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Aliases for SOBP Gene

Aliases for SOBP Gene

  • Sine Oculis Binding Protein Homolog 2 3 5
  • Jackson Circler Protein 1 3 4
  • JXC1 3 4
  • Sine Oculis Binding Protein Homolog (Drosophila) 2
  • Sine Oculis-Binding Protein Homolog 3
  • MRAMS 3

External Ids for SOBP Gene

Previous GeneCards Identifiers for SOBP Gene

  • GC06P107920
  • GC06P107811
  • GC06P105382

Summaries for SOBP Gene

Entrez Gene Summary for SOBP Gene

  • The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea. Defects in this gene have also been linked to intellectual disability. [provided by RefSeq, Mar 2011]

GeneCards Summary for SOBP Gene

SOBP (Sine Oculis Binding Protein Homolog) is a Protein Coding gene. Diseases associated with SOBP include Mental Retardation, Anterior Maxillary Protrusion, And Strabismus and Postcholecystectomy Syndrome. Gene Ontology (GO) annotations related to this gene include SUMO polymer binding.

UniProtKB/Swiss-Prot for SOBP Gene

  • Implicated in development of the cochlea.

Gene Wiki entry for SOBP Gene

Additional gene information for SOBP Gene

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

Genomics for SOBP Gene

GeneHancer (GH) Regulatory Elements for SOBP Gene

Promoters and enhancers for SOBP Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I107488 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 556 +2.5 2480 7.9 PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 ZNF213 SOBP PDSS2 ENSG00000234206 GC06M107466
GH06I106509 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 20 -976.6 -976614 7.7 PKNOX1 MLX ZNF493 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF48 ETS1 BEND3 SOBP ATG5 CRYBG1 QRSL1 LOC101927405 GC06P106528
GH06I107458 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 5.6 -30.4 -30432 2.3 PKNOX1 FOXA2 SMAD1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SLC30A9 PDSS2 PIR39325 SOBP
GH06I107329 Enhancer 0.6 ENCODE 13.1 -159.4 -159391 1.1 SRF USF1 ZNF133 MAX POLR2A IKZF1 ZNF143 RUNX3 SOBP LINC02526 PIR39423 GC06P107268 PDSS2
GH06I107241 Enhancer 1 Ensembl ENCODE 7.7 -248.0 -247999 1.8 SOX13 CTCF FOXA2 SAP130 CEBPG ZNF644 RAD21 SCRT2 HOMEZ SCRT1 SOBP PDSS2 GC06P107237 GC06P107246
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SOBP on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SOBP gene promoter:

Genomic Locations for SOBP Gene

Genomic Locations for SOBP Gene
chr6:107,489,958-107,661,309
(GRCh38/hg38)
Size:
171,352 bases
Orientation:
Plus strand
chr6:107,811,162-107,982,513
(GRCh37/hg19)

Genomic View for SOBP Gene

Genes around SOBP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SOBP Gene

Proteins for SOBP Gene

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

    Protein Symbol:
    A7XYQ1-SOBP_HUMAN
    Recommended name:
    Sine oculis-binding protein homolog
    Protein Accession:
    A7XYQ1
    Secondary Accessions:
    • B0QZ12
    • Q5BJD4
    • Q8N2B2

    Protein attributes for SOBP Gene

    Size:
    873 amino acids
    Molecular mass:
    92658 Da
    Quaternary structure:
    • Interacts (via SIM domains) with SUMO1 and SUMO2.
    SequenceCaution:
    • Sequence=AAH91526.2; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305}; Sequence=BAC03537.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};

neXtProt entry for SOBP Gene

Post-translational modifications for SOBP Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SOBP Gene

Domains & Families for SOBP Gene

Gene Families for SOBP Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SOBP Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SOBP Gene

Graphical View of Domain Structure for InterPro Entry

A7XYQ1

UniProtKB/Swiss-Prot:

SOBP_HUMAN :
  • Belongs to the SOBP family.
Family:
  • Belongs to the SOBP family.
genes like me logo Genes that share domains with SOBP: view

Function for SOBP Gene

Molecular function for SOBP Gene

UniProtKB/Swiss-Prot Function:
Implicated in development of the cochlea.

Phenotypes From GWAS Catalog for SOBP Gene

Gene Ontology (GO) - Molecular Function for SOBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032184 SUMO polymer binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SOBP: view
genes like me logo Genes that share phenotypes with SOBP: view

Human Phenotype Ontology for SOBP Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SOBP Gene

Localization for SOBP Gene

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 SOBP gene
Compartment Confidence
nucleus 4
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SOBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with SOBP: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SOBP Gene

Pathways & Interactions for SOBP Gene

No Data Available

Interacting Proteins for SOBP Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000318900%0d%0a9606.ENSP00000405965%0d%0a
Selected Interacting proteins: A7XYQ1-SOBP_HUMAN ENSP00000318900 for SOBP Gene via IID MINT STRING

Gene Ontology (GO) - Biological Process for SOBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007605 sensory perception of sound IEA --
GO:0007626 locomotory behavior IEA --
GO:0042472 inner ear morphogenesis IEA --
GO:0050890 cognition IMP 21035105
GO:0090102 cochlea development IEA --
genes like me logo Genes that share ontologies with SOBP: view

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

Drugs & Compounds for SOBP Gene

No Compound Related Data Available

Transcripts for SOBP Gene

Unigene Clusters for SOBP Gene

Sine oculis binding protein homolog (Drosophila):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for SOBP Gene

GeneLoc Exon Structure for
SOBP
ECgene alternative splicing isoforms for
SOBP

Expression for SOBP Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SOBP Gene

This gene is overexpressed in Fetal Brain (69.0).

