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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SHROOM1 Gene

protein-coding   GIFtS: 44
GCID: GC05M132157

shroom family member 1
  Search for SHROOM1
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SHROOM1    

Aliases
for SHROOM1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Shroom Family Member 11 2
APXL21 2 3
KIAA19601 3
Apical Protein 22 3
Protein Shroom12

External Ids:    HGNC: 240841   Entrez Gene: 1345492   Ensembl: ENSG000001644037   OMIM: 6111795   UniProtKB: Q2M3G43   

Export aliases for SHROOM1 gene to outside databases

Previous GC identifers: GC05M132186 GC05M127350


Summaries
for SHROOM1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for SHROOM1:
SHROOM family members play diverse roles in the development of the nervous system and other tissues (Hagens et al.,
2006 (PubMed 16615870)).(supplied by OMIM, Mar 2008)

UniProtKB/Swiss-Prot: SHRM1_HUMAN, Q2M3G4
Function: May be involved in the assembly of microtubule arrays during cell elongation (By similarity)




Genomic Views
for SHROOM1 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NC_018916.1  NT_034772.6  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SHROOM1 gene promoter:
         Tal-1beta   AP-2gamma   E47   Ik-2   Hand1   SEF-1 (1)   NF-Y   CBF(2)   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SHROOM1 promoter sequence
   Search SABiosciences Chromatin IP Primers for SHROOM1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SHROOM1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31.1   Ensembl cytogenetic band:  5q31.1   HGNC cytogenetic band: 5q31.1

SHROOM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHROOM1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M132157:  view genomic region     (about GC identifiers)

Start:
 132,157,833 bp from pter      End:
 132,166,590 bp from pter
Size:
 8,758 bases      Orientation:
 minus strand

Proteins
for SHROOM1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: SHRM1_HUMAN, Q2M3G4 (See protein sequence)
Recommended Name: Protein Shroom1  
Size: 852 amino acids; 90786 Da
Subunit: Interacts with F-actin (By similarity)
Subcellular location: Cytoplasm, cytoskeleton (By similarity)
Sequence caution: Sequence=BAB85546.1; Type=Erroneous initiation;
Secondary accessions: B7WP40 B7ZL01 Q8TDP0 Q8TF41
Alternative splicing: 2 isoforms:  Q2M3G4-1   Q2M3G4-2   

Explore the universe of human proteins at neXtProt for SHROOM1: NX_Q2M3G4

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q2M3G4

    • SHROOM1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001166171.1  NP_597713.2  

    ENSEMBL proteins: 
     ENSP00000367950   ENSP00000324245   ENSP00000367947   ENSP00000388049  

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    Uscn Proteins for SHROOM1

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0005874microtubule IEA--
    GO:0016460colocalizes with myosin II complex ISS16684770


    SHROOM1 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for SHROOM1

    Protein Domains /
    Families
    for SHROOM1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    SHROOM1 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR014799 ASD2
     IPR014800 ASD1

    Graphical View of Domain Structure for InterPro Entry Q2M3G4

    ProtoNet protein and cluster: Q2M3G4

    UniProtKB/Swiss-Prot: SHRM1_HUMAN, Q2M3G4
    Domain: The ASD1 domain mediates F-actin binding (By similarity)
    Similarity: Belongs to the shroom family
    Similarity: Contains 1 ASD1 domain
    Similarity: Contains 1 ASD2 domain


    Function
    for SHROOM1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: SHRM1_HUMAN, Q2M3G4
    Function: May be involved in the assembly of microtubule arrays during cell elongation (By similarity)

    miRNA
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    hsa-miR-302d hsa-miR-520e hsa-miR-429 hsa-miR-509-5p hsa-miR-302e hsa-miR-520a-3p hsa-miR-372 hsa-miR-520d-3p
    SwitchGear 3'UTR luciferase reporter plasmid: SHROOM1 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    Clone
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    Cell Line
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    Search LifeMap BioReagents cell lines for SHROOM1

    In Situ Assay
    Products:       
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0051015actin filament binding ISS16684770


    SHROOM1 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for SHROOM1:
     Decreased Hepatitis C virus re 


    Pathways & Interactions
    for SHROOM1 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SHROOM1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 22)

    5/24 Interacting proteins for SHROOM1 (Q2M3G42, 3 ENSP000003242454) via UniProtKB, MINT, STRING, and/or I2D (see all 24)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SFNP319472, 3MINT-3974770 I2D: score=1 
    RPS6KA1Q154183I2D: score=2 
    MYBPC3ENSP000003821934STRING: ENSP00000382193
    MYH1ENSP000002262074STRING: ENSP00000226207
    MYH10ENSP000002692434STRING: ENSP00000269243
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000902cell morphogenesis ISS16684770
    GO:0051017actin filament bundle assembly ISS16684770


    SHROOM1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for SHROOM1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SHROOM1
    Search CenterWatch for drugs/clinical trials and news about SHROOM1 / SHRM1 

    Transcripts
    for SHROOM1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for SHROOM1 gene (2 alternative transcripts): 
    NM_001172700.1  NM_133456.2  

    Unigene Cluster for SHROOM1:

    Shroom family member 1
    Hs.519574  [show with all ESTs]
    Unigene Representative Sequence: NM_001172700
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000378679(uc003kxy.2 uc003kxx.3) ENST00000319854 ENST00000378676
    ENST00000488072 ENST00000495680 ENST00000440118

