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SHROOM2 shroom family member 2 [ Homo sapiens (human) ]

Gene ID: 357, updated on 11-Sep-2019

Summary

Official Symbol
SHROOM2provided by HGNC
Official Full Name
shroom family member 2provided by HGNC
Primary source
HGNC:HGNC:630
See related
Ensembl:ENSG00000146950 MIM:300103
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
APXL; HSAPXL
Summary
This gene represents the human homolog of Xenopus laevis apical protein (APX) gene, which is implicated in amiloride-sensitive sodium channel activity. It is expressed in endothelial cells and facilitates the formation of a contractile network within endothelial cells. Depletion of this gene results in an increase in endothelial sprouting, migration, and angiogenesis. This gene is highly expressed in the retina, and is a strong candidate for ocular albinism type 1 syndrome. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2016]
Expression
Broad expression in ovary (RPKM 2.6), placenta (RPKM 2.6) and 21 other tissues See more
Orthologs

Genomic context

See SHROOM2 in Genome Data Viewer
Location:
Xp22.2
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (9786406..9949443)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (9754496..9917585)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene transducin beta like 1 X-linked Neighboring gene uncharacterized LOC105373126 Neighboring gene G protein-coupled receptor 143 Neighboring gene uncharacterized LOC107985658 Neighboring gene eukaryotic translation initiation factor 5 pseudogene 1 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 33 Neighboring gene claudin 34 Neighboring gene WWC family member 3

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

Phenotypes

NHGRI GWAS Catalog

Description
Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk.
NHGRI GWA Catalog
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ39277, DKFZp781J074

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
actin filament binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
actin filament binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
beta-catenin binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
ligand-gated sodium channel activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NOT actin filament bundle assembly ISS
Inferred from Sequence or Structural Similarity
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
 
brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
camera-type eye development ISS
Inferred from Sequence or Structural Similarity
more info
 
camera-type eye morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
NOT cell morphogenesis IDA
Inferred from Direct Assay
more info
PubMed 
NOT cell morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cellular pigment accumulation ISS
Inferred from Sequence or Structural Similarity
more info
 
ear development ISS
Inferred from Sequence or Structural Similarity
more info
 
establishment of melanosome localization ISS
Inferred from Sequence or Structural Similarity
more info
 
eye pigment granule organization ISS
Inferred from Sequence or Structural Similarity
more info
 
lens morphogenesis in camera-type eye ISS
Inferred from Sequence or Structural Similarity
more info
 
melanosome organization ISS
Inferred from Sequence or Structural Similarity
more info
 
sodium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apical junction complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
bicellular tight junction ISS
Inferred from Sequence or Structural Similarity
more info
 
cell-cell adherens junction ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cortical actin cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with cortical actin cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with cortical actin cytoskeleton ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cytoskeleton ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular exosome HDA PubMed 
microtubule IEA
Inferred from Electronic Annotation
more info
 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
protein Shroom2
Names
APX homolog of Xenopus
apical-like 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_012493.2 RefSeqGene

    Range
    4974..167988
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001320663.2NP_001307592.1  protein Shroom2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate promoter and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AK299907, BC140866, BM678914, X83543
    UniProtKB/Swiss-Prot
    Q13796
    UniProtKB/TrEMBL
    B7Z682
    Conserved Domains (1) summary
    pfam08687
    Location:153444
    ASD2; Apx/Shroom domain ASD2
  2. NM_001320664.1NP_001307593.1  protein Shroom2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate promoter, has an alternate in-frame acceptor splice site at the penultimate exon, and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (3) has a shorter N-terminus and lacks an internal amino acid compared to isoform 1.
    Source sequence(s)
    AK299907, BC140866, BM678914, CR749271, X83543
    Consensus CDS
    CCDS83453.1
    UniProtKB/Swiss-Prot
    Q13796
    UniProtKB/TrEMBL
    B7Z682, F5H3B6, Q68DU3
    Related
    ENSP00000415229.3, ENST00000418909.6
    Conserved Domains (1) summary
    pfam08687
    Location:153443
    ASD2; Apx/Shroom domain ASD2
  3. NM_001649.4NP_001640.1  protein Shroom2 isoform 1

    See identical proteins and their annotated locations for NP_001640.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC090481, BC140866, BM678914, X83543
    Consensus CDS
    CCDS14135.1
    UniProtKB/Swiss-Prot
    Q13796
    Related
    ENSP00000370299.3, ENST00000380913.8
    Conserved Domains (3) summary
    cd00992
    Location:25105
    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:13181609
    ASD2; Apx/Shroom domain ASD2
    pfam08688
    Location:640802
    ASD1; Apx/Shroom domain ASD1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    9786406..9949443
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005274500.4XP_005274557.2  protein Shroom2 isoform X1

    Conserved Domains (3) summary
    cd00992
    Location:25105
    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:13181608
    ASD2; Apx/Shroom domain ASD2
    pfam08688
    Location:640802
    ASD1; Apx/Shroom domain ASD1
  2. XM_011545506.1XP_011543808.1  protein Shroom2 isoform X2

    Conserved Domains (1) summary
    pfam08687
    Location:153444
    ASD2; Apx/Shroom domain ASD2
  3. XM_017029492.1XP_016884981.1  protein Shroom2 isoform X3

    UniProtKB/TrEMBL
    F5H3B6
    Conserved Domains (1) summary
    pfam08687
    Location:153443
    ASD2; Apx/Shroom domain ASD2
  4. XM_017029493.2XP_016884982.1  protein Shroom2 isoform X2

    Related
    ENSP00000406724.1, ENST00000452575.1
    Conserved Domains (1) summary
    pfam08687
    Location:153444
    ASD2; Apx/Shroom domain ASD2
  5. XM_017029494.2XP_016884983.1  protein Shroom2 isoform X3

    UniProtKB/TrEMBL
    F5H3B6
    Conserved Domains (1) summary
    pfam08687
    Location:153443
    ASD2; Apx/Shroom domain ASD2
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