference, frameshift-variant
rs886039774 Pathogenic 33,554,780(+) AAAGA(-/GA)TCATC intron-variant, nc-transcript-variant, reference, frameshift-variant
rs886039775 Pathogenic 33,555,233(+) AGATC(-/CC)AAGGT intron-variant, nc-transcript-variant, reference, frameshift-variant

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

Variant ID Type Subtype PubMed ID
nsv1115615 CNV duplication 24896259
nsv1078502 CNV duplication 25765185
esv2723356 CNV deletion 23290073
esv2723355 CNV deletion 23290073
esv2723354 CNV deletion 23290073

Variation tolerance for SON Gene

Residual Variation Intolerance Score: 0.699% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.07; 80.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SON Gene

Human Gene Mutation Database (HGMD)
SON
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SON

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

Disorders for SON Gene

MalaCards: The human disease database

(8) MalaCards diseases for SON Gene - From: HGMD, OMIM, ClinVar, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SON in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SON_HUMAN
  • ZTTK syndrome (ZTTKS) [MIM:617140]: An autosomal dominant syndrome characterized by intellectual disability, developmental delay, malformations of the cerebral cortex, epilepsy, vision problems, musculo-skeletal abnormalities, and congenital malformations. {ECO:0000269 PubMed:25590979, ECO:0000269 PubMed:27256762, ECO:0000269 PubMed:27545676, ECO:0000269 PubMed:27545680}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SON

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SON
genes like me logo Genes that share disorders with SON: view

No data available for Genatlas for SON Gene

Publications for SON Gene

  1. Transcription repression of human hepatitis B virus genes by negative regulatory element-binding protein/SON. (PMID: 11306577) Sun CT … Ting LP (The Journal of biological chemistry 2001) 3 4 22 60
  2. De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome. (PMID: 27545680) Kim JH … Ahn EY (American journal of human genetics 2016) 3 4 60
  3. De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive. (PMID: 27545676) Tokita MJ … Walkiewicz MA (American journal of human genetics 2016) 3 4 60
  4. Establishing SON in 21q22.11 as a cause a new syndromic form of intellectual disability: Possible contribution to Braddock-Carey syndrome phenotype. (PMID: 27256762) Takenouchi T … Kosaki K (American journal of medical genetics. Part A 2016) 3 4 60
  5. The origins, evolution, and functional potential of alternative splicing in vertebrates. (PMID: 21551269) Mudge JM … Harrow J (Molecular biology and evolution 2011) 2 3 60

Products for SON Gene

Sources for SON Gene

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