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Aliases for USHBP1 Gene

Aliases for USHBP1 Gene

  • USH1 Protein Network Component Harmonin Binding Protein 1 2 3 5
  • Usher Syndrome 1C Binding Protein 1 2 3
  • Mutated In Colon Cancer Protein 2 3 4
  • USH1C-Binding Protein 1 3 4
  • AIE-75-Binding Protein 3 4
  • AIEBP 3 4
  • MCC2 3 4
  • Usher Syndrome Type-1C Protein-Binding Protein 1 3
  • MCC-2 4

External Ids for USHBP1 Gene

Previous GeneCards Identifiers for USHBP1 Gene

  • GC19M017222
  • GC19M017223
  • GC19M017360
  • GC19M016927

Summaries for USHBP1 Gene

GeneCards Summary for USHBP1 Gene

USHBP1 (USH1 Protein Network Component Harmonin Binding Protein 1) is a Protein Coding gene. Diseases associated with USHBP1 include Usher Syndrome and Usher Syndrome, Type Ic. Gene Ontology (GO) annotations related to this gene include PDZ domain binding. An important paralog of this gene is MCC.

Additional gene information for USHBP1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USHBP1 Gene

Genomics for USHBP1 Gene

GeneHancer (GH) Regulatory Elements for USHBP1 Gene

Promoters and enhancers for USHBP1 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
GH19I017264 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.4 +16.3 16258 5.1 HDGF PKNOX1 SMAD1 ARID4B SIN3A ZNF2 YY1 SLC30A9 POLR2B ZNF766 BABAM1 ENSG00000269307 USHBP1 CHERP ABHD8 PLVAP F2RL3 OCEL1 GTPBP3 ENSG00000269427
GH19I017281 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +0.7 706 2.1 ARID4B SIN3A ZNF2 ZNF48 TCF12 ZNF121 ARID2 ZNF143 ATF7 RUNX3 ANKLE1 USHBP1 MRPL34 OCEL1 ABHD8 ENSG00000269307 BABAM1
GH19I017239 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 0.3 +37.8 37770 10.4 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 NR2F6 GC19M017243 CHERP ENSG00000267904 MVB12A GTPBP3 C19orf44 ENSG00000268087 OCEL1 ENSG00000268743
GH19I017261 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 0.3 +21.9 21867 0.9 HDGF MLX ARNT ARID4B SIN3A ZNF2 ZNF213 ZNF143 KLF13 DEK ENSG00000269578 ENSG00000267904 CHERP MVB12A ENSG00000268087 COLGALT1 ENSG00000268743 C19orf44 OCEL1 GTPBP3
GH19I017286 Enhancer 0.5 ENCODE 0.8 -4.2 -4179 1.1 MITF ZSCAN4 ID3 RELA MRPL34 OCEL1 ABHD8 USHBP1 ANKLE1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around USHBP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the USHBP1 gene promoter:

Genomic Locations for USHBP1 Gene

Genomic Locations for USHBP1 Gene
chr19:17,249,176-17,282,786
(GRCh38/hg38)
Size:
33,611 bases
Orientation:
Minus strand
chr19:17,359,985-17,393,595
(GRCh37/hg19)

Genomic View for USHBP1 Gene

Genes around USHBP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USHBP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USHBP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USHBP1 Gene

Proteins for USHBP1 Gene

  • Protein details for USHBP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N6Y0-USBP1_HUMAN
    Recommended name:
    Usher syndrome type-1C protein-binding protein 1
    Protein Accession:
    Q8N6Y0
    Secondary Accessions:
    • A8K7L6
    • B2RCR9
    • Q8NBX7
    • Q96KH3
    • Q9BYI8

    Protein attributes for USHBP1 Gene

    Size:
    703 amino acids
    Molecular mass:
    76068 Da
    Quaternary structure:
    • Interacts via its C-terminus with the first PDZ domain of USH1C.
    SequenceCaution:
    • Sequence=BAC11443.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for USHBP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USHBP1 Gene

Post-translational modifications for USHBP1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for USHBP1 Gene

Domains & Families for USHBP1 Gene

Gene Families for USHBP1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for USHBP1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for USHBP1 Gene

Graphical View of Domain Structure for InterPro Entry

Q8N6Y0

UniProtKB/Swiss-Prot:

USBP1_HUMAN :
  • Belongs to the MCC family.
Family:
  • Belongs to the MCC family.
genes like me logo Genes that share domains with USHBP1: view

Function for USHBP1 Gene

Phenotypes From GWAS Catalog for USHBP1 Gene

Gene Ontology (GO) - Molecular Function for USHBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0030165 PDZ domain binding IPI 11311560
genes like me logo Genes that share ontologies with USHBP1: view
genes like me logo Genes that share phenotypes with USHBP1: view

