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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
  • Vel Blood Group Antigen 3 4
  • Vel 3

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 Blood Group Incompatibility.

UniProtKB/Swiss-Prot for SMIM1 Gene

  • Regulator of red blood cell formation.

Additional gene information for SMIM1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMIM1 Gene

Genomics for SMIM1 Gene

GeneHancer (GH) Regulatory Elements for SMIM1 Gene

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
GH01I003771 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 581.7 +1.5 1494 5.2 HDGF SMAD1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 SMIM1 CEP104 C1orf174 WRAP73 ENSG00000272153 TP73-AS1 LRRC47 GC01P003777 CCDC27
GH01I003795 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 18.4 +23.5 23545 2.4 PKNOX1 ARNT MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B LRRC47 PIR46973 C1orf174 CEP104 SMIM1 WRAP73 ENSG00000272153
GH01I003856 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 15.7 +84.5 84530 2.2 HDGF SMAD1 ARID4B SIN3A YBX1 DMAP1 ZNF2 YY1 POLR2B ZNF207 CEP104 DFFB C1orf174 WRAP73 SMIM1 ENSG00000272153
GH01I003787 Enhancer 0.7 ENCODE 21.7 +15.1 15060 1.4 PKNOX1 BACH1 EBF1 BATF IRF4 NFATC1 ATF7 ETV6 BCLAF1 IKZF2 SMIM1 CEP104 ENSG00000272153 LRRC47 PIR46973
GH01I003792 Enhancer 0.8 ENCODE 18.5 +20.9 20854 1.8 HDAC1 ATF1 SIN3A ZBTB40 TCF12 POLR3A FOS CEBPB ATF4 KLF16 SMIM1 CEP104 LRRC47 PIR46973 ENSG00000272153
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SMIM1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SMIM1 Gene

Genomic Locations for SMIM1 Gene
chr1:3,772,761-3,775,982
(GRCh38/hg38)
Size:
3,222 bases
Orientation:
Plus strand
chr1:3,689,352-3,692,546
(GRCh37/hg19)

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 StructureGene Density

RefSeq DNA sequence for SMIM1 Gene

Proteins for SMIM1 Gene

  • 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

Post-translational modifications for SMIM1 Gene

No Post-translational modifications

Other Protein References for SMIM1 Gene

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

Molecular function for SMIM1 Gene

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

Phenotypes From GWAS Catalog for SMIM1 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , 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
extracellular 5
plasma membrane 3

Gene Ontology (GO) - Cellular Components for SMIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome HDA,IDA 23376485
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

SuperPathways for SMIM1 Gene

No Data Available

Interacting Proteins for SMIM1 Gene

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

No Compound Related Data Available

Transcripts for SMIM1 Gene

Unigene Clusters for SMIM1 Gene

Small integral membrane protein 1:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for SMIM1 Gene

GeneLoc Exon Structure for
SMIM1
ECgene alternative splicing isoforms for
SMIM1

Expression for SMIM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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



NURSA nuclear receptor signaling pathways regulating expression of SMIM1 Gene:

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(4.1)
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 33
  • 98.72 (n)
rat
(Rattus norvegicus)
Mammalia Smim1 33
  • 82.91 (n)
mouse
(Mus musculus)
Mammalia Smim1 33 16 34
  • 82.48 (n)
dog
(Canis familiaris)
Mammalia SMIM1 33 34
  • 81.2 (n)
cow
(Bos Taurus)
Mammalia SMIM1 33 34
  • 79.91 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia smim1 33
  • 66.23 (n)
Species where no ortholog for SMIM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

Paralogs for SMIM1 Gene

No data available for Paralogs for SMIM1 Gene

Variants for SMIM1 Gene

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 from dbSNP and Humsavar for SMIM1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000308514 -- 3,772,261(+) C/T upstream_transcript_variant
rs1001074497 -- 3,771,965(+) C/A upstream_transcript_variant
rs1001232288 -- 3,773,192(+) G/A intron_variant
rs1001263621 -- 3,773,512(+) C/T intron_variant
rs1002088396 -- 3,770,981(+) A/G upstream_transcript_variant

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

Disorders for SMIM1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SMIM1 Gene - From: HGMD, OMIM, and DISEASES

Disorder Aliases PubMed IDs
blood group, vel system
  • vel
blood group incompatibility
- 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

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. Disruption of SMIM1 causes the Vel- blood type. (PMID: 23505126) Ballif BA … Arnaud L (EMBO molecular medicine 2013) 2 3 4 58
  2. 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 58
  3. SMIM1 underlies the Vel blood group and influences red blood cell traits. (PMID: 23563608) Cvejic A … Albers CA (Nature genetics 2013) 2 3 4 58
  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 58
  5. The c.64_80del SMIM1 allele is segregating in the Hutterite population. (PMID: 26666208) Coghlan G … Zelinski T (Transfusion 2016) 3 58

Products for SMIM1 Gene

Sources for SMIM1 Gene

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