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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
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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

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