The product of this gene has been localized within the split hand/split foot malformation locus SHFM1 at chromosome 7. It has been proposed to be a candidate gene for the autosomal dominant form of the heterogeneous limb developmental disorder split hand/split foot malformation type 1. In addition, it has been shown to directly interact with BRCA2. It also may play a role in th... See more...

Aliases for SEM1 Gene

Aliases for SEM1 Gene

  • SEM1 26S Proteasome Complex Subunit 2 3 5
  • DSS1 2 3 4
  • Split Hand/Foot Malformation (Ectrodactyly) Type 1 2 3
  • Split Hand/Foot Malformation Type 1 Protein 3 4
  • Deleted In Split Hand/Split Foot Protein 1 3 4
  • 26S Proteasome Complex Subunit SEM1 3 4
  • 26S Proteasome Complex Subunit DSS1 3 4
  • Split Hand/Foot Deleted Protein 1 3 4
  • C7orf76 3 4
  • Shfdg1 2 3
  • SHFM1 3 4
  • SHSF1 2 3
  • ECD 2 3
  • SEM1, 26S Proteasome Complex Subunit 2
  • Chromosome 7 Open Reading Frame 76 2
  • Deleted In Split-Hand/Split-Foot 1 3
  • Putative Protein SEM1, Isoform 2 4
  • Deleted In Split-Hand/Foot 1 2
  • FLJ42280 2
  • SHFDG1 4
  • SHFD1 3
  • SEM1 5

External Ids for SEM1 Gene

Previous HGNC Symbols for SEM1 Gene

  • SHFD1
  • SHFM1
  • C7orf76

Summaries for SEM1 Gene

Entrez Gene Summary for SEM1 Gene

  • The product of this gene has been localized within the split hand/split foot malformation locus SHFM1 at chromosome 7. It has been proposed to be a candidate gene for the autosomal dominant form of the heterogeneous limb developmental disorder split hand/split foot malformation type 1. In addition, it has been shown to directly interact with BRCA2. It also may play a role in the completion of the cell cycle. [provided by RefSeq, Jul 2008]

GeneCards Summary for SEM1 Gene

SEM1 (SEM1 26S Proteasome Complex Subunit) is a Protein Coding gene. Diseases associated with SEM1 include Split Hand-Foot Malformation and Isolated Split Hand-Split Foot Malformation. Among its related pathways are Regulation of activated PAK-2p34 by proteasome mediated degradation and Antigen processing-Cross presentation.

UniProtKB/Swiss-Prot Summary for SEM1 Gene

  • Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair (PubMed:15117943). Component of the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, SEM1, and either centrin CETN2 or CETN3 (PubMed:22307388). The TREX-2 complex functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. Binds and stabilizes BRCA2 and is thus involved in the control of R-loop-associated DNA damage and thus transcription-associated genomic instability. R-loop accumulation increases in SEM1-depleted cells.

Gene Wiki entry for SEM1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEM1 Gene

Genomics for SEM1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SEM1 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
GH07J096708 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +0.7 681 2.8 CREB1 GATAD2A TEAD4 ZNF629 RFX1 IKZF1 ZNF692 POLR2A BACH1 TARDBP SEM1 lnc-DLX5-7 lnc-DLX5-3 SLC25A13
GH07J097014 Promoter 0.5 EPDnew 600.1 -304.2 -304189 0.1 EZH2 CBX8 DLX6-AS1 ENSG00000274709 SEM1 DLX6 DLX5
GH07J096833 Enhancer 1 Ensembl ENCODE 10.7 -124.0 -124000 1.4 GATAD2A TFE3 NFKBIZ RXRB GABPA TOE1 CEBPA SOX13 ETS1 TCF7 SEM1 DLX6 piR-52680-324 lnc-SEM1-3
GH07J096596 Enhancer 1 Ensembl ENCODE 10.5 +113.4 113390 1.4 PRDM10 FOXA1 CTCF ZNF501 ZNF600 ZNF341 SCRT2 MNT ZBTB44 TCF7L2 SEM1 LOC107986825 NONHSAG048264.2 SLC25A13
GH07J096598 Enhancer 0.6 Ensembl CraniofacialAtlas 10.5 +110.7 110702 1 FOXA2 HNF4A RXRA SP1 SEM1 DLX5 LOC107986825 NONHSAG048264.2 SLC25A13
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEM1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEM1

