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Aliases for SHROOM3 Gene

Aliases for SHROOM3 Gene

  • Shroom Family Member 3 2 3 5
  • Shroom-Related Protein 3 4
  • ShrmL 3 4
  • F-Actin-Binding Protein 3
  • Protein Shroom3 3
  • KIAA1481 4
  • MSTP013 3
  • HShrmL 4
  • APXL3 3
  • SHRM 3

External Ids for SHROOM3 Gene

Previous GeneCards Identifiers for SHROOM3 Gene

  • GC04P077575
  • GC04P077356
  • GC04P073108

Summaries for SHROOM3 Gene

Entrez Gene Summary for SHROOM3 Gene

  • This gene encodes a PDZ-domain-containing protein that belongs to a family of Shroom-related proteins. This protein may be involved in regulating cell shape in certain tissues. A similar protein in mice is required for proper neurulation. [provided by RefSeq, Jan 2011]

GeneCards Summary for SHROOM3 Gene

SHROOM3 (Shroom Family Member 3) is a Protein Coding gene. Diseases associated with SHROOM3 include Macular Degeneration, Age-Related, 7 and Neural Tube Defects. Among its related pathways are Tight junction. GO annotations related to this gene include actin binding and actin filament binding. An important paralog of this gene is SHROOM2.

UniProtKB/Swiss-Prot for SHROOM3 Gene

  • Controls cell shape changes in the neuroepithelium during neural tube closure. Induces apical constriction in epithelial cells by promoting the apical accumulation of F-actin and myosin II, and probably by bundling stress fibers. Induces apicobasal cell elongation by redistributing gamma-tubulin and directing the assembly of robust apicobasal microtubule arrays (By similarity).

Gene Wiki entry for SHROOM3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SHROOM3 Gene

Genomics for SHROOM3 Gene

Regulatory Elements for SHROOM3 Gene

Enhancers for SHROOM3 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
GH04F076579 0.7 Ensembl ENCODE 25.1 +145.6 145570 2.6 SCRT1 KLF1 ZNF362 PKNOX1 ZNF501 OSR2 ZNF121 E2F1 JUND GATA3 SHROOM3 RNU6-145P ENSG00000233860 CXCL9 GC04P076578 ENSG00000231335
GH04F076722 0.5 Ensembl ENCODE 22.2 +289.9 289853 4.4 ZNF263 CTCF ZNF280D CEBPB NR3C1 RAD21 ZFHX2 ATF3 MYNN IKZF1 SHROOM3 ENSG00000233860 RNU6-145P SOWAHB GC04M076663
GH04F076606 1 Ensembl ENCODE 20 +172.6 172598 2.2 SCRT1 BCOR ZNF146 ZNF211 TBL1XR1 CBFB MAX JUNB TBX21 EP300 SHROOM3 RNU6-145P ENSG00000233860 GC04P076578 ENSG00000231335
GH04F076663 1.1 Ensembl ENCODE 16.8 +230.5 230490 4.7 TBP PKNOX1 BMI1 RAD21 BRCA1 CBX5 ETV6 CREM EGR2 CBFB SHROOM3 ENSG00000233860 RNU6-145P FAM47E SUMO2P11 LOC105377290
GH04F076610 0.9 Ensembl ENCODE 16.8 +176.5 176506 2.0 ZNF362 BHLHE40 SMC3 NR3C1 RAD21 EP300 NR2F2 SHROOM3 ENSG00000231335 GC04P076578
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SHROOM3 on UCSC Golden Path with GeneCards custom track

Promoters for SHROOM3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001860499 1100 2400 CTCF ZNF654 SMC3 REST RAD21 ZBTB20

Genomic Location for SHROOM3 Gene

Chromosome:
4
Start:
76,435,100 bp from pter
End:
76,783,253 bp from pter
Size:
348,154 bases
Orientation:
Plus strand

Genomic View for SHROOM3 Gene

Genes around SHROOM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHROOM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHROOM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHROOM3 Gene

Proteins for SHROOM3 Gene

  • Protein details for SHROOM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TF72-SHRM3_HUMAN
    Recommended name:
    Protein Shroom3
    Protein Accession:
    Q8TF72
    Secondary Accessions:
    • Q5QTQ3
    • Q6ZRW3
    • Q96IR9
    • Q9P247

