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SHROOM3 shroom family member 3 [ Homo sapiens (human) ]

Gene ID: 57619, updated on 20-Dec-2019

Summary

Official Symbol
SHROOM3provided by HGNC
Official Full Name
shroom family member 3provided by HGNC
Primary source
HGNC:HGNC:30422
See related
Ensembl:ENSG00000138771 MIM:604570
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SHRM; APXL3; ShrmL; MSTP013
Summary
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]
Expression
Broad expression in colon (RPKM 6.8), gall bladder (RPKM 5.4) and 20 other tissues See more
Orthologs

Genomic context

See SHROOM3 in Genome Data Viewer
Location:
4q21.1
Exon count:
11
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (76435229..76783253)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (77356253..77704406)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 158 Neighboring gene RNA, U6 small nuclear 1000, pseudogene Neighboring gene ribosomal protein L36a pseudogene 18 Neighboring gene RNA, U6 small nuclear 145, pseudogene Neighboring gene microRNA 548ah Neighboring gene microRNA 4450 Neighboring gene uncharacterized LOC105377290 Neighboring gene SUMO2 pseudogene 11 Neighboring gene uncharacterized LOC105377289 Neighboring gene Sharpr-MPRA regulatory region 8749 Neighboring gene microtubule affinity regulating kinase 2 pseudogene Neighboring gene ribosomal protein L26 pseudogene 17 Neighboring gene sosondowah ankyrin repeat domain family member B

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Common variants at 5q22 associate with pediatric eosinophilic esophagitis.
NHGRI GWA Catalog
Genetic loci influencing kidney function and chronic kidney disease.
NHGRI GWA Catalog
Genome-wide association studies of serum magnesium, potassium, and sodium concentrations identify six Loci influencing serum magnesium levels.
NHGRI GWA Catalog
Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.
NHGRI GWA Catalog
Multiple loci associated with indices of renal function and chronic kidney disease.
NHGRI GWA Catalog
New loci associated with kidney function and chronic kidney disease.
NHGRI GWA Catalog
Using multiple measures for quantitative trait association analyses: application to estimated glomerular filtration rate.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1481, AC107072.2

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin filament binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
actin filament organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apical protein localization ISS
Inferred from Sequence or Structural Similarity
more info
 
cell morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular pigment accumulation ISS
Inferred from Sequence or Structural Similarity
more info
 
epithelial cell development IEA
Inferred from Electronic Annotation
more info
 
neural tube closure IEA
Inferred from Electronic Annotation
more info
 
pattern specification process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell shape IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
adherens junction ISS
Inferred from Sequence or Structural Similarity
more info
 
apical junction complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apical junction complex ISS
Inferred from Sequence or Structural Similarity
more info
 
apical plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apical plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
cortical actin cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoskeleton ISS
Inferred from Sequence or Structural Similarity
more info
 
microtubule IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
protein Shroom3
Names
F-actin-binding protein
shroom-related protein

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_028077.1 RefSeqGene

    Range
    5130..353154
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_020859.4NP_065910.3  protein Shroom3

    See identical proteins and their annotated locations for NP_065910.3

    Status: REVIEWED

    Source sequence(s)
    AB055660, AC107072, AK127929, AK128677, AW025141
    Consensus CDS
    CCDS3579.2
    UniProtKB/Swiss-Prot
    Q8TF72
    UniProtKB/TrEMBL
    B3KY47
    Related
    ENSP00000296043.6, ENST00000296043.7
    Conserved Domains (3) summary
    cd00992
    Location:33107
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam08687
    Location:16711955
    ASD2; Apx/Shroom domain ASD2
    pfam08688
    Location:8841062
    ASD1; Apx/Shroom domain ASD1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    76435229..76783253
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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