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SHROOM1 Gene

protein-coding   GIFtS: 48
GCID: GC05M132157

Shroom Family Member 1

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Shroom Family Member 11 2
APXL22 3 5
Apical Protein 22 3
KIAA19603 5
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


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SHROOM1 Gene:
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)

GeneCards Summary for SHROOM1 Gene:
SHROOM1 (shroom family member 1) is a protein-coding gene. GO annotations related to this gene include actin filament binding. An important paralog of this gene is SHROOM3.

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




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000005.9  NT_034772.7  NC_018916.2  
Regulatory elements:
   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 plasmidSHROOM1 promoter sequence
   Search Chromatin IP Primers for SHROOM1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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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)
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

Explore proteomics data for SHROOM1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SHROOM1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

    ENSEMBL proteins: 
     ENSP00000367950   ENSP00000324245   ENSP00000367947   ENSP00000388049  

    SHROOM1 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for SHROOM1

     
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    antibodies-online peptides for SHROOM1

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    antibodies-online antibodies for SHROOM1 (9 products) 

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    antibodies-online kits for SHROOM1 (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR014800 ASD1
     IPR027685 Shroom_fam
     IPR014799 ASD2

    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


    Find genes that share domains with SHROOM1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

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

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0051015actin filament binding ISS16684770
         
    Find genes that share ontologies with SHROOM1           About GenesLikeMe


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

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SHROOM1
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    miRNA
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    Selected qRT-PCR 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 plasmidSHROOM1 3' UTR sequence
    Inhib. RNA
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    Browse Sino Biological Human cDNA Clones
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SHRM1_HUMAN, Q2M3G4: Cytoplasm, cytoskeleton (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton3
    nucleus3
    cytosol2

    Gene Ontology (GO): 3 cellular component terms:    About this table

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

    Find genes that share ontologies with SHROOM1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SHROOM1
    Interactions:

        Search GeneGlobe Interaction Network for SHROOM1

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

    Selected 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:    About this table

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

    Find genes that share ontologies with SHROOM1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SHROOM1 (SHRM1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    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
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000378679(uc003kxy.2 uc003kxx.3) ENST00000319854 ENST00000378676
    ENST00000488072 ENST00000495680 ENST00000606676 ENST00000440118
    miRNA
    Products:
         
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    Selected qRT-PCR 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 plasmidSHROOM1 3' UTR sequence
    Inhib. RNA
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    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SHROOM1
      QuantiTect SYBR Green Assays in human, mouse, rat SHROOM1
      QuantiFast Probe-based Assays in human, mouse, rat SHROOM1

    Additional mRNA 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 

    Selected AceView cDNA sequences (see all 52):

    NM_133456 AI309907 BQ221784 AI277049 AF314142 BQ437705 AB075840 AI348038 
    AW846931 AL138455 CB216252 BE889777 AA326450 BG983381 BX358281 AI799642 
    BQ448015 BF476431 BC040980 BQ718274 BM354088 BM507227 BF446355 BQ549586 

    GeneLoc Exon Structure


    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SHROOM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGGCCTCACC
    SHROOM1 Expression
    About this image


    SHROOM1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Heart (Cardiovascular System)    fully expand to see all 2 entries
             Atrioventricular Canal Cells Atrioventricular Canal
    SHROOM1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SHROOM1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.519574
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    In Situ
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    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for SHROOM1 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Shroom11 , 5 shroom family member 11, 5 73.45(n)1
    62.71(a)1
      11 (31.95 cM)5
    717741  NM_027917.21  NP_082193.21 
     534572055 
    chicken
    (Gallus gallus)
    Aves --
    --
    Uncharacterized protein
    16(a)
    14(a)
    many → 1
    many → 1
    13(16362007-16369506)
    AADN03010540.1(5182-24316)
    lizard
    (Anolis carolinensis)
    Reptilia SHROOM16
    shroom family member 1
    42(a)
    1 ↔ 1
    2(127406156-127410645)
    zebrafish
    (Danio rerio)
    Actinopterygii shroom16
    shroom family member 1
    12(a)
    1 ↔ 1
    21(41659350-41716266) ENSDARG00000094181
    fruit fly
    (Drosophila melanogaster)
    Insecta Shroom6
    Shroom
    9(a)
    1 → many
    2R(10195667-10239312)


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

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

    Find genes that share paralogs with SHROOM1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SHROOM1 (see all 273)    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
         Database of Genomic Variants (DGV) 4 variations for SHROOM1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1003435CNV Deletion20482838
    nsv882920CNV Loss21882294
    nsv830489CNV Loss17160897
    nsv882919CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SHROOM1
    DNA2.0 Custom Variant and Variant Library Synthesis for SHROOM1

    (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.)
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    OMIM gene information: 611179    OMIM disorders: --


    Find genes that share disorders with SHROOM1           About GenesLikeMe


    Export disorders for SHROOM1 gene to outside databases

    (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)
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    PubMed articles for SHROOM1 gene integrated from 10 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. (BMC Cell Biol. 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. (DNA Res. 2001)
    3. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    4. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    5. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 2008)
    6. Differential actin-dependent localization modulates the evolutionarily conserved activity of Shroom family proteins. (PubMed id 16684770)1 Dietz M.L.... Hildebrand J.D. (J. Biol. Chem. 2006)
    7. 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. (Genome Res. 2004)
    8. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (Nature 2004)
    9. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    10. (PubMed id )2 

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 134549 HGNC: 24084 AceView: APXL2 Ensembl:ENSG00000164403 euGenes: HUgn134549
    ECgene: SHROOM1 H-InvDB: SHROOM1

    (According to HUGE)
    About This Section

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    HUGE: KIAA1960

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

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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