Genomic Locations for SEM1 Gene

Genomic Locations for SEM1 Gene
chr7:96,481,626-96,709,891
(GRCh38/hg38)
Size:
228,266 bases
Orientation:
Minus strand
chr7:96,110,938-96,132,835
(GRCh37/hg19)
Size:
21,898 bases
Orientation:
Minus strand

Genomic View for SEM1 Gene

Genes around SEM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEM1 Gene

Proteins for SEM1 Gene

  • Protein details for SEM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P60896-SEM1_HUMAN
    Recommended name:
    26S proteasome complex subunit SEM1
    Protein Accession:
    P60896
    Secondary Accessions:
    • Q13437
    • Q61067

    Protein attributes for SEM1 Gene

    Size:
    70 amino acids
    Molecular mass:
    8278 Da
    Quaternary structure:
    • Component of the 19S proteasome regulatory particle complex. The 26S proteasome consists of a 20S core particle (CP) and two 19S regulatory subunits (RP). The regulatory particle is made of a lid composed of 9 subunits including SEM1, a base containing 6 ATPases and few additional components (PubMed:27428775, PubMed:27342858). Belongs to the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, SEM1, and either centrin CETN2 or CETN3 (PubMed:22307388). Interacts with the C-terminal of BRCA2 (PubMed:10373512, PubMed:21719596).

    Three dimensional structures from OCA and Proteopedia for SEM1 Gene

    Alternative splice isoforms for SEM1 Gene

    UniProtKB/Swiss-Prot:
  • Protein details for SEM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZVN7-SEML_HUMAN
    Recommended name:
    Putative protein SEM1, isoform 2
    Protein Accession:
    Q6ZVN7

    Protein attributes for SEM1 Gene

    Size:
    128 amino acids
    Molecular mass:
    14085 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SEM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEM1 Gene

Post-translational modifications for SEM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SEM1 Gene

Domains & Families for SEM1 Gene

Gene Families for SEM1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SEM1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SEM1 Gene

GenScript: Design optimal peptide antigens:
  • FLJ42280 protein (B7ZVW6_HUMAN)
  • Split hand/foot malformation type 1 protein (DSS1_HUMAN)
  • cDNA FLJ76393, highly similar to Homo sapiens split hand/foot malformation (ectrodactyly) type 1 (SHFM1), mRNA (Q6IBB7_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P60896

UniProtKB/Swiss-Prot:

SEML_HUMAN :
  • Belongs to the DSS1/SEM1 family.
Family:
  • Belongs to the DSS1/SEM1 family.
genes like me logo Genes that share domains with SEM1: view

Function for SEM1 Gene

Molecular function for SEM1 Gene

UniProtKB/Swiss-Prot Function:
Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair (PubMed:15117943). Component of the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, SEM1, and either centrin CETN2 or CETN3 (PubMed:22307388). The TREX-2 complex functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. Binds and stabilizes BRCA2 and is thus involved in the control of R-loop-associated DNA damage and thus transcription-associated genomic instability. R-loop accumulation increases in SEM1-depleted cells.

Phenotypes From GWAS Catalog for SEM1 Gene

Gene Ontology (GO) - Molecular Function for SEM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI --
genes like me logo Genes that share ontologies with SEM1: view
genes like me logo Genes that share phenotypes with SEM1: view

Human Phenotype Ontology for SEM1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SEM1

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SEM1 Gene

Localization for SEM1 Gene

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 SEM1 gene
Compartment Confidence
nucleus 5
cytosol 4
extracellular 3
mitochondrion 2
plasma membrane 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SEM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000502 proteasome complex IBA --
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol TAS --
GO:0008541 proteasome regulatory particle, lid subcomplex IEA --
GO:0032039 integrator complex IDA --
genes like me logo Genes that share ontologies with SEM1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SEM1 Gene

Pathways & Interactions for SEM1 Gene

PathCards logo

SuperPathways for SEM1 Gene

SuperPathway Contained pathways
1 Regulation of activated PAK-2p34 by proteasome mediated degradation
.78
2 RET signaling
3 HIV Life Cycle
.45
4 Parkinson disease
5 Class I MHC mediated antigen processing and presentation
genes like me logo Genes that share pathways with SEM1: view