    Protein attributes for SHROOM3 Gene

    Size:
    1996 amino acids
    Molecular mass:
    216857 Da
    Quaternary structure:
    • Interacts with F-actin.
    SequenceCaution:
    • Sequence=AAQ13515.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB84689.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for SHROOM3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SHROOM3 Gene

Post-translational modifications for SHROOM3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SHROOM3 Gene

Domains & Families for SHROOM3 Gene

Gene Families for SHROOM3 Gene

Protein Domains for SHROOM3 Gene

Suggested Antigen Peptide Sequences for SHROOM3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TF72

UniProtKB/Swiss-Prot:

SHRM3_HUMAN :
  • The ASD1 domain mediates F-actin binding.
  • Belongs to the shroom family.
Domain:
  • The ASD1 domain mediates F-actin binding.
  • The ASD2 domain is required for apical constriction induction.
  • Contains 1 ASD1 domain.
  • Contains 1 ASD2 domain.
  • Contains 1 PDZ (DHR) domain.
Family:
  • Belongs to the shroom family.
genes like me logo Genes that share domains with SHROOM3: view

Function for SHROOM3 Gene

Molecular function for SHROOM3 Gene

UniProtKB/Swiss-Prot Function:
Controls cell shape changes in the neuroepithelium during neural tube closure. Induces apical constriction in epithelial cells by promoting the apical accumulation of F-actin and myosin II, and probably by bundling stress fibers. Induces apicobasal cell elongation by redistributing gamma-tubulin and directing the assembly of robust apicobasal microtubule arrays (By similarity).

Gene Ontology (GO) - Molecular Function for SHROOM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0051015 actin filament binding IEA --
genes like me logo Genes that share ontologies with SHROOM3: view
genes like me logo Genes that share phenotypes with SHROOM3: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SHROOM3 Gene

Localization for SHROOM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHROOM3 Gene

Cell junction, adherens junction. Cytoplasm, cytoskeleton. Note=Colocalizes with F-actin in stress fibers and adherens junctions. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SHROOM3 Gene COMPARTMENTS Subcellular localization image for SHROOM3 gene
Compartment Confidence
cytoskeleton 4
cytosol 4
nucleus 4
plasma membrane 3

Gene Ontology (GO) - Cellular Components for SHROOM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA,ISS --
GO:0005874 microtubule IEA --
GO:0005912 adherens junction IEA,ISS --
GO:0016324 apical plasma membrane ISS --
genes like me logo Genes that share ontologies with SHROOM3: view

Pathways & Interactions for SHROOM3 Gene

SuperPathways for SHROOM3 Gene

SuperPathway Contained pathways
1 Tight junction
genes like me logo Genes that share pathways with SHROOM3: view

Pathways by source for SHROOM3 Gene

1 KEGG pathway for SHROOM3 Gene

Gene Ontology (GO) - Biological Process for SHROOM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis ISS --
GO:0001843 neural tube closure IEA --
GO:0002064 epithelial cell development IEA --
GO:0007275 multicellular organism development IEA --
GO:0007389 pattern specification process ISS --
genes like me logo Genes that share ontologies with SHROOM3: view

No data available for SIGNOR curated interactions for SHROOM3 Gene

Drugs & Compounds for SHROOM3 Gene

(2) Drugs for SHROOM3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for SHROOM3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SHROOM3: view

Transcripts for SHROOM3 Gene

Unigene Clusters for SHROOM3 Gene

Shroom family member 3:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SHROOM3 Gene

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

ExUns: 17 ^ 18 ^ 19 ^ 20a · 20b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for SHROOM3 Gene

GeneLoc Exon Structure for
SHROOM3
ECgene alternative splicing isoforms for
SHROOM3

Expression for SHROOM3 Gene

mRNA expression in normal human tissues for SHROOM3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SHROOM3 Gene

This gene is overexpressed in Stomach (41.9), Lung (6.9), and Adrenal (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SHROOM3 Gene



NURSA nuclear receptor signaling pathways regulating expression of SHROOM3 Gene:

SHROOM3

SOURCE GeneReport for Unigene cluster for SHROOM3 Gene:

Hs.702168
genes like me logo Genes that share expression patterns with SHROOM3: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SHROOM3 Gene

