SMIM1 Gene (Protein Coding)

Small Integral Membrane Protein 1 (Vel Blood Group)

GC01P003772
GIFtS:
28
This gene encodes a small, conserved protein that participates in red blood cell formation. The encoded protein is localized to the cell membrane and is the antigen for the Vel blood group. Alternative splicing results in different transcript variants that encode the same protein. [provided by RefSeq, Dec 2013] See more...

Aliases for SMIM1 Gene

Aliases for SMIM1 Gene

  • Small Integral Membrane Protein 1 (Vel Blood Group) 2 3 5
  • Small Integral Membrane Protein 1 2 3 4
  • Vel Blood Group Antigen 3 4
  • Vel 2 3
  • SMIM1 5

External Ids for SMIM1 Gene

Previous GeneCards Identifiers for SMIM1 Gene

  • GC01P003691

Summaries for SMIM1 Gene

Entrez Gene Summary for SMIM1 Gene

  • This gene encodes a small, conserved protein that participates in red blood cell formation. The encoded protein is localized to the cell membrane and is the antigen for the Vel blood group. Alternative splicing results in different transcript variants that encode the same protein. [provided by RefSeq, Dec 2013]

GeneCards Summary for SMIM1 Gene

SMIM1 (Small Integral Membrane Protein 1 (Vel Blood Group)) is a Protein Coding gene. Diseases associated with SMIM1 include Blood Group, Vel System and Slate Pneumoconiosis.

UniProtKB/Swiss-Prot Summary for SMIM1 Gene

Additional gene information for SMIM1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMIM1 Gene

Genomics for SMIM1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SMIM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J003771 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 631.6 +1.6 1583 5.3 HNRNPL GATAD2A CTCF ZBTB33 TFE3 LEF1 IKZF1 NFKBIZ KDM1A ZNF692 SMIM1 MN308894 CEP104 C1orf174 WRAP73 ENSG00000272153 TP73-AS1 LRRC47 CCDC27
GH01J003116 Promoter/Enhancer 0.8 EPDnew CraniofacialAtlas dbSUPER 600 -656.0 -656018 0.8 BCL11A SMIM1 MIR4251 PRDM16 PRDM16-DT ARHGEF16
GH01J003792 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 18.5 +22.5 22503 4.9 CREB1 GATAD2A HNRNPL PRDM10 ZNF629 TFE3 ZNF512 RFX1 SIX5 LEF1 LRRC47 piR-52974 CEP104 C1orf174 SMIM1 WRAP73 ENSG00000272153 piR-57460-002
GH01J003856 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 15.7 +84.5 84546 3.2 HNRNPL CREB1 GATAD2A ZBTB33 PRDM10 RFX1 SIX5 IKZF1 CTCF BACH1 CEP104 DFFB C1orf174 WRAP73 SMIM1 ENSG00000272153 lnc-LRRC47-3 LRRC47
GH01J003787 Enhancer 0.9 Ensembl ENCODE 21.7 +15.3 15311 1.7 BACH1 IKZF2 PKNOX1 EED DPF2 RUNX3 BCLAF1 CBFB TCF12 BCL11A CEP104 SMIM1 LRRC47 ENSG00000272153 piR-57460-002
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMIM1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMIM1

Genomic Locations for SMIM1 Gene

Genomic Locations for SMIM1 Gene
chr1:3,772,655-3,775,982
(GRCh38/hg38)
Size:
3,328 bases
Orientation:
Plus strand
chr1:3,689,352-3,692,546
(GRCh37/hg19)
Size:
3,195 bases
Orientation:
Plus strand

Genomic View for SMIM1 Gene

Genes around SMIM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMIM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMIM1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SMIM1 Gene

Proteins for SMIM1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for SMIM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    B2RUZ4-SMIM1_HUMAN
    Recommended name:
    Small integral membrane protein 1
    Protein Accession:
    B2RUZ4

    Protein attributes for SMIM1 Gene

    Size:
    78 amino acids
    Molecular mass:
    8749 Da
    Quaternary structure:
    • Homooligomer; disulfide-linked.

neXtProt entry for SMIM1 Gene

Protein Expression for SMIM1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SMIM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMIM1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SMIM1 Gene

Domains & Families for SMIM1 Gene

Gene Families for SMIM1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Blood group antigen proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SMIM1 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

B2RUZ4

UniProtKB/Swiss-Prot:

SMIM1_HUMAN :
  • The extracellular domain carries the Vel antigen.
  • Belongs to the SMIM1 family.
Domain:
  • The extracellular domain carries the Vel antigen.
Family:
  • Belongs to the SMIM1 family.
genes like me logo Genes that share domains with SMIM1: view

No data available for Suggested Antigen Peptide Sequences for SMIM1 Gene

Function for SMIM1 Gene

Products:

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  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for SMIM1 Gene

UniProtKB/Swiss-Prot Function:
Regulator of red blood cell formation.

