Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SEM1 Gene

Aliases for SEM1 Gene

  • SEM1, 26S Proteasome Complex Subunit 2 3 5
  • 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 DSS1 3 4
  • Split Hand/Foot Deleted Protein 1 3 4
  • C7orf76 3 4
  • Shfdg1 3 4
  • SHFM1 3 4
  • DSS1 3 4
  • 26S Proteasome Complex Subunit SEM1 3
  • Chromosome 7 Open Reading Frame 76 2
  • Deleted In Split-Hand/Split-Foot 1 3
  • Deleted In Split-Hand/Foot 1 2
  • SHSF1 3
  • SHFD1 3
  • ECD 3

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 Foot and Split Hand-Split Foot Malformation. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and RET signaling.

UniProtKB/Swiss-Prot 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

Additional gene information for SEM1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEM1 Gene

Genomics for SEM1 Gene

Regulatory Elements for SEM1 Gene

Enhancers for SEM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07H096833 0.9 ENCODE 10.7 -124.0 -124001 1 FOXA2 MLX DNMT3B THRB ZSCAN9 RARA CREM MIXL1 THAP11 HMG20B SEM1 DLX6 MARK2P10 LOC105375414
GH07H096596 0.6 ENCODE 10.5 +113.2 113228 0 CTCF L3MBTL2 ZNF341 MYNN MAX MNT PRDM10 SEM1 GC07M096611 LOC105375412
GH07H096666 0.3 FANTOM5 11.4 +43.3 43321 0 SEM1 GC07M096611
GH07H096708 1.1 ENCODE 0.7 +0.4 445 2 HDGF ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF143 SP3 ZHX2 SEM1 GC07M096611
GH07H096727 0.3 FANTOM5 0.4 -17.9 -17922 0 SEM1 LOC105375414
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEM1 on UCSC Golden Path with GeneCards custom track

Promoters for SEM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000215458 291 1600 HDGF ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF143 FOS ZHX2

Genomic Location for SEM1 Gene

Chromosome:
7
Start:
96,481,626 bp from pter
End:
96,709,891 bp from pter
Size:
228,266 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

Protein Domains for SEM1 Gene

InterPro:
ProtoNet:

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

miRNA for SEM1 Gene

miRTarBase miRNAs that target SEM1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SEM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 5
extracellular 3
mitochondrion 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 IEA --
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

SuperPathway Contained pathways
1 CDK-mediated phosphorylation and removal of Cdc6
.78
.31
2 RET signaling
3 HIV Life Cycle
.45
4 Class I MHC mediated antigen processing and presentation
5 Cell Cycle, Mitotic
.60
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:0000209 protein polyubiquitination TAS --
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 --
GO:0006406 mRNA export from nucleus IEA --
GO:0006521 regulation of cellular amino acid metabolic process 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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SEM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

No ASD Table

Relevant External Links for SEM1 Gene

GeneLoc Exon Structure for
SEM1
ECgene alternative splicing isoforms for
SEM1

Expression for SEM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of SEM1 Gene:

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

  • Liver(4.6)
  • Nervous system(4.6)
  • Heart(3.1)
  • Thyroid gland(2.9)
  • Muscle(2.8)
  • Intestine(2.6)
  • Adrenal gland(2.4)
  • Kidney(2.4)
  • Lung(2.4)
  • Skin(2.3)
  • Blood(2.2)

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
Organs:
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 33 34
  • 100 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SHFM1 34
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SHFM1 33 34
  • 93.33 (n)
mouse
(Mus musculus)
Mammalia Shfm1 33 34
  • 88.57 (n)
Sem1 16
rat
(Rattus norvegicus)
Mammalia Shfm1 33
  • 88.57 (n)
dog
(Canis familiaris)
Mammalia SHFM1 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves SHFM1 33 34
  • 85.71 (n)
lizard
(Anolis carolinensis)
Reptilia SHFM1 34
  • 100 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii shfm1 33 34
  • 79.05 (n)
wufb55c02 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1217 33
Species where no ortholog for SEM1 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)
  • 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 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)

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 from dbSNP and Humsavar for SEM1 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs1000193520 -- 96,711,322(+) GATTG(-/TTGAT)TTAAA upstream-variant-2KB
rs1000280227 -- 96,691,275(+) ATGTG(C/G)AAAGT intron-variant
rs1000462450 -- 96,704,056(+) AGAAG(A/G)GACTA intron-variant
rs1000500893 -- 96,690,705(+) TTACT(-/A)TCCAA intron-variant
rs1000612987 -- 96,689,787(+) CATCC(C/T)TGTCT intron-variant

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)

Relevant External Links 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

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

Disorder Aliases PubMed IDs
split foot
split hand-split foot malformation
  • lobster-claw deformity
split hand
  • ectrodactyly of hand
split hand-foot malformation 2
  • shfm2
ovarian mucinous adenofibroma
- elite association - COSMIC cancer census association via MalaCards
Search SEM1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SEM1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEM1
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. The proteasome is involved in determining differential utilization of double-strand break repair pathways. (PMID: 17563742) Gudmundsdottir K … Ashworth A (Oncogene 2007) 3 22 60
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  3. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier LW … Wilson RK (Nature 2003) 3 4 60
  4. SEM1, a homologue of the split hand/split foot malformation candidate gene Dss1, regulates exocytosis and pseudohyphal differentiation in yeast. (PMID: 9927667) Jäntti J … Keränen S (Proceedings of the National Academy of Sciences of the United States of America 1999) 3 22 60
  5. 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 60

Products for SEM1 Gene

Sources for SEM1 Gene

Content
Loading form....