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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 Blue Color Blindness and Lethal Congenital Contracture Syndrome 1. 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

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
GH21G033378 2.1 FANTOM5 Ensembl ENCODE dbSUPER 4.1 -160.5 -160486 6.7 HDGF PKNOX1 FOXA2 MLX ZFP64 WRNIP1 ARID4B DMAP1 YBX1 ZNF143 IFNGR2 GART IFNAR2 IL10RB IFNAR1 TMEM50B SON GC21P033366
GH21G033363 1.5 FANTOM5 Ensembl ENCODE dbSUPER 5.5 -178.3 -178318 1.4 ELF3 CTCF PKNOX1 CEBPG ZBTB40 GATA3 FOXK2 ZNF350 MAFK CREM IFNGR2 IL10RB IFNAR1 LINC01548 IFNAR2 SON GART OLIG1 GC21P033366
GH21G033298 1.9 FANTOM5 Ensembl ENCODE dbSUPER 3.8 -241.7 -241652 4.7 PKNOX1 FOXA2 ATF1 TCF12 ZNF766 GATA2 ZNF143 KLF13 CAVIN1 TBX21 IFNAR1 IFNAR2 IL10RB IFNGR2 ENSG00000249624 GART TMEM50B URB1 SON OLIG1
GH21G033400 1.7 FANTOM5 ENCODE dbSUPER 3.3 -138.7 -138669 6.7 FOXA2 MLX CREB3L1 AGO1 WRNIP1 ARID4B SIN3A ZNF2 YY1 FOS IFNGR2 TMEM50B IFNAR2 RPS5P3 ENSG00000231355 ENSG00000249624 DNAJC28 IL10RB GART IFNAR1
GH21G033359 1.9 FANTOM5 Ensembl ENCODE dbSUPER 2.9 -181.1 -181141 3.1 HDGF PKNOX1 ARID4B ZNF48 ZNF2 YY1 GATA2 ZNF143 ZNF207 FOS IFNGR2 IFNAR2 IFNAR1 IL10RB GART SON OLIG1 GC21P033366 USF1P1
- 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 262 4201 CREB3L1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 MEF2D SSRP1

Genomic Location for SON Gene

Chromosome:
21
Start:
33,542,618 bp from pter
End:
33,577,514 bp from pter
Size:
34,897 bases
Orientation:
Plus strand

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 isoforms=2, 3, 4, 5, 6, 7, 8, 9, 1016, isoforms=2, 3, 4, 5, 7, 9, 102173, and isoforms=2, 5, 7, 92382
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SON Gene

Domains & Families for SON Gene

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).

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 IDA,IEA 21504830
GO:0005515 protein binding IPI 21504830
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

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 IDA,IEA 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 34 35
  • 99.52 (n)
rat
(Rattus norvegicus)
Mammalia Son 34
  • 93.53 (n)
dog
(Canis familiaris)
Mammalia LOC100856585 34
  • 91.61 (n)
-- 35
  • 90 (a)
OneToMany
-- 35
  • 90 (a)
OneToMany
cow
(Bos Taurus)
Mammalia SON 34 35
  • 89.41 (n)
mouse
(Mus musculus)
Mammalia Son 34 16 35
  • 87.54 (n)
oppossum
(Monodelphis domestica)
Mammalia SON 35
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SON 35
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves SON 35
  • 36 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SON 35
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.16651 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.21268 34
zebrafish
(Danio rerio)
Actinopterygii SON 35
  • 52 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10141 34
fruit fly
(Drosophila melanogaster)
Insecta CG8273 36 35
  • 38 (a)
worm
(Caenorhabditis elegans)
Secernentea D1037.1 36 35
  • 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
esv2723354 CNV deletion 23290073
esv2723355 CNV deletion 23290073
esv2723356 CNV deletion 23290073
nsv1078502 CNV duplication 25765185
nsv1115615 CNV duplication 24896259

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

(7) MalaCards diseases for SON Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
blue color blindness
  • tritanopia
lethal congenital contracture syndrome 1
  • lccs1
anterior horn cell disease
colorblindness, tritan
  • tritanopia
hepatitis b
  • chronic hepatitis b
- 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 C.-T. … Ting L.-P. (J. Biol. Chem. 2001) 3 4 22 64
  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 J.H. … Ahn E.Y. (Am. J. Hum. Genet. 2016) 3 4 64
  3. De novo truncating variants in SON cause intellectual disability, congenital malformations, and failure to thrive. (PMID: 27545676) Tokita M.J. … Walkiewicz M.A. (Am. J. Hum. Genet. 2016) 3 4 64
  4. The origins, evolution, and functional potential of alternative splicing in vertebrates. (PMID: 21551269) Mudge J.M. … Harrow J. (Mol. Biol. Evol. 2011) 2 3 64
  5. SON controls cell-cycle progression by coordinated regulation of RNA splicing. (PMID: 21504830) Ahn E.Y. … Zhang D.E. (Mol. Cell 2011) 3 4 64

Products for SON Gene

Sources for SON Gene

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