Phenotypes From GWAS Catalog for SMIM1 Gene

Gene Ontology (GO) - Molecular Function for SMIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042803 protein homodimerization activity IDA 23563606
genes like me logo Genes that share ontologies with SMIM1: view

Phenotypes for SMIM1 Gene

MGI mutant phenotypes for SMIM1:
inferred from 1 alleles
genes like me logo Genes that share phenotypes with SMIM1: view

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMIM1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SMIM1 Gene

Localization for SMIM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMIM1 Gene

Cell membrane. Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMIM1 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 2
nucleus 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for SMIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IMP 26452714
GO:0009986 cell surface IMP 23563606
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SMIM1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SMIM1 Gene

Pathways & Interactions for SMIM1 Gene

PathCards logo

SuperPathways for SMIM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SMIM1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SMIM1 Gene

Drugs & Compounds for SMIM1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SMIM1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SMIM1 Gene

4 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMIM1

Alternative Splicing Database (ASD) splice patterns (SP) for SMIM1 Gene

No ASD Table

Relevant External Links for SMIM1 Gene

GeneLoc Exon Structure for
SMIM1

Expression for SMIM1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMIM1 Gene

mRNA expression in normal human tissues for SMIM1 Gene
mRNA expression by BioGPS for SMIM1 GenemRNA expression by GTEx for SMIM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMIM1 Gene

This gene is overexpressed in Whole Blood (x12.8), Testis (x6.0), and Heart - Atrial Appendage (x5.6).

Protein differential expression in normal tissues from HIPED for SMIM1 Gene

This gene is overexpressed in Ovary (17.8), Peripheral blood mononuclear cells (9.2), and Fetal Liver (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMIM1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMIM1

SOURCE GeneReport for Unigene cluster for SMIM1 Gene:

Hs.22047

mRNA Expression by UniProt/SwissProt for SMIM1 Gene:

B2RUZ4-SMIM1_HUMAN
Tissue specificity: Highly expressed in the bone marrow and expressed at lower levels in non-hematopoietic tissues. Highly expressed in erythroleukemia cell lines. Up-regulated in CD34+ hematopoietic progenitors cultured toward red blood cells.

Evidence on tissue expression from TISSUES for SMIM1 Gene

  • Liver(4.3)
  • Heart(2.2)
  • Blood(2.1)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with SMIM1: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMIM1 Gene

Orthologs for SMIM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SMIM1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SMIM1 30
  • 98.72 (n)
Rat
(Rattus norvegicus)
 Mammalia Smim1 30
  • 82.91 (n)
Mouse
(Mus musculus)
 Mammalia Smim1 30 17 31
  • 82.48 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia SMIM1 30 31
  • 81.2 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia SMIM1 30 31
  • 79.91 (n)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia smim1 30
  • 66.23 (n)
Species where no ortholog for SMIM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for SMIM1 Gene

ENSEMBL:
Gene Tree for SMIM1 (if available)
TreeFam:
Gene Tree for SMIM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMIM1: view image

Paralogs for SMIM1 Gene

No data available for Paralogs for SMIM1 Gene

Variants for SMIM1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Polymorphic Variants from UniProtKB/Swiss-Prot for SMIM1 Gene

SMIM1_HUMAN-B2RUZ4
SMIM1 is responsible for the Vel blood group system (VEL) [MIM:615264]. The Vel antigen is present on red blood cells from all people except rare Vel-negative individuals who can form antibodies to Vel in response to transfusion or pregnancy. These antibodies may cause severe hemolytic reactions in blood recipients. In most cases, Vel-negative individuals are homozygous for a 17 nucleotide frameshift deletion in exon 3. In some cases, Vel-negative are heterozygous for the 17 nucleotide frameshift deletion and a missense variant at position 51.

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMIM1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
50826 Affects: Vel blood group system 3,775,433(+) AGTCAGCCTAGGGGCT FRAMESHIFT_VARIANT
rs1182690110 - p.Met51Lys
VAR_069361 - p.Met51Arg

Additional dbSNP identifiers (rs#s) for SMIM1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SMIM1 Gene

Variant ID Type Subtype PubMed ID
dgv13n100 CNV gain 25217958
esv3585042 CNV gain 21293372
nsv1012423 CNV gain 25217958
nsv830314 CNV gain+loss 17160897
nsv830425 CNV gain 17160897
nsv951959 CNV deletion 24416366

Variation tolerance for SMIM1 Gene

Gene Damage Index Score: 0.06; 1.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMIM1 Gene

Human Gene Mutation Database (HGMD)
SMIM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMIM1

SNP Genotyping and Copy Number Assay Products

Disorders for SMIM1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SMIM1 Gene - From: OMIM and DISEASES

Disorder Aliases PubMed IDs
blood group, vel system
  • vel
slate pneumoconiosis
  • schistosis
schwartz-jampel syndrome, type 1
  • kniest-like dysplasia with pursed lips and ectopia lentis
dieulafoy lesion
  • dieulafoy lesion of intestine
tinea nigra
  • infection by cladosporium werneckii
- elite association - COSMIC cancer census association via MalaCards
Search SMIM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SMIM1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SMIM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SMIM1 Gene

Publications for SMIM1 Gene

  1. Homozygosity for a null allele of SMIM1 defines the Vel-negative blood group phenotype. (PMID: 23563606) Storry JR … Olsson ML (Nature genetics 2013) 2 3 4
  2. SMIM1 underlies the Vel blood group and influences red blood cell traits. (PMID: 23563608) Cvejic A … Albers CA (Nature genetics 2013) 2 3 4
  3. Disruption of SMIM1 causes the Vel- blood type. (PMID: 23505126) Ballif BA … Arnaud L (EMBO molecular medicine 2013) 2 3 4
  4. SMIM1 is a type II transmembrane phosphoprotein and displays the Vel blood group antigen at its carboxyl-terminus. (PMID: 26452714) Arnaud L … Ballif BA (FEBS letters 2015) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

ExternalLinks

View latest publications for SMIM1 gene in Mastermind

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