Gene Ontology (GO) - Biological Process for SEM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000165 MAPK cascade TAS --
GO:0000209 protein polyubiquitination TAS --
GO:0000724 double-strand break repair via homologous recombination IBA --
GO:0002223 stimulatory C-type lectin receptor signaling pathway TAS --
GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent TAS --
genes like me logo Genes that share ontologies with SEM1: view

No data available for SIGNOR curated interactions for SEM1 Gene

Drugs & Compounds for SEM1 Gene

No Compound Related Data Available

Transcripts for SEM1 Gene

mRNA/cDNA for SEM1 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SEM1

Alternative Splicing Database (ASD) splice patterns (SP) for SEM1 Gene

No ASD Table

Relevant External Links for SEM1 Gene

GeneLoc Exon Structure for
SEM1

Expression for SEM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEM1

mRNA Expression by UniProt/SwissProt for SEM1 Gene:

P60896-SEM1_HUMAN
Tissue specificity: Expressed in limb bud, craniofacial primordia and skin.

Evidence on tissue expression from TISSUES for SEM1 Gene

  • Nervous system(4.5)
  • Liver(4.3)
  • Thyroid gland(3.1)
  • Blood(2.5)
  • Heart(2.3)
  • Muscle(2.2)
  • Lung(2.1)
  • Skin(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SEM1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • chin
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • outer ear
  • skull
Abdomen:
  • kidney
Pelvis:
  • testicle
  • ureter
  • urinary bladder
Limb:
  • ankle
  • arm
  • digit
  • finger
  • foot
  • forearm
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • coagulation system
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with SEM1: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for SEM1 Gene

Orthologs for SEM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SEM1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SHFM1 30 31
  • 100 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SHFM1 31
  • 97 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SHFM1 30 31
  • 93.33 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Shfm1 30
  • 88.57 (n)
Mouse
(Mus musculus)
Mammalia Shfm1 30 31
  • 88.57 (n)
OneToOne
Sem1 17
Dog
(Canis familiaris)
Mammalia SHFM1 31
  • 71 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SHFM1 30 31
  • 85.71 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SHFM1 31
  • 100 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii shfm1 30 31
  • 79.05 (n)
OneToOne
wufb55c02 30
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.1217 30
Species where no ortholog for SEM1 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)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SEM1 Gene

ENSEMBL:
Gene Tree for SEM1 (if available)
TreeFam:
Gene Tree for SEM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEM1: view image

Paralogs for SEM1 Gene

Pseudogenes.org Pseudogenes for SEM1 Gene

genes like me logo Genes that share paralogs with SEM1: view

No data available for Paralogs for SEM1 Gene

Variants for SEM1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEM1 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
738972 Likely Benign: not provided 96,688,954(-) C/T SYNONYMOUS_VARIANT
744701 Likely Benign: not provided 96,709,731(-) A/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
rs1802882 - p.Asp17Gly

Additional dbSNP identifiers (rs#s) for SEM1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SEM1 Gene

Variant ID Type Subtype PubMed ID
esv2660164 CNV deletion 23128226
esv27008 CNV loss 19812545
esv3614213 CNV loss 21293372
nsv831064 CNV gain 17160897
nsv831065 CNV gain 17160897

Variation tolerance for SEM1 Gene

Residual Variation Intolerance Score: 59.1% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEM1 Gene

Human Gene Mutation Database (HGMD)
SEM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEM1 Gene

Disorders for SEM1 Gene

MalaCards: The human disease database

(24) MalaCards diseases for SEM1 Gene - From: Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SEM1 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with SEM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEM1 Gene

Publications for SEM1 Gene

  1. Characterization of the split hand/split foot malformation locus SHFM1 at 7q21.3-q22.1 and analysis of a candidate gene for its expression during limb development. (PMID: 8733122) Crackower MA … Tsui LC (Human molecular genetics 1996) 2 3 4
  2. A comprehensive functional characterization of BRCA2 variants associated with Fanconi anemia using mouse ES cell-based assay. (PMID: 21719596) Biswas K … Sharan SK (Blood 2011) 3 4
  3. Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. (PMID: 17323924) Wang X … Huang L (Biochemistry 2007) 3 4
  4. The proteasome is involved in determining differential utilization of double-strand break repair pathways. (PMID: 17563742) Gudmundsdottir K … Ashworth A (Oncogene 2007) 3 23
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for SEM1 Gene

Sources for SEM1 Gene