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    SHROOM1 shroom family member 1 [ Homo sapiens (human) ]

    Gene ID: 134549, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SHROOM1provided by HGNC
    Official Full Name
    shroom family member 1provided by HGNC
    Primary source
    HGNC:HGNC:24084
    See related
    Ensembl:ENSG00000164403 MIM:611179; AllianceGenome:HGNC:24084
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    APXL2
    Summary
    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]
    Expression
    Broad expression in prostate (RPKM 16.8), urinary bladder (RPKM 6.1) and 15 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    5q31.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132822141..132830647, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (133341872..133351357, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (132157833..132166339, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23096 Neighboring gene cyclin I family member 2 Neighboring gene septin 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16337 Neighboring gene Sharpr-MPRA regulatory region 2681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:132150138-132150638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:132150639-132151139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16339 Neighboring gene sosondowah ankyrin repeat domain family member A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16341 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16343 Neighboring gene U7 small nuclear RNA Neighboring gene RNA, U7 small nuclear 15 pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 192

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Suppression of SHROOM1 Improves In Vitro and In Vivo Gene Integration by Promoting Homology-Directed Repair. Zhao Z, et al. Int J Mol Sci, 2020 Aug 13. PMID 32823670, Free PMC Article
    2. Structure of the Shroom-Rho Kinase Complex Reveals a Binding Interface with Monomeric Shroom That Regulates Cell Morphology and Stimulates Kinase Activity. Zalewski JK, et al. J Biol Chem, 2016 Dec 2. PMID 27758857, Free PMC Article
    3. Identification of differentially methylated regions in new genes associated with knee osteoarthritis. Bonin CA, et al. Gene, 2016 Jan 15. PMID 26484395, Free PMC Article
    4. hShroom1 links a membrane bound protein to the actin cytoskeleton. Dye DE, et al. Cell Mol Life Sci, 2009 Feb. PMID 19137261
    5. A new standard nomenclature for proteins related to Apx and Shroom. Hagens O, et al. BMC Cell Biol, 2006 Apr 14. PMID 16615870, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Suppression of SHROOM1 Improves In Vitro and In Vivo Gene Integration by Promoting Homology-Directed Repair.
      Title: Suppression of SHROOM1 Improves In Vitro and In Vivo Gene Integration by Promoting Homology-Directed Repair.
    2. These data provide molecular insight into the Shroom-Rock interface and demonstrate that Shroom directly participates in regulating cytoskeletal dynamics, adding to its known role in Rock localization.
      Title: Structure of the Shroom-Rho Kinase Complex Reveals a Binding Interface with Monomeric Shroom That Regulates Cell Morphology and Stimulates Kinase Activity.
    3. FOXP4 and SHROOM1 genes are hypermethylated in the knee osteoarthritic cartilage.
      Title: Identification of differentially methylated regions in new genes associated with knee osteoarthritis.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1960

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables actin filament binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables myosin II binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in actin filament bundle assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in actin filament bundle assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in apical junction complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cortical actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein Shroom1
    Names
    apical protein 2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001172700.2 → NP_001166171.1  protein Shroom1 isoform 1

      See identical proteins and their annotated locations for NP_001166171.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB075840, EB387851
      Consensus CDS
      CCDS54902.1
      UniProtKB/Swiss-Prot
      B7WP40, B7ZL01, Q2M3G4, Q8TDP0, Q8TF41
      Related
      ENSP00000367950.3, ENST00000378679.8
      Conserved Domains (2) summary
      pfam08687
      Location:544 → 823
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:140 → 233
      ASD1; Apx/Shroom domain ASD1

    2. NM_001410779.1 → NP_001397708.1  protein Shroom1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC004500, AC004775
      Consensus CDS
      CCDS93780.1
      UniProtKB/TrEMBL
      A6NN40
      Related
      ENSP00000367947.1, ENST00000378676.1