Animal Models for USHBP1 Gene

MGI Knock Outs for USHBP1:

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for USHBP1 Gene

Localization for USHBP1 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 USHBP1 gene
Compartment Confidence
nucleus 3
cytosol 2
mitochondrion 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for USHBP1 Gene

Pathways & Interactions for USHBP1 Gene

SuperPathways for USHBP1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for USHBP1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for USHBP1 Gene

Drugs & Compounds for USHBP1 Gene

No Compound Related Data Available

Transcripts for USHBP1 Gene

Unigene Clusters for USHBP1 Gene

Usher syndrome 1C binding protein 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for USHBP1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b
SP1: - - - -
SP2: - - - - -
SP3: - - -
SP4: - - - - -
SP5: -
SP6:

Relevant External Links for USHBP1 Gene

GeneLoc Exon Structure for
USHBP1
ECgene alternative splicing isoforms for
USHBP1

Expression for USHBP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for USHBP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for USHBP1 Gene

This gene is overexpressed in Thyroid (41.1) and Placenta (24.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for USHBP1 Gene



Protein tissue co-expression partners for USHBP1 Gene

NURSA nuclear receptor signaling pathways regulating expression of USHBP1 Gene:

USHBP1

SOURCE GeneReport for Unigene cluster for USHBP1 Gene:

Hs.512773

mRNA Expression by UniProt/SwissProt for USHBP1 Gene:

Q8N6Y0-USBP1_HUMAN
Tissue specificity: Highest level of expression in heart, and moderate to low expression in skeletal muscle, kidney, liver, small intestine, placenta and lung.

Evidence on tissue expression from TISSUES for USHBP1 Gene

  • Spleen(4.1)
genes like me logo Genes that share expression patterns with USHBP1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for USHBP1 Gene

Orthologs for USHBP1 Gene

This gene was present in the common ancestor of animals.

Orthologs for USHBP1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia USHBP1 33 34
  • 98.81 (n)
dog
(Canis familiaris)
Mammalia USHBP1 33 34
  • 80.7 (n)
cow
(Bos Taurus)
Mammalia USHBP1 33 34
  • 80.56 (n)
rat
(Rattus norvegicus)
Mammalia Ushbp1 33
  • 72.16 (n)
mouse
(Mus musculus)
Mammalia Ushbp1 33 16 34
  • 71.16 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia USHBP1 34
  • 42 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia USHBP1 34
  • 41 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USHBP1 34
  • 31 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC100148935 33
  • 45.56 (n)
CT573239.1 34
  • 23 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG34404 34
  • 14 (a)
OneToMany
Species where no ortholog for USHBP1 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)
  • chicken (Gallus gallus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for USHBP1 Gene

ENSEMBL:
Gene Tree for USHBP1 (if available)
TreeFam:
Gene Tree for USHBP1 (if available)

Paralogs for USHBP1 Gene

Paralogs for USHBP1 Gene

(1) SIMAP similar genes for USHBP1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with USHBP1: view

Variants for USHBP1 Gene

Sequence variations from dbSNP and Humsavar for USHBP1 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000166186 -- 17,256,002(-) CAAA/ genic_downstream_transcript_variant, intron_variant
rs1000304838 -- 17,251,188(-) T/A genic_downstream_transcript_variant, intron_variant
rs1000467902 -- 17,266,444(-) G/A upstream_transcript_variant
rs1000553602 -- 17,260,805(-) G/C intron_variant
rs1001177979 -- 17,255,293(-) A/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for USHBP1 Gene

Variant ID Type Subtype PubMed ID
nsv470129 CNV loss 18288195
nsv578740 CNV loss 21841781

Variation tolerance for USHBP1 Gene

Residual Variation Intolerance Score: 88.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.03; 90.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USHBP1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
USHBP1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USHBP1 Gene

Disorders for USHBP1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for USHBP1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
usher syndrome
  • retinitis pigmentosa-deafness syndrome
usher syndrome, type ic
  • ush1c
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for USHBP1

genes like me logo Genes that share disorders with USHBP1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for USHBP1 Gene

Publications for USHBP1 Gene

  1. Interaction of MCC2, a novel homologue of MCC tumor suppressor, with PDZ-domain Protein AIE-75. (PMID: 11311560) Ishikawa S … Moriuchi T (Gene 2001) 2 3 4 22 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. (PMID: 26871637) Yang X … Vidal M (Cell 2016) 3 58
  5. An inter-species protein-protein interaction network across vast evolutionary distance. (PMID: 27107014) Zhong Q … Vidal M (Molecular systems biology 2016) 3 58

Products for USHBP1 Gene

Sources for USHBP1 Gene

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