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] See more...

Aliases for SOBP Gene

Aliases for SOBP Gene

  • Sine Oculis Binding Protein Homolog 2 3 5
  • Sine Oculis-Binding Protein Homolog 3 4
  • Jackson Circler Protein 1 3 4
  • JXC1 3 4
  • Sine Oculis Binding Protein Homolog (Drosophila) 2
  • 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 Deafness, Autosomal Dominant 66. Gene Ontology (GO) annotations related to this gene include SUMO polymer binding. An important paralog of this gene is RAI2.

UniProtKB/Swiss-Prot Summary for SOBP Gene

Gene Wiki entry for SOBP Gene

Additional gene information for SOBP Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification 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
GH06J107488 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 505.9 +2.1 2148 8.1 FOXK2 EP300 ZSCAN5C POLR2G NCOR1 PHF8 ZNF639 ZNF10 ZIC2 KDM6A SOBP PDSS2 ENSG00000253090 RF00017-5712
GH06J106509 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 20 -977.1 -977099 7.6 POLR2G NCOR1 ZNF354C ZIC2 POLR2A ZNF623 CTCF ZNF510 KLF7 TGIF2 SOBP ATG5 CRYBG1 BEND3 QRSL1 lnc-RTN4IP1-1 lnc-ATG5-4
GH06J107458 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 5.6 -30.5 -30498 3.2 FOXK2 ZNF217 EP300 CTCF SIN3A NRF1 TCF12 POLR2G SP1 GTF2E2 PDSS2 lnc-SOBP-3 piR-46326 ENSG00000253090 SOBP
GH06J107329 Enhancer 0.8 Ensembl ENCODE 13.1 -159.4 -159397 1.8 USF1 POLR2A NFYB USF2 SRF SPI1 HLF ZNF133 BHLHE40 MAX SOBP PDSS2 LINC02526 piR-42172-005 FJ601684-409 RF00017-5702
GH06J107323 Enhancer 0.6 Ensembl ENCODE 14.9 -166.9 -166935 1.5 FOS EGR2 SCRT2 CEBPB SOBP piR-42172-005 FJ601684-409 RF00017-5702 PDSS2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SOBP on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SOBP

Top Transcription factor binding sites by QIAGEN in the SOBP gene promoter:
  • AREB6
  • CREB
  • deltaCREB
  • FOXI1
  • HFH-3
  • Hlf
  • Pax-2
  • Pax-2a
  • Pbx1a
  • SRY

Genomic Locations for SOBP Gene

Genomic Locations for SOBP Gene
chr6:107,490,098-107,661,309
(GRCh38/hg38)
Size:
171,212 bases
Orientation:
Plus strand
chr6:107,811,162-107,982,513
(GRCh37/hg19)
Size:
171,352 bases
Orientation:
Plus strand

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

GenScript: Design optimal peptide antigens:
  • SOBP protein (Q24K27_HUMAN)
  • cDNA FLJ10159 fis, clone HEMBA1003528 (Q9NWB3_HUMAN)
  • Jackson circler protein 1 (SOBP_HUMAN)

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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SOBP

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
cytoskeleton 1
mitochondrion 1
cytosol 1
extracellular 0
peroxisome 0

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

PathCards logo

SuperPathways for SOBP Gene

No Data Available
;

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

mRNA/cDNA for SOBP Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SOBP

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

No ASD Table

Relevant External Links for SOBP Gene

GeneLoc Exon Structure for
SOBP

Expression for SOBP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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 31 30
  • 97.79 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SOBP 31 30
  • 94.89 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SOBP 31 30
  • 94.67 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 92 (a)
OneToMany
-- 31
  • 79 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Sobp 30
  • 91.17 (n)
mouse
(Mus musculus)
Mammalia Sobp 17 31 30
  • 90.93 (n)
oppossum
(Monodelphis domestica)
Mammalia SOBP 31
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves SOBP 31 30
  • 81.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SOBP 31
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sobp 30
  • 73.01 (n)
zebrafish
(Danio rerio)
Actinopterygii sobpa 31 30
  • 58.86 (n)
OneToMany
sobpb 31
  • 41 (a)
OneToMany
SOBP (3 of 3) 31
  • 40 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Sobp 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SOBP: view image

Paralogs for SOBP Gene

Paralogs for SOBP Gene

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

  • SOBP_HUMAN
  • Q24K27_HUMAN
genes like me logo Genes that share paralogs with SOBP: view

Variants for SOBP Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SOBP Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
710658 Likely Benign: not provided 107,635,253(+) C/T SYNONYMOUS_VARIANT
716742 Likely Benign: not provided 107,634,591(+) T/C MISSENSE_VARIANT
716871 Benign: not provided 107,635,075(+) A/AGCC INFRAME_INSERTION
722121 Likely Benign: not provided 107,506,288(+) A/G SYNONYMOUS_VARIANT
730166 Likely Benign: not provided 107,634,641(+) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SOBP Gene

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

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

Disorder Aliases PubMed IDs
mental retardation, anterior maxillary protrusion, and strabismus
  • mrams
deafness, autosomal dominant 66
  • dfna66
postcholecystectomy syndrome
strabismus
  • strabismus, susceptibility to
biliary dyskinesia
  • sphincter of oddi dysfunction
- 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 54
  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 41 54
  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 54
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 54

Products for SOBP Gene

Sources for SOBP Gene