    3. NM_133456.3 → NP_597713.2  protein Shroom1 isoform 2

      See identical proteins and their annotated locations for NP_597713.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, uses a downstream start codon, and uses an alternate in-frame splice site, compared to variant 1. The resulting isoform (2) has a shorter N-terminus and lacks a 5-aa segment near the C-terminus, compared to isoform 1.
      Source sequence(s)
      AF314142, BC104916, EB387851
      Consensus CDS
      CCDS4161.1
      UniProtKB/Swiss-Prot
      Q2M3G4
      Related
      ENSP00000324245.3, ENST00000319854.7
      Conserved Domains (2) summary
      pfam08687
      Location:544 → 818
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:140 → 233
      ASD1; Apx/Shroom domain ASD1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      132822141..132830647 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416730.1 → XP_047272686.1  protein Shroom1 isoform X1

      UniProtKB/Swiss-Prot
      B7WP40, B7ZL01, Q2M3G4, Q8TDP0, Q8TF41

    2. XM_047416733.1 → XP_047272689.1  protein Shroom1 isoform X2

      UniProtKB/TrEMBL
      A6NN40

    3. XM_047416731.1 → XP_047272687.1  protein Shroom1 isoform X1

      UniProtKB/Swiss-Prot
      B7WP40, B7ZL01, Q2M3G4, Q8TDP0, Q8TF41

    4. XM_005271885.5 → XP_005271942.1  protein Shroom1 isoform X1

      See identical proteins and their annotated locations for XP_005271942.1

      UniProtKB/Swiss-Prot
      B7WP40, B7ZL01, Q2M3G4, Q8TDP0, Q8TF41
      Conserved Domains (2) summary
      pfam08687
      Location:544 → 823
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:140 → 233
      ASD1; Apx/Shroom domain ASD1

    5. XM_047416732.1 → XP_047272688.1  protein Shroom1 isoform X1

      UniProtKB/Swiss-Prot
      B7WP40, B7ZL01, Q2M3G4, Q8TDP0, Q8TF41

    6. XM_005271886.4 → XP_005271943.1  protein Shroom1 isoform X1

      See identical proteins and their annotated locations for XP_005271943.1

      UniProtKB/Swiss-Prot
      B7WP40, B7ZL01, Q2M3G4, Q8TDP0, Q8TF41
      Conserved Domains (2) summary
      pfam08687
      Location:544 → 823
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:140 → 233
      ASD1; Apx/Shroom domain ASD1

    7. XM_047416735.1 → XP_047272691.1  protein Shroom1 isoform X4

    8. XM_006714534.3 → XP_006714597.1  protein Shroom1 isoform X3

      Conserved Domains (1) summary
      pfam08688
      Location:140 → 233
      ASD1; Apx/Shroom domain ASD1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      133341872..133351357 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351648.1 → XP_054207623.1  protein Shroom1 isoform X2

      UniProtKB/TrEMBL
      A6NN40

    2. XM_054351647.1 → XP_054207622.1  protein Shroom1 isoform X1

      UniProtKB/Swiss-Prot
      B7WP40, B7ZL01, Q2M3G4, Q8TDP0, Q8TF41

    3. XM_054351646.1 → XP_054207621.1  protein Shroom1 isoform X1

      UniProtKB/Swiss-Prot
      B7WP40, B7ZL01, Q2M3G4, Q8TDP0, Q8TF41

    4. XM_054351645.1 → XP_054207620.1  protein Shroom1 isoform X1

      UniProtKB/Swiss-Prot
      B7WP40, B7ZL01, Q2M3G4, Q8TDP0, Q8TF41

    5. XM_054351650.1 → XP_054207625.1  protein Shroom1 isoform X4

    6. XM_054351649.1 → XP_054207624.1  protein Shroom1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2M3G4.1 GenPept UniProtKB/Swiss-Prot:Q2M3G4

    Gene LinkOut

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