Orthologs for SHROOM3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SHROOM3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SHROOM3 34 35
  • 98.63 (n)
dog
(Canis familiaris)
Mammalia SHROOM3 34 35
  • 81.36 (n)
cow
(Bos Taurus)
Mammalia SHROOM3 34 35
  • 81.04 (n)
mouse
(Mus musculus)
Mammalia Shroom3 34 16 35
  • 78.43 (n)
rat
(Rattus norvegicus)
Mammalia Shroom3 34
  • 77.92 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SHROOM3 35
  • 68 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SHROOM3 35
  • 54 (a)
OneToOne
chicken
(Gallus gallus)
Aves SHROOM3 34 35
  • 60.73 (n)
lizard
(Anolis carolinensis)
Reptilia SHROOM3 35
  • 47 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia shroom3 34
  • 50.3 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.5622 34
zebrafish
(Danio rerio)
Actinopterygii SHROOM3 35
  • 56 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Shroom 35
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5284 35
  • 43 (a)
ManyToMany
-- 35
  • 41 (a)
ManyToMany
Species where no ortholog for SHROOM3 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 SHROOM3 Gene

ENSEMBL:
Gene Tree for SHROOM3 (if available)
TreeFam:
Gene Tree for SHROOM3 (if available)

Paralogs for SHROOM3 Gene

Paralogs for SHROOM3 Gene

(1) SIMAP similar genes for SHROOM3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SHROOM3: view

Variants for SHROOM3 Gene

Sequence variations from dbSNP and Humsavar for SHROOM3 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs761601802 Uncertain significance 76,739,349(+) AGTTA(C/T)GCAGC reference, synonymous-codon
rs863225433 Uncertain significance 76,741,021(+) GGGGG(-/G)CGCCC reference, frameshift-variant
rs10000169 -- 76,435,093(+) AACTT(C/T)CTACG upstream-variant-2KB
rs10001658 -- 76,706,668(+) TTCAA(A/G)CTTCT intron-variant
rs10001789 -- 76,535,596(+) GAAAC(C/T)AGATG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SHROOM3 Gene

Variant ID Type Subtype PubMed ID
esv2664574 CNV deletion 23128226
esv2727846 CNV deletion 23290073
esv2727847 CNV deletion 23290073
esv275302 CNV loss 21479260
esv2759262 CNV loss 17122850
esv3601055 CNV loss 21293372
esv3601056 CNV loss 21293372
esv3601062 CNV loss 21293372
esv3601063 CNV loss 21293372
esv8702 CNV gain 19470904
nsv1136879 CNV deletion 24896259
nsv1143289 CNV deletion 24896259
nsv289572 CNV insertion 16902084
nsv292270 CNV deletion 16902084
nsv478414 CNV novel sequence insertion 20440878
nsv478526 CNV novel sequence insertion 20440878
nsv594696 CNV gain 21841781
nsv7363 OTHER inversion 18451855
nsv829972 CNV loss 17160897
nsv829973 CNV loss 17160897
nsv967767 CNV duplication 23825009

Variation tolerance for SHROOM3 Gene

Residual Variation Intolerance Score: 93.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.26; 97.63% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SHROOM3 Gene

Human Gene Mutation Database (HGMD)
SHROOM3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHROOM3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHROOM3 Gene

Disorders for SHROOM3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SHROOM3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
macular degeneration, age-related, 7
  • macular degeneration, age-related, neovascular type
neural tube defects
  • spina bifida
macular degeneration, age-related, 1
  • macular degeneration, age-related, 2
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SHROOM3

Genetic Association Database (GAD)
SHROOM3
Human Genome Epidemiology (HuGE) Navigator
SHROOM3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SHROOM3
genes like me logo Genes that share disorders with SHROOM3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHROOM3 Gene

Publications for SHROOM3 Gene

  1. A new standard nomenclature for proteins related to Apx and Shroom. (PMID: 16615870) Hagens O. … Wallingford J.B. (BMC Cell Biol. 2006) 2 3 4 64
  2. Common variants at 5q22 associate with pediatric eosinophilic esophagitis. (PMID: 20208534) Rothenberg M.E. … Hakonarson H. (Nat. Genet. 2010) 3 46 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. Genetic loci influencing kidney function and chronic kidney disease. (PMID: 20383145) Chambers J.C. … Kooner J.S. (Nat. Genet. 2010) 3 46 64
  5. New loci associated with kidney function and chronic kidney disease. (PMID: 20383146) KAPttgen A. … Fox C.S. (Nat. Genet. 2010) 3 46 64

Products for SHROOM3 Gene

Sources for SHROOM3 Gene

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