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SHROOM1
    8/19 QIAGEN miScript miRNA Assays for microRNAs that regulate SHROOM1 (see all 19):
    hsa-miR-302d hsa-miR-520e hsa-miR-429 hsa-miR-509-5p hsa-miR-302e hsa-miR-520a-3p hsa-miR-372 hsa-miR-520d-3p
    SwitchGear 3'UTR luciferase reporter plasmid: SHROOM1 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SHROOM1 (see all 4)
    OriGene shRNA RFP: SHROOM1
    OriGene siRNA: SHROOM1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SHROOM1
    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 2): SHROOM1 (NM_133456)
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SHROOM1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SHROOM1

    Additional cDNA sequence: 

    AB075840.1 AF314142.1 BC040980.1 BC104914.1 BC104916.1 BC143494.1 

    9 DOTS entries:

    DT.405835  DT.100022033  DT.70101999  DT.95263595  DT.75116182  DT.75170038  DT.86839198  DT.97784779 
    DT.121645433 

    24/52 AceView cDNA sequences (see all 52):

    NM_133456 AB075840 BQ221784 BQ437705 AI277049 AI348038 AI309907 AF314142 
    BQ549586 BG983381 BF446355 AW846931 BM507227 BQ718274 AA588854 BQ650755 
    AA343553 AL138454 BC040980 BM272376 CB216252 AI799642 BX358281 AA326450 

    GeneLoc Exon Structure


    Expression
    for SHROOM1 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SHROOM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGGCCTCACC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    SHROOM1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    HeartAtrioventricular NodeAtrioventricular Node CellsMyocardium
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SHROOM1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SHROOM1

    SOURCE GeneReport for Unigene cluster: Hs.519574
        SABiosciences Custom PCR Arrays for SHROOM1
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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SHROOM1

    Orthologs
    for SHROOM1 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for SHROOM1 gene from 5/15 species (see all 15)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Shroom11 , 5 shroom family member 11, 5 73.12(n)1
    61.89(a)1    		   11 (31.95 cM)5
    717741  NM_027917.21  NP_082193.21 
     534572055 
    chicken
    (Gallus gallus)    		 Aves SHROOM16
    		 Uncharacterized protein
    		 17(a)
    		 1 ↔ 1
    		 13(17619314-17627138)
    lizard
    (Anolis carolinensis)    		 Reptilia SHROOM16
    		 --
    		 41(a)
    		 1 ↔ 1
    		 2(127406198-127410645)
    zebrafish
    (Danio rerio)    		 Actinopterygii si:ch211-225b14.66
    		 si:ch211-225b14.6
    		 12(a)
    		 1 ↔ 1
    		 21(41659350-41716266)
    fruit fly
    (Drosophila melanogaster)    		 Insecta Shroom6
    		 Shroom
    		 7(a)
    		 1 → many
    		 2R(10195667-10239312)


    ENSEMBL Gene Tree for SHROOM1 (if available)
    TreeFam Gene Tree for SHROOM1 (if available) 

    Paralogs
    for SHROOM1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SHROOM1 gene
    SHROOM32  SHROOM42  SHROOM22  

    SHROOM1 for paralogs           About GeneDecksing



    Genomic Variants
    for SHROOM1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/193 NCBI SNPs in SHROOM1 are shown (see all 193)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 5 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1485264711,2
    		--132157517(+) CTACTG/TCTCTA 2 -- int10--------
    rs1919471371,2
    		--132157531(+) AAGCTG/TGGATG 2 -- int10--------
    rs1841549411,2
    		--132157650(+) GAAAGC/TGCAGT 2 -- int10--------
    rs609868821,2
    		C,F,--132157699(+) AGACTA/GACTAG 2 -- int14Minor allele frequency- G:0.32WA EA 242
    rs1875478681,2
    		--132157996(+) AATAAC/TACACA 2 -- ut310--------
    rs2010385001,2
    		C--132158043(+) AGTATC/TTTTTT 2 -- ut310--------
    rs1911429971,2
    		--132158078(+) TGAGAC/TGGAGT 2 -- ut310--------
    rs1822701081,2
    		--132158208(+) CCGCCA/TCCACG 2 -- ut310--------
    rs2014619131,2
    		--132158444(+) TACGTC/GGGTGA 2 -- ut310--------
    rs1429310021,2
    		C,--132158564(+) ACGGGA/GCATGA 4 A V mis10--------

    HapMap Linkage Disequilibrium report for SHROOM1 (132157833 - 132166590 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SHROOM1: --

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    Disorders / Diseases
    for SHROOM1 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    SHROOM1 for disorders           About MalaCards

    SHROOM1 for disorders           About GeneDecksing

    OMIM gene information: 611179    OMIM disorders: --


    Export disorders for SHROOM1 gene to outside databases

    Publications
    for SHROOM1 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SHROOM1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SHROOM1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. A new standard nomenclature for proteins related to Apx and Shroom. (PubMed id 16615870)1, 2, 3 Hagens O....Wallingford J.B. (2006)
    2. Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins. (PubMed id 11853319)1, 2, 3 Nagase T.... Ohara O. (2001)
    3. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    4. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    5. Differential actin-dependent localization modulates the evolutionarily conserved activity of Shroom family proteins. (PubMed id 16684770)1 Dietz M.L.... Hildebrand J.D. (2006)
    6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    7. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    9. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

    External Searches for SHROOM1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing SHROOM1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 134549 HGNC: 24084 AceView: APXL2 Ensembl:ENSG00000164403 euGenes: HUgn134549
    ECgene: SHROOM1 H-InvDB: SHROOM1

    Other Databases showing SHROOM1 gene

    (According to HUGE)
    About This Section
    HUGE: KIAA1960

    Specialized Databases showing SHROOM1 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SHROOM1 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for SHROOM1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for SHROOM1 gene:
    Search GeneIP for patents involving SHROOM1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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