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



Protein tissue co-expression partners for SOBP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SOBP Gene:

SOBP

SOURCE GeneReport for Unigene cluster for SOBP Gene:

Hs.445244

Evidence on tissue expression from TISSUES for SOBP Gene

  • Nervous system(2.8)
  • Lung(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SOBP Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeleton
Regions:
Head and neck:
  • brain
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • skull
  • tooth
genes like me logo Genes that share expression patterns with SOBP: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SOBP Gene

Orthologs for SOBP Gene

This gene was present in the common ancestor of animals.

Orthologs for SOBP Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SOBP 33 34
  • 97.79 (n)
dog
(Canis familiaris)
Mammalia SOBP 33 34
  • 94.89 (n)
cow
(Bos Taurus)
Mammalia SOBP 33 34
  • 94.67 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 92 (a)
OneToMany
-- 34
  • 79 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Sobp 33
  • 91.17 (n)
mouse
(Mus musculus)
Mammalia Sobp 33 16 34
  • 90.93 (n)
oppossum
(Monodelphis domestica)
Mammalia SOBP 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves SOBP 33 34
  • 81.4 (n)
lizard
(Anolis carolinensis)
Reptilia SOBP 34
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sobp 33
  • 73.01 (n)
zebrafish
(Danio rerio)
Actinopterygii sobpa 33 34
  • 58.86 (n)
sobpb 34
  • 41 (a)
OneToMany
SOBP (3 of 3) 34
  • 40 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Sobp 34
  • 24 (a)
OneToOne
Species where no ortholog for SOBP 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 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)
  • worm (Caenorhabditis elegans)

Evolution for SOBP Gene

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

Paralogs for SOBP Gene

(1) SIMAP similar genes for SOBP Gene using alignment to 2 proteins:

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

No data available for Paralogs for SOBP Gene

Variants for SOBP Gene

Sequence variations from dbSNP and Humsavar for SOBP Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs146747167 likely-benign, benign, not specified, not provided 107,634,459(+) A/G coding_sequence_variant, missense_variant
rs148915050 likely-benign, not specified, not provided 107,506,325(+) A/C/G 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, upstream_transcript_variant
rs267607078 pathogenic, Mental retardation, anterior maxillary protrusion, and strabismus 107,634,825(+) C/T coding_sequence_variant, stop_gained
rs541688197 benign, likely-benign, uncertain-significance, not specified, not provided 107,635,076(+) GCCGCCGCCGCCGCCGCCGCC/GCCGCCGCCGCC/GCCGCCGCCGCCGCC/GCCGCCGCCGCCGCCGCC/GCCGCCGCCGCCGCCGCCGCCGCC/GCCGCCGCCGCCGCCGCCGCCGCCGCC/GCCGCCGCCGCCGCCGCCGCCGCCGCCGCC/GCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC/GCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC coding_sequence_variant, inframe_deletion, inframe_insertion
rs587780464 likely-benign, not specified 107,634,226(+) A/C coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
dgv1012e201 CNV deletion 23290073
esv2732551 CNV deletion 23290073
nsv1073579 CNV deletion 25765185
nsv1073580 CNV deletion 25765185
nsv1122136 CNV deletion 24896259
nsv1146719 CNV insertion 26484159
nsv349993 CNV insertion 16902084
nsv830762 CNV gain 17160897
nsv830763 CNV gain 17160897

Variation tolerance for SOBP Gene

Residual Variation Intolerance Score: 21.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.20; 52.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SOBP Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for SOBP Gene

MalaCards: The human disease database

(10) MalaCards diseases for SOBP Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, anterior maxillary protrusion, and strabismus
  • mrams
postcholecystectomy syndrome
common bile duct disease
  • common bile duct diseases
biliary dyskinesia
  • sphincter of oddi dysfunction
esotropia
  • convergence in manifest squint
- elite association - COSMIC cancer census association via MalaCards
Search SOBP in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SOBP_HUMAN
  • Mental retardation, anterior maxillary protrusion, and strabismus (MRAMS) [MIM:613671]: A syndrome characterized by severe mental retardation, strabismus and dysmorphic features such as anterior maxillary protrusion with vertical maxillary excess, open bite and prominent crowded teeth. Some patients may lack dysmorphic features and manifest temporal lobe epilepsy and psychosis. Esotropia and amblyopia are present in some individuals. {ECO:0000269 PubMed:21035105}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SOBP

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SOBP: view

No data available for Genatlas for SOBP Gene

Publications for SOBP Gene

  1. Poly-small ubiquitin-like modifier (PolySUMO)-binding proteins identified through a string search. (PMID: 23086935) Sun H … Hunter T (The Journal of biological chemistry 2012) 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system. (PMID: 21035105) Birk E … Basel-Vanagaite L (American journal of human genetics 2010) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. (PMID: 28112733) Hendriks IA … Nielsen ML (Nature structural & molecular biology 2017) 4 58

Products for SOBP Gene

Sources for SOBP Gene

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